WO2021203053A1 - Immunotherapy targeting a conserved region in sars coronaviruses - Google Patents
Immunotherapy targeting a conserved region in sars coronaviruses Download PDFInfo
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- WO2021203053A1 WO2021203053A1 PCT/US2021/025653 US2021025653W WO2021203053A1 WO 2021203053 A1 WO2021203053 A1 WO 2021203053A1 US 2021025653 W US2021025653 W US 2021025653W WO 2021203053 A1 WO2021203053 A1 WO 2021203053A1
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Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
- C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
- C07K16/1002—Coronaviridae
- C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
- C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
- C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
- C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
- C07K2317/52—Constant or Fc region; Isotype
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
- C07K2317/55—Fab or Fab'
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
- C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
- C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
Definitions
- Figures 1A and 1B show binding by antibodies (1A) S303 (VH SEQ ID NO.:63; VL SEQ ID NO.:67) and (1B) S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) to recombinant SARS-CoV-2 RBD.
- Figures 2A and 2B shows the SARS-CoV-2 neutralization capacity of certain antibodies.
- Figures 3A-3I show SARS-CoV-2 neutralization of infection.
- Figure 3A shows neutralization by donor plasma from SARS-CoV-1 survivors.
- Figures 3B-3D and 3I show neutralization by supernatant from B cells expressing certain antibodies.
- Figures 3E-3H show neutralization by certain recombinant IgG1 antibodies.
- Figures 4A and 4B show binding of antibody-containing B cell supernatant to SARS-CoV-2 S protein expressed on ExpiCHO cells. Graphs showing binding profiles of antibodies S300-S310 are indicated with boxes.
- Figures 5A and 5B show binding of antibodies S311 and S312 in the supernatant of cultured B cells to SARS-CoV-1 and SARS-CoV-2. Antibody concentrations are estimates.
- SARS S1 Sino protein from Sino Biological.
- RBD2 RBD of SARS-CoV-2 produced in-house.
- Figures 6A-6E show (top) binding curves of certain antibodies for SARS-CoV- 1 (SARS1) RBD and SARS-CoV-2 (SARS2) RBD, as measured by Octet, and (bottom) KD values. KD values for antibodies (e.g., ⁇ 1.0x10-12M) with very strong binding and slow dissociation are estimates.
- Figure 7 shows neutralization of infection by S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83) and S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) antibodies, alone or in combination, against SARS-CoV-2 pseudotyped virus.
- Figures 8A-8K show binding curves of certain antibodies for RBD of SARS- CoV-1, RBD of SARS-CoV-2, and ectodomains of various coronaviruses, as measured by ELISA.
- Figure 9 shows neutralization of infection by S309 rIgG1 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) and S315 rIgG1 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) against SARS-CoV-2 pseudotyped virus.
- Figure 10 shows neutralization of infection by S309 full-length rIgG1 and S309 rFab (both of which comprise a VH of SEQ ID NO.:105 and a VL of SEQ ID NO.:168) against SARS-CoV-2 pseudotyped virus.
- Figure 11 shows binding of antibody S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) to SARS-CoV-1 and SARS-CoV-2 spike protein expressed on ExpiCHO cells. Stacked histograms of flow cytometry graphs show antibody dose-dependent binding of S309 to SARS-CoV and SARS-CoV-2.
- Figure 12A and 12B show concentration-dependent binding measured by flow cytometry for certain antibodies.
- Figure 12A shows binding to SARS-CoV-2.
- Figure 12B shows binding to SARS-CoV-1.
- Figure 13 shows neutralization of infection by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) against SARS-CoV-2 pseudotyped virus.
- S303 VH SEQ ID NO.:63; VL SEQ ID NO:67
- S304 VH SEQ ID NO.:79; VL SEQ ID NO.:83
- S306 VH SEQ ID NO.:87; VL SEQ ID NO.:91
- S309 VH SEQ ID NO.:105; VL SEQ ID NO.:
- Figure 14A-14D show binding affinity/avidity of antibodies S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) to RBD of SARS-CoV-1 (right panels) and SARS-CoV-2 (left panels).
- Figure 15A and 15B show competition of pairs of antibodies for binding to the RBD of SARS-CoV-1 ( Figure 15A) and SARS-CoV-2 ( Figure 15B).
- the x-axis shows time (0 to 1000 seconds), and the y-axis shows the binding to RBD as measured by BLI (0 to 3 nm).
- the first antibody is indicated on the left of the matrix and the second antibody is indicated on the top of the matrix.
- the dashed vertical lines in Figure 15B show the switch from the first antibodyto the second antibody.
- At right are antigenic sites as determined by structural information, escape mutant analysis, and BLI-based epitope binning.
- Figure 16 shows the ability of S309 to interfere with RBD of SARS-CoV-1 (left) or SARS-CoV-2 (right) binding to human ACE2 (hACE2).
- FIG. 17A and 17B show antibody-dependent effects of certain antibodies against model infected cells.
- Figure 17A shows antibody-dependent cytotoxicity using primary NK effector cells and SARS-CoV-2-expressing ExpiCHO cells as target cells.
- FIG. 17B Bar graph at right shows ADCC for the indicated antibody(ies), calculated as area under the curve (AUC).
- Figure 17B shows antibody-dependent cellular phagocytosis using PBMCs as phagocytic cells and PKF67-labelled SARS-CoV-2-expressing ExpiCHO as target cells.
- Line graphs show mean fluorescence intensity (MFI) of PBMCs after incubation with target cells and antibodies, determined for one representative donor with high affinity Fc ⁇ RIIIa (symbols show means ⁇ SD of duplicates).
- MFI mean fluorescence intensity
- Figure 18A-18J show binding curves of certain recombinant antibodies for RBD of SARS-CoV-1, RBD of SARS-CoV-2, and ectodomains of various coronavirus strains, as measured by ELISA.
- Recombinant mAbs were tested by ELISA at a concentration range of 5 to 0.00028mg/ml.
- RBD2 Receptor binding domain of SARS- CoV-2.
- RBD1 Receptor binding domain of SARS-CoV (also referred-to herein as SARS-CoV-1).
- Spike stabilized prefusion trimer of the indicated coronavirus.
- FIG. 19A and 19B show ability of certain antibodies to interfere with RBD binding to human ACE2.
- Human ACE2 hACE2 was loaded onto BLI sensors, followed by incubation of the sensors with RBD alone or RBD in combination with recombinant antibody. The vertical dashed line indicates the start of the loading of RBD with or without antibody.
- RBD Receptor binding domain.
- Figure 19A shows SARS-CoV-1 RBD binding to ACE2.
- Figure 19B shows SARS-CoV-2 RBD binding to ACE2.
- Figure 20A and 20B show binding affinity and avidity of antibody S309 IgG (Figure 20A) versus S309 Fab (Figure 20B) for SARS-CoV-1 RBD (bottom of each figure) and SARS-CoV-2 RBD (top of each figure).
- IgG and the Fab VH SEQ ID NO.:105; VL SEQ ID NO.:168.
- RBD was loaded to BLI pins and association of different concentrations of S309-IgG-MLNS or S309 Fab was measured.
- Vertical dashed lines indicate the start of the dissociation phase when BLI pins were switched to buffer.
- Figure 21A-21C show reactivity of S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), and S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159) antibodies against SARS-CoV-2.
- Figure 21A shows reactivity of S304, S306, S309, and S310 antibodies against TX100 extracted lysate of SARS-CoV-2 infected Vero E6 cells.
- Figure 21B shows reactivity of the same antibodies against SDS extracted lysate of SARS-CoV-2 infected Vero E6 cells.
- Figure 21C shows reactivity of human SARS-CoV-1 convalescent serum against TX100 extracted or SDS extracted lysate of SARS-CoV-2 infected Vero E6 cells.
- Figures 21A and 21B also show data for comparator antibody LCA57, which is specific for spike protein of MERS-CoV (Corti et al. PNAS 112(33):10473-10478 (2015).
- Figure 22A-22D show neutralization of SARS-CoV-2 infection by antibodies as assessed by inhibition of nucleoprotein (NP) expression at 24 and 45 hours post infection.
- NP nucleoprotein
- Figure 22A shows neutralization of SARS-CoV-2 infection by S304 S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83).
- Figure 22B shows neutralization of SARS- CoV-2 infection by S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168.
- Figure 22C shows neutralization of SARS-CoV-2 infection by the combination of S304 and S309.
- Figure 22D shows control neutralization of SARS-CoV-2 infection by comparator antibody LCA57, which is specific for spike protein of MERS-CoV (Corti et al. PNAS 112(33):10473-10478 (2015)).
- Figure 23 shows neutralization of infection by antibodies S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182), alone or in combination, against SARS-CoV-2 pseudotyped virus.
- Figure 24A and 24B show antibody-dependent effects of certain antibodies against model infected cells.
- Figure 24A shows antibody-dependent cell-mediated cytotoxicity (ADCC) using primary NK effector cells and SARS-CoV-2-expressing ExpiCHO cells as target cells.
- the graph shows the % killing of target cells after incubation with antibody or combination of antibodies shown in the legend.
- Figure 24B shows ADCC for the indicated antibody(ies), calculated as area under the curve (AUC).
- FIG. 25A shows antibody-dependent cellular phagocytosis (ADCP) using PBMCs as phagocytic cells and PKF67-labelled SARS-CoV-2-expressing ExpiCHO cells as target cells.
- the graph shows mean fluorescence intensity (MFI) of PBMCs after incubation with target cells and antibodies, determined for one representative donor with high affinity Fc ⁇ RIIIa (symbols show means ⁇ SD of duplicates).
- Figure 25B shows ADCP for the indicated antibody(ies), calculated as area under the curve (AUC).
- Figure 26 shows antibody binding as measured by flow cytometry. Binding of antibody S309 to SARS-CoV-2 Spike protein expressed in Expi-CHO cells was detected with a fluorescently labeled secondary antibody.
- Figure 27 shows binding of antibody S309 (labeled as "11” in the figure key) and four engineered variants of S309 (labeled as "12” through “15”, respectively) to S protein, as measured by flow cytometry.
- S309 N55Q comprises an N55Q mutation in CDRH2, resulting in a variant VH sequence (SEQ ID NO:.113), and the wild-type VL sequence (SEQ ID NO.:168) of S309
- S309 W50F comprises a W50F variant VH sequence (SEQ ID NO: 129) and the wild-type VL sequence (SEQ ID NO.:168) of S309
- S309 W105F comprises a W105F variant VH sequence (SEQ ID NO: 119) and the wild-type VL sequence (SEQ ID NO.:168) of S309
- S309 W50F/G56A/W105F comprises a W50F/G56A/W105F variant VH sequence (SEQ ID NO.:172) and the wild-type VL sequence of S309.
- S309 N55Q is labeled as "12”
- S309 W50F is labeled as “13”
- S309 W105F is labeled as “14”
- S309 W50F-G56A-W105F is labeled as "15.”
- Antibody binding to SARS-CoV-2 Spike protein expressed on Expi-CHO cells was detected with a fluorescently labeled secondary antibody. Data from two experiments are shown.
- Figure 28 shows neutralization of infection by antibody S309 (referred to in the figure as "Variant-11 (wt)") and four S309 variant antibodies against SARS-CoV-2 pseudotyped viruses.
- S309 N55Q is labeled as “Variant-12”
- S309 W50F is labeled as “Variant-13”
- S309 W105F is labeled as “Variant-14”
- S309 W50F- G56A-W105F is labeled as "Variant-15.”
- Pseudotyped viruses are VSV pseudotyped with SARS-CoV-2 Spike protein.
- Figure 29 shows a summary of results from binding and pseudovirus neutralization assays for antibody S309 (“S309-WT”) and four engineered variants of S309 ("N55Q"; "W50F”; “W105F”; “W50F/G56A/W105F”).
- the dashed horizontal line shows change of function of engineered variant versus S309-WT baseline. Differently hatched bars show binding to glycosylated RBD as measured by SPR, binding to deglycosylated RBD as measured by SPR, binding to antigen-expressing cells, as measured by FACS, and neutralization as measured using SARS-CoV-2 pseudoviruses.
- Figures 30A-30F show binding kinetics of certain monoclonal antibodies to SARS-CoV-2 glycosylated or deglycosylated RBD as measured by SPR.
- Figure 30A shows binding kinetics of S309 wild type antibody (2 replicate experiments).
- Figure 30B shows binding kinetics of S309 variant N55Q (bottom), as compared to S309 wild type antibody (top).
- Figure 30C shows binding kinetics of S309 variant W50F (bottom) as compared to S309 wild type antibody (top).
- Figure 30D shows binding kinetics of S309 variant W105F (bottom) as compared to S309 wild type antibody (top).
- Figure 30E shows binding of S309 variant W50F/G56A/W105F (bottom) as compared to S309 wild type antibody (top).
- Figure 30F shows binding of S309 variant W50F/G56A/W105F using 10 minute injection period (top panel) or 3 minute injection period (bottom panel).
- Figure 31 shows activation of high affinity (158V) Fc ⁇ RIIIa (left panel) or low affinity (158F) Fc ⁇ RIIIa (right panel) by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), and a combination of S309 and S315, along with comparator antibody S230.
- S303 VH SEQ ID NO.:63; VL SEQ ID NO:67
- S304 VH SEQ ID NO.:79; VL SEQ ID NO.:83
- S306 VH SEQ ID NO.:87; VL SEQ ID NO.:91
- S309 VH SEQ ID NO.:105; VL SEQ ID NO.:168
- Activation was measured using SARS-CoV-2 S-expressing ExpiCHO cells as target cells and Jurkat reporter cells stably transfected with NFAT-driven luciferase reporter gene. Activation of Fc ⁇ RIIIa results in NFAT-mediated expression of the luciferase reporter gene. Results are from one experiment, one or two measurements per mAb.
- Figure 32 shows activation of Fc ⁇ RIIa by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO.:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), and a combination of S309 and S315, along with comparator monoclonal antibody S230.
- Activation was measured using SARS-CoV-2 S-expressing ExpiCHO cells as target cells and Jurkat reporter cells stably transfected with NFAT-driven luciferase reporter gene.
- FIGS 33A and 33B show binding of antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182), along with comparator antibodies S110, S230, and S109, to S protein expressed on a cell surface.
- Figure 33A shows binding to ExpiCHO cells transfected with SARS-CoV-2 S protein.
- Figure 33B shows binding to ExpiCHO cells transfected with SARS-CoV-1 S protein. Mean fluorescence intensity was measured by flow cytometry for each antibody. Antibody concentrations tested are indicated in the x-axis.
- Figure 34 shows neutralization of infection by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) against SARS-CoV-1 pseudotyped virus.
- Figure 35A and 35B show conservation of Spike protein residues.
- FIG 35A shows Spike protein variants occurring with a frequency of n>1 as spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain.
- Figure 35B shows the prevalence of variants in Spike glycoprotein by amino acid. Each dot is a distinct variant. The locations of Domain A and RBD are shown. Variants passing a frequency threshold of 0.1% are as indicated.
- Figure 36 shows neutralization of SARS-CoV-2-MLV by antibody S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) combined with an equimolar amount of antibody S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83).
- the concentration shown on the x axis is that of the individual antibodies.
- Figure 37 shows neutralization of SARS-CoV2-MLV by S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) combined with an equimolar amount of antibody S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) antibodies.
- Figure 38 shows neutralization of SARS-CoV-2-MLV, SARS-CoV-MLV (bearing S from various isolates) and other sarbecovirus isolates by mAb S309.
- Figures 39A-39C show structures of SARS-CoV-2 S glycoprotein in complex with the S309 antibody Fab fragment, as determined by cryoEM. For these data, resolution was 4.2 ⁇ (Fab bound to open SARS-CoV-2 S protein trimer) and 3.6 ⁇ (Fab bound to closed SARS-CoV-2 S protein trimer) resolution.
- Figure 39A shows a ribbon diagram of the partially open SARS-CoV-2 S protein trimer with one RBD (S B ) domain open, bound to three S309 Fab fragments (left) and the closed SARS-CoV-2 S protein trimer bound to three S309 Fab fragments shown in two orthogonal orientations (center and right).
- Figure 39B shows close-up views of the S309 epitope (as determined using cryoEM at the above resolution) showing the contacts formed with the core fucose (labeled with a star) and the core N-acetyl-glucosamine of the oligosaccharide at position N343 (left) and the 20-residue long CDRH3 sitting atop the RBD (S B ) helix comprising residues 337-344 (right).
- the oligosaccharide at position N343 is omitted for clarity.
- Figures 39A and 39B show selected residues involved in interactions between S309 and SARS-CoV-2 S protein.
- Figure 39C shows a molecular surface representation of the SARS-CoV-2 S protein trimer, showing the S309 footprint indicated by residue conservation (conserved amino acid residue or conservative substitution) on one protomer among SARS-CoV-2 and SARS-CoV-1 S glycoproteins. Data were refined at higher resolution (3.7 ⁇ for open trimer, and 3.1 ⁇ for closed trimer; see Figures 47A-48C; in Figure 48B, R509 should be indicated part of the S309 epitope).
- Figures 40 shows ribbon diagrams of S309 and ACE2 bound to SARS-CoV-2 S protein RBD (S B ).
- FIG. 41A-41C show conservation of Spike and RBD residues in relation to the binding footprints of ACE2 and S309.
- Figure 41A shows the ACE2 and S309 footprints mapped onto the structure of the SARS-CoV-2 RBD (PDB ID: 6M0J).
- the ACE2 footprint was defined by residues being within 5 ⁇ of the receptor in 6M0J.
- FIG. 41B shows alignments of the full RBD sequences of multiple sarbecoviruses.
- the ACE2 and S309 footprints are indicated; subsequent analysis determined that D442 was not in the S309 footprint (epitope).
- the three high frequency variant residues are indicated.
- Figure 41C shows conservation analysis of spike glycoprotein residues making contact with S309 across clades of sarbecoviruses. Residue coordinates for both SARS-CoV-2 and SARS-CoV-1 are shown.
- the NAT motif enabling glycosylation of N343 is indicated.
- the SARS-CoV-1 and SARS-CoV- 2 sequence differences are indicated.
- the column labeled “n” indicates the number of sequences used for this analysis.
- the IC50 is the half maximal neutralizing concentration of S309 against SARS-CoV-1-MLV or SARS-CoV-2-MLV.
- Figure 42 shows competition of antibodies with RBD for binding to ACE2.
- SARS-CoV-2 S protein ectodomain was loaded onto BLI sensors, followed by incubation of the sensors with hACE2 or S309 IgG (left panel) or Fab (right panel). In a third step, sensors were incubated with hACE2 or S309 IgG/Fab as indicated.
- Figures 43A-43D show cryoEM data processing and validation of the SARS- CoV-2 S protein structure.
- Figure 43A shows a representative electron micrograph (top panel) and class averages (bottom panel) of SARS-CoV-2 S protein embedded in vitreous ice. Scale bar: 100nm.
- Figure 43B shows gold-standard Fourier shell correlation curves for the closed and partially open trimers. The 0.143 cutoff is indicated by horizontal dashed lines.
- Figure 43C shows a local resolution map calculated using cryoSPARC for the closed reconstruction.
- Figure 43D shows the atomic model fit into the cryoEM density.
- Figures 44A and 44B show binding of certain antibodies to S glycoproteins of SARS-CoV-2 ( Figure 44A) or SARS-CoV-1 ( Figure 44B) expressed at the surface of ExpiCHO cells. Symbols are means of duplicates from one experiment.
- Figures 45A and 45B show binding affinity and avidity of S309 IgG (Figure 45A) and S309 Fab (Figure 45B) for SARS-CoV-2 RBD (top panel) or SARS-CoV-2 Spike protein (bottom panel). For both IgG and Fab: VH SEQ ID NO.:105 and VL SEQ ID NO.:168.
- Biotinylated RBD of SARS-CoV-2 or biotinylated SARS-CoV-2 prefusion S ectodomain trimer were loaded onto Streptavidin biosensors, and association of different concentrations of S309-IgG-MLNS (comprising M428L and N434S Fc mutations (EU numbering)) or S309 Fab was measured.
- Vertical dashed lines indicate the start of the dissociation phase when biosensors were switched to buffer.
- Figures 46A and 46B show binding of antibodies S303, S304, S306, S309, S310, and S315, along with comparator antibodies S110, S124, S230, and S109, to S protein expressed on a cell surface.
- Figure 42A shows binding to ExpiCHO cells transfected with SARS-CoV-2 S protein.
- Figure 42B shows binding to ExpiCHO cells transfected with SARS-CoV-1 S protein. Mean fluorescence intensity was measured by flow cytometry for each antibody. Antibody concentrations tested are indicated in the x axis.
- Figures 47A-47D show cryoEM data processing and validation of the SARS- CoV-2 S protein structure.
- Figure 47A shows a representative electron micrograph (top panel) and class averages (bottom panel) of SARS-CoV-2 S protein embedded in virtreous ice. Scale bar: 100nm.
- Figure 47B shows gold-standard (solid line) and map/model (dashed line) Fourier shell correlation curves for the closed and partially open trimers.
- Figures 47C and 47D show local resolution maps calculated using cryoSPARC for the closed state (Figure 47C) and open state (Figure 47D) reconstructions.
- Figures 48A-48C show conservation of Spike and RBD residues in relation to the binding footprints of ACE2 and S309 at the higher resolution (as determined by cryo-EM at 3.7 ⁇ for open trimer, and 3.1 ⁇ for closed trimer).
- Figure 48A shows the ACE2 and S309 footprints mapped onto the structure of the SARS-CoV-2 RBD (PDB ID: 6M0J). The ACE2 footprint was defined by residues being within 5 ⁇ of the receptor in 6M0J.
- FIG. 48B shows alignments of the full RBD sequences of multiple sarbecoviruses.
- the ACE2 and S309 footprints also indicated; R509, not shown in Figure 48B, is part of the S309 antibody footprint (epitope).
- Dashed boxes indicate glycosylation sites and asterisks indicate the N343 glycosylation site. The three high frequency variant residues are indicated.
- Figure 48C shows conservation analysis of spike glycoprotein residues making contact with S309 across clades of sarbecoviruses. Residue coordinates for both SARS-CoV-2 and SARS-CoV-1 are shown. The NAT motif enabling glycosylation of N343 is indicated. The SARS-CoV-1 and SARS-CoV-2 sequence differences are indicated. Dashes indicate identity to SARS-CoV-2 consensus residues. Blanks indicate deletions. When multiple variants are found, they are listed in order of prevalence (high to low). For SARS-CoV-2, where more than 10,000 sequences were analyzed, variants found in a single sequence are not shown and variants found in only two sequences are parenthesized.
- Figures 49A and 49B show conservation of Spike protein residues.
- Figure 49A shows Spike protein variants supported by at least two sequences as spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. The RBD and other Spike protein domains are shown in the colors indicated. 171 variants (out of 11,839 total Spike protein sequences analyzed) are shown.
- Figure 49B shows the prevalence of variants in Spike glycoprotein by amino acid position. Each dot is a distinct variant. The location of the RBD is shown. Location within the RBD, RBM, or S309 epitope is indicated. Variants are labeled if their prevalence is greater than 1% (D614G only) or if they are located within the RBD or S309 epitope. The location of conserved N343 is also indicated.
- Figures 50A and 50B show binding of various concentrations of monoclonal antibodies to immobilized SARS-CoV-2 DS Spike protein (green curve) or SARS- CoV-2 wild-type ("WT”) Spike protein (black curve).
- the "DS" Spike protein comprises the following mutations and is stabilized in a prefusion "closed” conformation: S383C, R682S, R683G, R685G, D985C, K986P, V987P (numbering in reference to SEQ ID NO.:165).
- Figure 50A shows binding of antibody S309.
- Figure 50B shows binding of antibody S304. Calculated IC50 values are shown above each graph.
- Figure 51 shows binding of various concentrations of monoclonal antibody S309 to immobilized SARS-CoV-1 DS Spike protein or SARS-CoV-1 Spike protein. Calculated IC50 values are shown above the graph.
- Figure 52 shows conservation of the S309 N55Q (VH: SEQ ID NO.:113; VL: SEQ ID NO.:168) MLNS epitope in SARS-CoV-2, based on analysis of SARS-CoV-2 variants as of March 12, 2021 (GISAID (human spike protein seqs; ⁇ 10% Xs; >1018 aa (80% full length)).
- GISAID human spike protein seqs; ⁇ 10% Xs; >1018 aa (80% full length)
- Epitope residues in accordance with SEQ ID NO.:165 surface glycoprotein [Wuhan seafood market pneumonia virus]; GenBank: QHD43416.1; January 23, 2020, are shown along the x-axis.
- the bars in the graph show (1) variant amino acid residues (substitution mutants) that have been identified at each of the epitope residue positions along the x-axis , (2) whether SARS-CoV-2 having the indicated amino acid variation(s) has a greater than 3-fold or less than 3-fold reduction in neutralization potency by antibody S309 N55Q MLNS, as compared to SARS-CoV-2 having the surface glycoprotein amino acid sequence shown in SEQ ID NO.:165, (3) the number of identified counts of variants (y-axis, left hand side of graph) at the indicated epitope residue position, and (4) conservation of the epitope residue shown on the x-axis, expressed as percentage of SARS-CoV-2 sequences comprising the epitope residue shown on the x-axis.
- the present disclosure provides, in part, antibodies and antigen-binding fragments that recognize a novel target region present in SARS CoV-2 surface glycoprotein receptor binding domain (RBD, also referred to as "SB"), which target region is highly conserved in other SARS coronaviruses, such as SARS-CoV (e.g., Urbani, CHUK-1, GZ02, HC_SZ_61_03, A031G, WIV1 SARS-like bat).
- SARS-CoV surface glycoprotein receptor binding domain
- the target region can include amino acid residues that are distinct from those RBD amino acid residues that interact with human ACE2.
- antibodies and antigen-binding fragments can bind to and optionally neutralize a SARS-CoV-2 variant comprising one or more amino acid substitution mutation within the target region.
- the target region comprises or consists of epitope amino acid residues contacted (e.g., as determined by X-ray crystallography, cryo-electron microscopy, or the like) by certain antibodies or antigen-binding fragments of the present disclosure, such as an antibody or antigen-binding fragment comprising a VH having the amino acid sequence set forth in SEQ ID NO.:105 and a VL having the amino acid sequence set forth in SEQ ID NO.:168.
- the target region or epitope comprises any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, R509, C336, and K444, according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike”) glycoprotein).
- the target region or epitope comprises any one or more of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike”) glycoprotein).
- the target region or epitope comprises any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike”) glycoprotein).
- the target region further comprses D442 according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or “spike”) glycoprotein).
- the target region or epitope comprises amino acid residue N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated.
- antibodies and antigen-binding fragments that can bind to SARS-CoV-2 S protein RBD when the SARS-CoV-2 S protein RBD is in an open confirmation, in a closed conformation, or both.
- immunogenic compositions that comprise a polypeptide or polypeptides that comprise(s) all or a portion of a target region or epitope.
- polynucleotides that encode an antibody or antigen-binding fragment, and/or that encode a polypeptide or polypeptides that comprise(s) all or a portion of a target region or epitope.
- vectors that comprise a polynucleotide, host cells that comprise a polynucleotide and/or a vector, compositions, and uses of the same to, for example, treat a SARS coronavirus infection in a subject and/or to induce an immune response against a SARS coronavirus infection in a subject.
- SARS-CoV-2 also referred to herein as "Wuhan coronavirus", or “Wuhan seafood market pneumonia virus”, or “Wuhan CoV”, or “novel CoV”, or “nCoV”, or “2019 nCoV”, or “Wuhan nCoV” is a betacoronavirus believed to be of lineage B (sarbecovirus).
- SARS-CoV-2 was first identified in Wuhan, Hubei province, China, in late 2019 and spread within China and to other parts of the world by early 2020. Symptoms of SARS-CoV-2 include fever, dry cough, and dyspnea.
- SARS-CoV-2 The genomic sequence of SARS-CoV-2 isolate Wuhan-Hu-1 is provided in SEQ ID NO.:163 (see also GenBank MN908947.3, January 23, 2020), and the amino acid translation of the genome is provided in SEQ ID NO.:164 (see also GenBank QHD43416.1, January 23, 2020).
- SARS- CoV-2 comprises a "spike” or surface (“S") type I transmembrane glycoprotein containing a receptor binding domain (RBD). RBD is believed to mediate entry of the lineage B SARS coronavirus to respiratory epithelial cells by binding to the cell surface receptor angiotensin-converting enzyme 2 (ACE2).
- ACE2 cell surface receptor angiotensin-converting enzyme 2
- a receptor binding motif (RBM) in the virus RBD is believed to interact with ACE2.
- the amino acid sequence of the SARS-CoV-2 Wuhan-Hu-1 surface glycoprotein (S) is provided in SEQ ID NO.:165.
- the amino acid sequence of SARS-CoV-2 Wuhan-Hu-1 RBD is provided in SEQ ID NO.:166.
- SARS-CoV-2 Wuhan-Hu-1 S protein has approximately 73% amino acid sequence identity with SARS-CoV S protein.
- the amino acid sequence of SARS- CoV-2 Wuhan-Hu-1 RBM is provided in SEQ ID NO.:167.
- SARS-CoV-2 RBD has approximately 75% to 77% amino acid sequence similarity to SARS coronavirus RBD
- SARS-CoV-2 Wuhan Hu-1RBM has approximately 50% amino acid sequence similarity to SARS coronavirus RBM.
- SARS-CoV-2 Wuhan Hu-1 refers to a virus comprising the amino acid sequence set forth in any one or more of SEQ ID NOs.:164, 165, and 166, optionally with the genomic sequence set forth in SEQ ID NO.:163. There have been a number of emerging SARS-CoV-2 variants.
- SARS- CoV-2 variants contain an N439K mutation, which has enhanced binding affinity to the human ACE2 receptor (Thomson, E.C., et al., The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. bioRxiv, 2020).
- SARS-CoV-2 variants contain an N501Y mutation, which is associated with increased transmissibility, including the lineages B.1.1.7 (also known as 20I/501Y.V1 and VOC 202012/01; (del69-70, del144, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H mutations)) and B.1.351 (also known as 20H/501Y.V2; L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and A701V mutations), which were discovered in the United Kingdom and South Africa, respectively (Tegally, H., et al., Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
- SARS-CoV-2 severe acute respiratory syndrome-related coronavirus 2
- B.1.351 also include two other mutations in the RBD domain of SARS-CoV2 spike protein, K417N and E484K (Tegally, H., et al., Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv, 2020: p.2020.12.21.20248640).
- SARS-CoV-2 variants include the Lineage B.1.1.28, which was first reported in Brazil; the Variant P.1, lineage B.1.1.28 (also known as 20J/501Y.V3), which was first reported in Japan; Variant L452R, which was first reported in California in the United States (Pan American Health Organization, Epidemiological update: Occurrence of variants of SARS-CoV-2 in the Americas, January 20, 2021, available at reliefweb.int/sites/reliefweb.int/files/resources/2021-jan-20-phe-epi-update-SARS- CoV-2.pdf).
- SARS-CoV-2 variants include a SARS CoV-2 of clade 19A; SARS CoV-2 of clade 19B; a SARS CoV-2 of clade 20A; a SARS CoV-2 of clade 20B; a SARS CoV-2 of clade 20C; a SARS CoV-2 of clade 20D; a SARS CoV-2 of clade 20E (EU1); a SARS CoV-2 of clade 20F; a SARS CoV-2 of clade 20G; and SARS CoV-2 B1.1.207; and other SARS CoV-2 lineages described in Rambaut, A., et al., A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
- SARS-CoV-2 variants also include: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K; N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q
- any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
- any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness are to be understood to include any integer within the recited range, unless otherwise indicated.
- the term "about” means ⁇ 20% of the indicated range, value, or structure, unless otherwise indicated.
- a protein domain, region, or module e.g., a binding domain
- a protein "consists essentially of" a particular amino acid sequence when the amino acid sequence of a domain, region, module, or protein includes extensions, deletions, mutations, or a combination thereof (e.g., amino acids at the amino- or carboxy-terminus or between domains) that, in combination, contribute to at most 20% (e.g., at most 15%, 10%, 8%, 6%, 5%, 4%, 3%, 2% or 1%) of the length of a domain, region, module, or protein and do not substantially affect (i.e., do not reduce the activity by more than 50%, such as no more than 40%, 30%, 25%, 20%, 15%, 10%, 5%, or 1%) the activity of the domain(s), region(s), module(s), or protein (e.g., the target binding affinity of a binding protein).
- extensions, deletions, mutations, or a combination thereof e.g., amino acids at the amino- or carboxy-
- amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
- Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, ⁇ -carboxyglutamate, and O-phosphoserine.
- Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an ⁇ -carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
- Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
- mutation refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively.
- a mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s).
- a “conservative substitution” refers to amino acid substitutions that do not significantly affect or alter binding characteristics of a particular protein. Generally, conservative substitutions are ones in which a substituted amino acid residue is replaced with an amino acid residue having a similar side chain.
- Conservative substitutions include a substitution found in one of the following groups: Group 1: Alanine (Ala or A), Glycine (Gly or G), Serine (Ser or S), Threonine (Thr or T); Group 2: Aspartic acid (Asp or D), Glutamic acid (Glu or Z); Group 3: Asparagine (Asn or N), Glutamine (Gln or Q); Group 4: Arginine (Arg or R), Lysine (Lys or K), Histidine (His or H); Group 5: Isoleucine (Ile or I), Leucine (Leu or L), Methionine (Met or M), Valine (Val or V); and Group 6: Phenylalanine (Phe or F), Tyrosine (Tyr or Y), Tryptophan (Trp or W).
- Group 1 Alanine (Ala or A), Glycine (Gly or G), Serine (Ser or S), Threonine (Thr or T);
- Group 2 Aspartic acid (
- amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing).
- an aliphatic grouping may include, for purposes of substitution, Gly, Ala, Val, Leu, and Ile.
- Other conservative substitutions groups include: sulfur-containing: Met and Cysteine (Cys or C); acidic: Asp, Glu, Asn, and Gln; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gln; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, Ile, Val, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information can be found in Creighton (1984) Proteins, W.H. Freeman and Company.
- protein or “polypeptide” refers to a polymer of amino acid residues. Proteins apply to naturally occurring amino acid polymers, as well as to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, and non-naturally occurring amino acid polymers. Variants of proteins, peptides, and polypeptides of this disclosure are also contemplated.
- variant proteins, peptides, and polypeptides comprise or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.9% identical to an amino acid sequence of a defined or reference amino acid sequence as described herein.
- Nucleic acid molecule or “polynucleotide” or “polynucleic acid” refers to a polymeric compound including covalently linked nucleotides, which can be made up of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g., morpholine ring).
- Nucleic acid molecules include polyribonucleic acid (RNA), which includes mRNA, microRNA, siRNA, viral genomic RNA, and synthetic RNA, and polydeoxyribonucleic acid (DNA), which includes cDNA, genomic DNA, and synthetic DNA, either of which may be single or double stranded. If single-stranded, the nucleic acid molecule may be the coding strand or non-coding (anti-sense) strand.
- RNA polyribonucleic acid
- DNA polydeoxyribonucleic acid
- a nucleic acid molecule encoding an amino acid sequence includes all nucleotide sequences that encode the same amino acid sequence.
- nucleotide sequences may also include intron(s) to the extent that the intron(s) would be removed through co- or post-transcriptional mechanisms.
- different nucleotide sequences may encode the same amino acid sequence as the result of the redundancy or degeneracy of the genetic code, or by splicing.
- Variants of nucleic acid molecules of this disclosure are also contemplated.
- Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and are preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical a nucleic acid molecule of a defined or reference polynucleotide as described herein, or that hybridize to a polynucleotide under stringent hybridization conditions of 0.015M sodium chloride, 0.0015M sodium citrate at about 65-68oC or 0.015M sodium chloride, 0.0015M sodium citrate, and 50% formamide at about 42oC. Nucleic acid molecule variants retain the capacity to encode a binding domain thereof having a functionality described herein, such as binding a target molecule.
- Percent sequence identity refers to a relationship between two or more sequences, as determined by comparing the sequences. Preferred methods to determine sequence identity are designed to give the best match between the sequences being compared. For example, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment). Further, non-homologous sequences may be disregarded for comparison purposes. The percent sequence identity referenced herein is calculated over the length of the reference sequence, unless indicated otherwise. Methods to determine sequence identity and similarity can be found in publicly available computer programs.
- Sequence alignments and percent identity calculations may be performed using a BLAST program (e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX).
- BLAST program e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX.
- the mathematical algorithm used in the BLAST programs can be found in Altschul et al., Nucleic Acids Res.25:3389-3402, 1997.
- sequence analysis software is used for analysis, the results of the analysis are based on the "default values" of the program referenced. "Default values" mean any set of values or parameters which originally load with the software when first initialized.
- isolated means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring).
- nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated.
- nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide.
- isolated can, in some embodiments, also describe an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition that is outside of a human body.
- gene means the segment of DNA or RNA involved in producing a polypeptide chain; in certain contexts, it includes regions preceding and following the coding region (e.g., 5’ untranslated region (UTR) and 3’ UTR) as well as intervening sequences (introns) between individual coding segments (exons).
- regions preceding and following the coding region e.g., 5’ untranslated region (UTR) and 3’ UTR
- intervening sequences introns between individual coding segments (exons).
- a “functional variant” refers to a polypeptide or polynucleotide that is structurally similar or substantially structurally similar to a parent or reference compound of this disclosure, but differs slightly in composition (e.g., one base, atom or functional group is different, added, or removed), such that the polypeptide or encoded polypeptide is capable of performing at least one function of the parent polypeptide with at least 50% efficiency, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide.
- a functional variant of a polypeptide or encoded polypeptide of this disclosure has "similar binding,” “similar affinity” or “similar activity” when the functional variant displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide, such as an assay for measuring binding affinity (e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (K D ) constant).
- binding affinity e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (K D ) constant.
- a “functional portion” or “functional fragment” refers to a polypeptide or polynucleotide that comprises only a domain, portion or fragment of a parent or reference compound, and the polypeptide or encoded polypeptide retains at least 50% activity associated with the domain, portion or fragment of the parent or reference compound, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide, or provides a biological benefit (e.g., effector function).
- a biological benefit e.g., effector function
- a “functional portion” or “functional fragment” of a polypeptide or encoded polypeptide of this disclosure has “similar binding” or “similar activity” when the functional portion or fragment displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide (preferably no more than 20% or 10%, or no more than a log difference as compared to the parent or reference with regard to affinity).
- the term "engineered,” “recombinant,” or “non-natural” refers to an organism, microorganism, cell, nucleic acid molecule, or vector that includes at least one genetic alteration or has been modified by introduction of an exogenous or heterologous nucleic acid molecule, wherein such alterations or modifications are introduced by genetic engineering (i.e., human intervention). Genetic alterations include, for example, modifications introducing expressible nucleic acid molecules encoding functional RNA, proteins, fusion proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of a cell’s genetic material.
- Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a polynucleotide, gene, or operon.
- heterologous or “non-endogenous” or “exogenous” refers to any gene, protein, compound, nucleic acid molecule, or activity that is not native to a host cell or a subject, or any gene, protein, compound, nucleic acid molecule, or activity native to a host cell or a subject that has been altered.
- Heterologous, non-endogenous, or exogenous includes genes, proteins, compounds, or nucleic acid molecules that have been mutated or otherwise altered such that the structure, activity, or both is different as between the native and altered genes, proteins, compounds, or nucleic acid molecules.
- heterologous, non-endogenous, or exogenous genes, proteins, or nucleic acid molecules may not be endogenous to a host cell or a subject, but instead nucleic acids encoding such genes, proteins, or nucleic acid molecules may have been added to a host cell by conjugation, transformation, transfection, electroporation, or the like, wherein the added nucleic acid molecule may integrate into a host cell genome or can exist as extra-chromosomal genetic material (e.g., as a plasmid or other self-replicating vector).
- homologous or homolog refers to a gene, protein, compound, nucleic acid molecule, or activity found in or derived from a host cell, species, or strain.
- a heterologous or exogenous polynucleotide or gene encoding a polypeptide may be homologous to a native polynucleotide or gene and encode a homologous polypeptide or activity, but the polynucleotide or polypeptide may have an altered structure, sequence, expression level, or any combination thereof.
- a non-endogenous polynucleotide or gene, as well as the encoded polypeptide or activity may be from the same species, a different species, or a combination thereof.
- a nucleic acid molecule or portion thereof native to a host cell will be considered heterologous to the host cell if it has been altered or mutated, or a nucleic acid molecule native to a host cell may be considered heterologous if it has been altered with a heterologous expression control sequence or has been altered with an endogenous expression control sequence not normally associated with the nucleic acid molecule native to a host cell.
- heterologous can refer to a biological activity that is different, altered, or not endogenous to a host cell.
- heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding an antibody or antigen-binding fragment (or other polypeptide), or any combination thereof.
- endogenous or “native” refers to a polynucleotide, gene, protein, compound, molecule, or activity that is normally present in a host cell or a subject.
- expression refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene.
- the process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post- translational modification, or any combination thereof.
- An expressed nucleic acid molecule is typically operably linked to an expression control sequence (e.g., a promoter).
- operably linked refers to the association of two or more nucleic acid molecules on a single nucleic acid fragment so that the function of one is affected by the other.
- heterologous nucleic acid molecules When two or more heterologous nucleic acid molecules are introduced into a host cell, it is understood that the two or more heterologous nucleic acid molecules can be introduced as a single nucleic acid molecule (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof.
- the number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of separate nucleic acid molecules introduced into a host cell.
- construct refers to any polynucleotide that contains a recombinant nucleic acid molecule (or, when the context clearly indicates, a fusion protein of the present disclosure).
- a (polynucleotide) construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome.
- a "vector” is a nucleic acid molecule that is capable of transporting another nucleic acid molecule. Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules.
- Vectors of the present disclosure also include transposon systems (e.g., Sleeping Beauty, see, e.g., Geurts et al., Mol. Ther.8:108, 2003: Mátés et al., Nat. Genet.41:753, 2009).
- Exemplary vectors are those capable of autonomous replication (episomal vector), capable of delivering a polynucleotide to a cell genome (e.g., viral vector), or capable of expressing nucleic acid molecules to which they are linked (expression vectors).
- expression vector refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host.
- control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation.
- the vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert.
- the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself or deliver the polynucleotide contained in the vector into the genome without the vector sequence.
- plasmid "expression plasmid,” “virus,” and “vector” are often used interchangeably.
- nucleic acid molecule in the context of inserting a nucleic acid molecule into a cell, means “transfection", “transformation,” or “transduction” and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
- polynucleotides of the present disclosure may be operatively linked to certain elements of a vector.
- Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion.
- Expression control sequences may be operatively linked if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
- the vector comprises a plasmid vector or a viral vector (e.g., a lentiviral vector or a ⁇ -retroviral vector).
- Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as ortho-myxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox, and canarypox).
- herpesvirus e.
- viruses include, for example, Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus.
- retroviruses include avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
- “Retroviruses” are viruses having an RNA genome, which is reverse-transcribed into DNA using a reverse transcriptase enzyme, the reverse-transcribed DNA is then incorporated into the host cell genome.
- “Gammaretrovirus” refers to a genus of the retroviridae family. Examples of gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses.
- "Lentiviral vectors” include HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types.
- Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope, and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells.
- the viral vector can be a gammaretrovirus, e.g., Moloney murine leukemia virus (MLV)-derived vectors.
- MMV Moloney murine leukemia virus
- the viral vector can be a more complex retrovirus-derived vector, e.g., a lentivirus-derived vector.
- HIV-1-derived vectors belong to this category.
- Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus).
- Methods of using retroviral and lentiviral viral vectors and packaging cells for transducing mammalian host cells with viral particles containing transgenes are known in the art and have been previous described, for example, in: U.S. Patent 8,119,772; Walchli et al., PLoS One 6:327930, 2011; Zhao et al., J.
- Retroviral and lentiviral vector constructs and expression systems are also commercially available.
- viral vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defective HSV and attenuated HSV (Krisky et al., Gene Ther.5:1517, 1998).
- HSVs herpes simplex viruses
- Other vectors that can be used with the compositions and methods of this disclosure include those derived from baculoviruses and ⁇ -viruses. (Jolly, D J.1999. Emerging Viral Vectors. pp 209-40 in Friedmann T. ed. The Development of Human Gene Therapy.
- plasmid vectors such as sleeping beauty or other transposon vectors
- the viral vector may also comprise additional sequences between the two (or more) transcripts allowing for bicistronic or multicistronic expression. Examples of such sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide, or any combination thereof.
- IRS internal ribosome entry sites
- the term "host” refers to a cell or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest (e.g., an antibody of the present disclosure).
- a host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids or express proteins. The term also encompasses progeny of the host cell, whether genetically or phenotypically the same or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells.
- a "host” refers to a cell or a subject (e.g., a human) infected with SARS-CoV-2.
- Antigen or "Ag”, as used herein, refers to an immunogenic molecule that provokes an immune response.
- This immune response may involve antibody production, activation of specific immunologically-competent cells, activation of complement, antibody dependent cytotoxicicity, or any combination thereof.
- An antigen immunological molecule
- An antigen may be, for example, a peptide, glycopeptide, polypeptide, glycopolypeptide, polynucleotide, polysaccharide, lipid, or the like. It is readily apparent that an antigen can be synthesized, produced recombinantly, or derived from a biological sample. Exemplary biological samples that can contain one or more antigens include tissue samples, stool samples, cells, biological fluids, or combinations thereof. Antigens can be produced by cells that have been modified or genetically engineered to express an antigen.
- Antigens can also be present in a SARS-CoV-2 (e.g., a surface glycoprotein or portion thereof), such as present in a virion, or expressed or presented on the surface of a cell infected by SARS-CoV-2.
- SARS-CoV-2 e.g., a surface glycoprotein or portion thereof
- epitope includes any molecule, structure, amino acid sequence, or protein determinant that is recognized and specifically bound by a cognate binding molecule, such as an immunoglobulin, or other binding molecule, domain, or protein.
- Epitopic determinants generally contain chemically active surface groupings of molecules, such as amino acids or sugar side chains, and can have specific three-dimensional structural characteristics, as well as specific charge characteristics.
- the epitope can be comprised of consecutive amino acids (e.g., a linear epitope), or can be comprised of amino acids from different parts or regions of the protein that are brought into proximity by protein folding (e.g., a discontinuous or conformational epitope), or non-contiguous amino acids that are in close proximity irrespective of protein folding.
- An epitope may also be referred to herein as a "footprint" of a cognate binding molecule (e.g., antibody or antigen-binding fragment) on the molecule (e.g., RBD or S protein) bound thereby.
- an antibody or antigen-binding fragment "contacts" an epitope structure (amino acid residue or glycan) as described herein when any atom of the antibody or antigen-binding fragment, when bound to a SARS or SARS-CoV-2 RBD, is within 5.0 ⁇ of the epitope structure (e.g., as determined by cryo-electron microscopy (e.g., single-particle cryo-EM) at 3.7 ⁇ resolution or at 3.1 ⁇ resolution; and/or as determined by x-ray crystallography, at 2.65 ⁇ resolution such as described herein).
- cryo-electron microscopy e.g., single-particle cryo-EM
- an antibody or antigen-binding fragment contacts an epitope structure (amino acid residue or glycan) as described herein when any atom of the antibody or antigen-binding fragment, when bound to the RBD, is within 3.7 ⁇ of the epitope structure.
- an antibody or antigen-binding fragment contacts an epitope structure (amino acid residue or glycan) as described herein when any atom of the antibody or antigen-binding fragment, when bound to a SARS or SARS-CoV-2 RBD, is within 3.1 ⁇ of the epitope structure.
- contacting comprises an electrostatic interaction between the antibody or antigen-binding fragment and the epitope structure.
- contacting comprises a hydrophobic contact or hydrophobic interaction between the antibody or antigen-binding fragment and the epitope structure.
- SARS-CoV-2 Target Region The present disclosure provides, in part, a target region in SARS-CoV-2 RBD that is highly conserved across other SARS coronaviruses and current SARS-CoV-2 variants.
- the target region comprises an epitope that is specifically recognized and bound by an antibody or antigen-binding fragment thereof, and can include additional structures (e.g. amino acids, sugar side chains) that are in proximity to and/or are between epitope residues in three-dimensional space.
- antibodies and antigen-binding fragments that are capable of binding to a SARS coronavirus (e.g., SARS-CoV-2 or a variant thereof) in a target region are provided, as well as immunogenic polypeptides that comprise amino acid residues, sequences, and/or features (e.g., helix, beta-sheet) of a target region.
- SARS coronavirus e.g., SARS-CoV-2 or a variant thereof
- immunogenic polypeptides that comprise amino acid residues, sequences, and/or features (e.g., helix, beta-sheet) of a target region.
- RBD epitope of antibody S309 (VH: SEQ ID NO.:105; VL: SEQ ID NO.:168) was determined by cryo-electron microscopy (initially at 4.2 ⁇ resolution of the Fab in complex with open-conformation RBD and 3.6 ⁇ resolution of the Fab in complex with closed-conformation RBD; refined at 3.7 ⁇ resolution of the Fab in complex with open-conformation RBD and 3.1 ⁇ resolution of the Fab in complex with closed-conformation RBD) and by x-ray crystal studies (2.65 ⁇ resolution, with epitope features identified as all RBD amino acid residues within 5.0 ⁇ of any atom of the Fab of antibody S309).
- cryo-electron microscopy studies at the higher resolution identified the following amino acids (numbering as in SEQ ID NO.:165) as the epitope of antibody S309: T333; N334; L335; P337; G339; E340; V341; N343 (bearing a glycan that contains a core fucose); A344; T345; R346; N354; K356; R357; I358; S359; N360; C361; N440; L441; K444; R509.
- cryo-EM 4.2 ⁇ resolution of the Fab in complex with open-conformation RBD and 3.6 ⁇ resolution of the Fab in complex with closed-conformation RBD
- C336 and D442 were included in the epitope.
- the higher resolution data are preferred.
- the x-ray crystal studies identified the following amino acids as the epitope of antibody S309: T333; N334; L335; C336; P337; G339; E340; V341; N343 (bearing a glycan that contains a core fucose); A344; T345; R346; N354; K356; R357; I358; S359; N360; C361; N440; L441; R509.
- a non-limiting example of procedures and parameters for performing cryo-electron microscopy using SARS-CoV-2 glycoprotein and an antibody or antigen- binding fragment comprises (1)-(4) below; see also Protein Data Bank codes 6WPS (Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment; DOI: 10.2210/pdb6WPS/pdb; EMDataResource: EMD-21864) and 6WPT (Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state); DOI: 10.2210/pdb6WPT/pdbEMDataResource: EMD-21865; Deposited: 2020-04- 27 Released: 2020-05-27): (1) Recombinant S-glycoprotein ectodomain and SB production: ⁇ Producing SARS-CoV-22P S glycoprotein (GenBank: YP_009724390.1) ectodomain in 500-(4) below
- ⁇ Resolutions can be based on the gold-standard Fourier shell correlation of 0.143 criterion and Fourier shell correlation curves, and may be corrected for the effects of e.g. soft masking by high-resolution noise substitution (see Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012)).
- Cryo-EM model building and analysis ⁇ Using UCSF Chimera (Goddard, T. D., Huang, C. C. & Ferrin, T. E. Visualizing density maps with UCSF Chimera. J. Struct.
- a target region in RBD comprises a helix that comprises amino acid residues 337-344 of SEQ ID NO.:165, a 5-stranded ⁇ -sheet (residues 356- 361 of SEQ ID NO.:165, and another helix that spans residues 440-444 of SEQ ID NO.:165 and is located near the three-fold molecular axis of an S glycoprotein trimer.
- This RBD epitope and portions thereof, and, in some embodiments, target region sequence that is not within the epitope but that is adjacent, is proximal to, and/or is between epitope residues or portions of the epitope, provides immunogenic polypeptides that are described in further detail in the present disclosure.
- an antibody or antigen-binding fragment is capable of binding in a target region comprising, or an immunogenic polypeptide comprises, any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- a target region and/or an immunogenic polypeptide further comprises D442 according to SEQ ID NO.:165.
- an antibody or antigen-binding fragment is capable of binding in a target region comprising, or an immunogenic polypeptide comprises, any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165).
- a target region and/or an immunogenic polypeptide further comprises D442 according to SEQ ID NO.:165.
- an antibody or antigen-binding fragment is capable of binding in a target region comprising, or an immunogenic polypeptide comprises, any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165).
- a target region and/or an immunogenic polypeptide further comprises D442 according to SEQ ID NO.:165.
- Table 1. shows SEQ ID NO.:165 with S309 antibody epitope residues (as determined by cryo-EM (higher-resolution settings) or X-ray studies) in bold. Table 1.
- Wuhan-Hu-1 CoV-2 S Glycoprotein Amino Acid Sequence (SEQ ID NO.:165) showing S309 Antibody Epitope Residues (bold) and human ACE2 Contact Residues (underlined), as Determined by X-Ray or Cryo-EM Studies Antibodies, Antigen-Binding Fragments, and Compositions
- the present disclosure provides an antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD) when the RBD is in an open conformation and/or when the RBD is in a closed conformation. Structure and function of antibodies and antigen-binding fragments is decribed further herein.
- SARS-CoV-2 surface glycoproteins has been observed in an "open” conformation, wherein the surface glycoprotein is present in a homotrimer of surface glycoprotein monomers and the RBD of one surface glycoprotein monomer of the trimer points upward relative to the other two RBDs, away from the C-terminal end of the surface glycoprotein, and also in a "closed” confrmation, where none of the three RBDs of a surface glycoprotein trimer point upward. See, for example, Figure 39A.
- "open" in the context of a surface glycoprotein conformation includes a partially open conformation and a fully open conformation.
- the antibody or antigen-binding fragment is capable of binding to the RBD when the RBD is in an open conformation, and is capable of binding to the RBD when the RBD is in a closed conformation.
- the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein is comprised in a trimer thereof, wherein, optionally, each surface glycoprotein of the trimer can be simultaneously bound to a separate antibody or antigen-binding fragment.
- one RBD of the trimer is in an open conformation.
- two or three RBDs of the trimer are in a closed conformation.
- the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein RBD of a SARS coronavirus and/or of another sarbecovirus that is not SARS-CoV-2.
- the SARS coronavirus comprises Urbani, CHUK-1, GZ02, HC_SZ_61_03, A031G, WIV1 SARS-like bat, or any combination thereof.
- the antibody or antigen-binding fragment is capable of binding to a SARS-CoV-2 surface glycoprotein when the SARS-CoV-2 surface glycoprotein is in a prefusion conformation.
- an antibody, or an antigen-binding fragment thereof that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD), wherein the binding comprises contacting one or more amino acid residues of the RBD that are different from the amino acid residues of the RBD that contact a human ACE2 when the SARS CoV-2 surface glycoprotein is bound to the human ACE2, wherein, optionally, the antibody or antigen-binding fragment does not compete with human ACE2 for binding to the RBD.
- RBD SARS-CoV-2 surface glycoprotein receptor binding domain
- binding to human ACE2 can be determined using, for example, biolayer interferometry (BLI), wherein human ACE2 is loaded onto a BLI sensor followed by incubation of RBD alone or RBD plus antibody aor antigen-binding fragment.
- binding of the antibody or antigen-binding fragment to the RBD does not comprise contacting an RBD amino acid residue that contacts a human ACE2 when the surface glycoprotein is bound to the human ACE2.
- RBD residues that contact human ACE2 are V445, G446, G447, Y449, Y453, L455, F456, Y473, A475, G476, E484, F486, N487, Y489, Q493, G496, F497, Q498, T500, N501, G502, and Y505 of SEQ ID NO.:165.
- an antibody or antigen-binding fragment that is capable of binding to a SARS-CoV-2 epitope that comprises or consists of any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- binding comprises contacting any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- binding comprises contacting amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- the antibody or antigen-binding fragment is capable of binding to a SARS-CoV-2 epitope that comprises or consists of any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- binding comprises contacting any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- binding comprises contacting amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- the antibody or antigen-binding fragment is capable of binding to a SARS-CoV-2 epitope that comprises or consists of any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165.
- binding comprises contacting any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165.
- binding comprises contacting amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165.
- binding of the antibody or antigen-binding fragment to the RBD can comprise contacting amino acid N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated, such as, for example, comprising a fucose.
- an antibody or antigen-binding fragment thereof is provided that is capable of binding to a target region in RBD that comprises (i) a helix that comprises amino acid residues 337-344 of SEQ ID NO.:165, (ii) a 5-stranded ⁇ - sheet (residues 356-361 of SEQ ID NO.:165, and (iii) a helix that spans residues 440- 444 of SEQ ID NO.:165 and is located near the three-fold molecular axis of an S glycoprotein trimer.
- an antibody, or an antigen-binding fragment thereof, that is capable of binding to an epitope in a sarbecovirus surface glycoprotein receptor binding domain (RBD), wherein the epitope comprises an asparagine amino acid residue that is or that corresponds to amino acid residue N343 of SEQ ID NO.:165, wherein the correspondence is determined according to sequence alignment of (i) a sarbecovirus surface glycoprotein or RBD amino acid sequence containing the asparagine amino acid residue with (ii) SEQ ID NO.:165.
- the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 is glycosylated.
- an asparagine amino acid residue that "corresponds to" N343 of SEQ ID NO.:165 refers to an asparagine amino acid of a coronavirus, betacoronavirus, sarbecovirus, or SARS-CoV amino acid sequence that is not SEQ ID NO.:165 or is not from Wuhan-Hu-1, wherein the asparagine amino acid has an equivalent position within the amino acid sequence as compared to the position of N343 in SEQ ID No.:365 – for example, the coronavirus, betacoronavirus, sarbecovirus, or SARS-CoV amino acid sequence that is not SEQ ID NO.:165 may be shorter or longer than the amino acid sequence comprising SEQ ID NO.:165, such that position 343 in the coronavirus, betacoronavirus, sarbecovirus, or SARS-CoV amino acid sequence that is not SEQ ID NO.:165 or from Wuhan-Hu-1 may not be the equivalent residue to N343 in SEQ ID
- viral genomic sequences can be downloaded from GISAID using the ‘complete (>29,000 bp)’ and ‘low coverage exclusion’ filters.
- Non-human sequences can be included or excluded.
- S glycoprotein ORF can be localized by aligning a reference protein sequence (e.g. YP_009724390.1) to the genomic sequence of isolates with Exonerate v.2.4.0 (-m protein2dna --refine full --minintron 999999 --percent 30 --showalignment false --showvulgar false --ryo “>%ti ⁇ n%tcs). Coding nucleotide sequences can be translated in silico using seqkit v.0.12.0.
- the glycosylation of the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 comprises a fucose.
- the asparagine amino acid residue (N) that is or that corresponds to N343 of SEQ ID NO.:165 is comprised in an amino acid sequence N-X- T, X being any amino acid except for P, and preferably being A.
- the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence NITNCLPFGEVFNATR (SEQ ID NO.:234), or a variant thereof having one, two, three, four or five amino acid substitutions, provided that the sequence N-X-T is present, X being any amino acid except for P, and preferably being A.
- the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence NITNCLPFGEVFNATRFASVYAWNRKRISNCV (SEQ ID NO.:235), or is comprised in a variant sequence of SEQ ID NO.:235 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions relative to SEQ ID NO.:235, provided that the amino acid sequence N-X-T is present, X being any amino acid except for P, and preferably being A, wherein optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:235 independently comprises a conservative substitution or a non-conservative substitution.
- the antibody or antigen-binding fragment is capable of binding to, and optionally is capable of neutralizing an infection (e.g., in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human) by, a SARS-CoV-2 that comprises any one or more of the following mutations relative to SEQ ID NO.:165: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K.
- the antibody or antigen-binding fragment is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2 that comprises any one or more of the following mutations in RBD relative to SEQ ID NO.:165: N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q; E340D; L335S; L441F; L441I; L441R; L441R; L44
- the antibody or antigen-binding fragment is capable of neutralizing the SARS-CoV-2 infection with a potency that is less than 3-fold reduced as compared to the potency with which the antibody or antigen-binding fragment neutralizes infection by a SARS-CoV-2 that comprises the amino acid sequence of SEQ ID NO.:165.
- An exemplary antibody or antigen-binding fragment according to the presently disclosed embodiments comprises the VH amino acid sequence of SEQ ID NO.:105 and the VL amino acid sequence of SEQ ID NO.:168 (e.g., antibody S309).
- Engineered variants of S309 that bind to SARS-CoV-2 include those having the VH amino acid sequence set forth in SEQ ID NO.:113, SEQ ID NO.:129, SEQ ID NO.:119, or SEQ ID NO.:172, and the VL amino acid sequence set forth in SEQ ID NO.:168.
- Terms understood by those in the art of antibody technology are each given the meaning acquired in the art, unless expressly defined differently herein.
- antibody refers to an intact antibody comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as any antigen-binding portion or fragment of an intact antibody that has or retains the ability to bind to the antigen target molecule recognized by the intact antibody, such as an scFv, Fab, or Fab'2 fragment.
- antibody herein is used in the broadest sense and includes polyclonal and monoclonal antibodies, including intact antibodies and functional (antigen-binding) antibody fragments thereof, including fragment antigen binding (Fab) fragments, F(ab')2 fragments, Fab' fragments, Fv fragments, recombinant IgG (rIgG) fragments, single chain antibody fragments, including single chain variable fragments (scFv), and single domain antibodies (e.g., sdAb, sdFv, nanobody) fragments.
- Fab fragment antigen binding
- F(ab')2 fragments fragment antigen binding
- Fab' fragments fragment antigen binding
- Fv fragments fragment antigen binding fragments
- rIgG recombinant IgG fragments
- single chain antibody fragments including single chain variable fragments (scFv), and single domain antibodies (e.g., sdAb, sdFv, nanobody) fragments.
- the term encompasses genetically engineered and/or otherwise modified forms of immunoglobulins, such as intrabodies, peptibodies, chimeric antibodies, fully human antibodies, humanized antibodies, and heteroconjugate antibodies, multispecific, e.g., bispecific antibodies, diabodies, triabodies, tetrabodies, tandem di-scFv, and tandem tri-scFv.
- antibody should be understood to encompass functional antibody fragments thereof.
- the term also encompasses intact or full-length antibodies, including antibodies of any class or sub-class, including IgG and sub-classes thereof (IgG1, IgG2, IgG3, IgG4), IgM, IgE, IgA, and IgD.
- V L or “VL” and “V H “ or “VH” refer to the variable binding region from an antibody light chain and an antibody heavy chain, respectively.
- a VL is a kappa ( ⁇ ) class (also “VK” herein).
- a VL is a lambda ( ⁇ ) class.
- the variable binding regions comprise discrete, well-defined sub-regions known as “complementarity determining regions” (CDRs) and “framework regions” (FRs).
- CDR complementarity determining region
- HVR hypervariable region
- an antibody VH comprises four FRs and three CDRs as follows: FR1-HCDR1-FR2-HCDR2-FR3-HCDR3-FR4; and an antibody VL comprises four FRs and three CDRs as follows: FR1-LCDR1-FR2- LCDR2-FR3-LCDR3-FR4.
- the VH and the VL together form the antigen- binding site through their respective CDRs.
- a "variant" of a CDR refers to a functional variant of a CDR sequence having up to 1-3 amino acid substitutions (e.g., conservative or non- conservative substitutions), deletions, or combinations thereof.
- Numbering of CDR and framework regions may be according to any known method or scheme, such as the Kabat, Chothia, EU, IMGT, and AHo numbering schemes (see, e.g., Kabat et al., "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5 th ed.; Chothia and Lesk, J. Mol. Biol.196:901-917 (1987)); Lefranc et al., Dev. Comp. Immunol.27:55, 2003; Honegger and Plückthun, J. Mol.
- CCG Chemical Computing Group
- MOE Molecular Operating Environment
- ANARCI Antigen receptor Numbering And Receptor Classification
- CH refers to an "immunoglobulin heavy chain constant region" or a "heavy chain constant region,” which is further divisible, depending on the antibody isotype into CH1, CH2, and CH3 (IgA, IgD, IgG), or CH1, CH2, CH3, and CH4 domains (IgE, IgM).
- the Fc region of an antibody heavy chain is described further herein.
- an antibody or antigen-binding fragment of the present disclosure comprises any one or more of CL, a CH1, a CH2, and a CH3.
- a CL comprises an amino acid sequence having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 975, 98%, 99%, or 100% identity to the amino acid sequence of SEQ ID NO.:174 or SEQ ID NO.: 193.
- a CH1-CH2-CH3 comprises an amino acid sequence having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 975, 98%, 99%, or 100% identity to the amino acid sequence of SEQ ID NO.:173 or SEQ ID NO.:175.
- a “Fab” fragment antigen binding is the part of an antibody that binds to antigens and includes the variable region and CH1 of the heavy chain linked to the light chain via an inter-chain disulfide bond. Each Fab fragment is monovalent with respect to antigen binding, i.e., it has a single antigen-binding site. Pepsin treatment of an antibody yields a single large F(ab')2 fragment that roughly corresponds to two disulfide linked Fab fragments having divalent antigen-binding activity and is still capable of cross-linking antigen.
- Both the Fab and F(ab’)2 are examples of "antigen- binding fragments.”
- Fab' fragments differ from Fab fragments by having additional few residues at the carboxy terminus of the CH1 domain including one or more cysteines from the antibody hinge region.
- Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
- F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
- Fab fragments may be joined, e.g., by a peptide linker, to form a single chain Fab, also referred to herein as "scFab.”
- a single chain Fab also referred to herein as "scFab.”
- an inter-chain disulfide bond that is present in a native Fab may not be present, and the linker serves in full or in part to link or connect the Fab fragments in a single polypeptide chain.
- a heavy chain- derived Fab fragment e.g., comprising, consisting of, or consisting essentially of VH + CH1, or "Fd
- a light chain-derived Fab fragment e.g., comprising, consisting of, or consisting essentially of VL + CL
- a scFab may be arranged, in N-terminal to C-terminal direction, according to (heavy chain Fab fragment – linker – light chain Fab fragment) or (light chain Fab fragment – linker – heavy chain Fab fragment).
- Peptide linkers and exemplary linker sequences for use in scFabs are discussed in further detail herein.
- a scFab can be comprise any combination of VH and VL sequences or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein.
- “Fv” is a small antibody fragment that contains a complete antigen-recognition and antigen-binding site.
- This fragment generally consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association.
- a single variable domain or half of an Fv comprising only three CDRs specific for an antigen
- sFv single-chain Fv
- scFv single-chain Fv
- the scFv polypeptide comprises a polypeptide linker disposed between and linking the VH and VL domains that enables the scFv to retain or form the desired structure for antigen binding.
- the antibody or antigen-binding fragment comprises a scFv comprising a VH domain, a VL domain, and a peptide linker linking the VH domain to the VL domain.
- a scFv comprises a VH domain linked to a VL domain by a peptide linker, which can be in a VH-linker- VL orientation or in a VL-linker-VH orientation.
- Any scFv of the present disclosure may be engineered so that the C-terminal end of the VL domain is linked by a short peptide sequence to the N-terminal end of the VH domain, or vice versa (i.e., (N)VL(C)-linker-(N)VH(C) or (N)VH(C)-linker-(N)VL(C).
- a linker may be linked to an N-terminal portion or end of the VH domain, the VL domain, or both.
- Peptide linker sequences may be chosen, for example, based on: (1) their ability to adopt a flexible extended conformation; (2) their inability or lack of ability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides and/or on a target molecule; and/or (3) the lack or relative lack of hydrophobic or charged residues that might react with the polypeptides and/or target molecule.
- linker design e.g., length
- linker design can include the conformation or range of conformations in which the VH and VL can form a functional antigen-binding site.
- peptide linker sequences contain, for example, Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala, may also be included in a linker sequence. Other amino acid sequences which may be usefully employed as linker include those disclosed in Maratea et al., Gene 40:3946 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:82588262 (1986); U.S. Pat. No. 4,935,233, and U.S. Pat. No.4,751,180.
- linkers may include, for example, Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys- Val-Asp (SEQ ID NO: 215) (Chaudhary et al., Proc. Natl. Acad. Sci.
- Any suitable linker may be used, and in general can be about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 1523, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100 amino acids in length, or less than about 200 amino acids in length, and will preferably comprise a flexible structure (can provide flexibility and room for conformational movement between two regions, domains, motifs, fragments, or modules connected by the linker), and will preferably be biologically inert and/or have a low risk of immunogenicity in a human.
- Exemplary linkers include those comprising or consisting of the amino acid sequence set forth in any one or more of SEQ ID NOs: 206-217.
- the linker comprises or consists of an amino acid sequence having at least 75% (i.e., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in any one of SEQ ID NOs: 206-217.
- linker sequences are not required; for example, when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
- DNA in the germline variable (V), joining (J), and diversity (D) gene loci may be rearranged and insertions and/or deletions of nucleotides in the coding sequence may occur. Somatic mutations may be encoded by the resultant sequence, and can be identified by reference to a corresponding known germline sequence.
- somatic mutations that are not critical to a desired property of the antibody e.g., binding to a Wuhan coronavirus antigen
- that confer an undesirable property upon the antibody e.g., an increased risk of immunogenicity in a subject administered the antibody
- the antibody or antigen-binding fragment of the present disclosure comprises at least one more germline-encoded amino acid in a variable region as compared to a parent antibody or antigen-binding fragment, provided that the parent antibody or antigen binding fragment comprises one or more somatic mutations.
- Variable region and CDR amino acid sequences of certain antibodies that bind to SARS-CoV-2 are provided in Table 2 herein.
- An exemplary antibody that binds to an epitope as described herein comprises the VH amino acid sequence set forth in SEQ ID NO.:105 and the VL amino acid sequence set forth in SEQ ID NO.:168.
- Engineered variants of S309 that bind to SARS-CoV-2 include those having the VH amino acid sequence set forth in SEQ ID NO.:113, SEQ ID NO.:129, SEQ ID NO.:119, or SEQ ID NO.:172, and the VL amino acid sequence set forth in SEQ ID NO.:168.
- an antibody or antigen-binding fragment comprises an amino acid modification (e.g., a substitution mutation) to remove an undesired risk of oxidation, deamidation, and/or isomerization.
- variant antibodies that comprise one or more amino acid alterations in a variable region (e.g., VH, VL, framework or CDR) as compared to a presently disclosed ("parent") antibody, wherein the variant antibody is capable of binding to a Wuhan coronavirus antigen.
- an antibody or antigen-binding fragment of the present disclosure is monospecific (e.g., binds to a single epitope) or is multispecific (e.g., binds to multiple epitopes and/or target molecules).
- Antibodies and antigen binding fragments may be constructed in various formats. Exemplary antibody formats disclosed in Spiess et al., Mol.
- FIT-Ig e.g., PCT Publication No.
- the antibody or antigen-binding fragment comprises two or more of VH domains, two or more VL domains, or both (i.e., two or more VH domains and two or more VL domains).
- an antigen-binding fragment comprises the format (N-terminal to C-terminal direction) VH-linker-VL- linker-VH-linker-VL, wherein the two VH sequences can be the same or different and the two VL sequences can be the same or different.
- Such linked scFvs can include any combination of VH and VL domains arranged to bind to a given target, and in formats comprising two or more VH and/or two or more VL, one, two, or more different eptiopes or antigens may be bound. It will be appreciated that formats incorporating multiple antigen-binding domains may include VH and/or VL sequences in any combination or orientation.
- the antigen-binding fragment can comprise the format VL-linker-VH-linker-VL-linker-VH, VH-linker-VL-linker-VL-linker-VH, or VL-linker-VH-linker-VH-linker-VL.
- a bispecific or multispecific antibody or antigen-binding fragment may, in some embodiments, comprise one, two, or more antigen-binding domains (e.g., a VH and a VL) of the instant disclosure.
- Two or more binding domains may be present that bind to the same or a different SARS-CoV-2 epitope, and a bispecific or multispecific antibody or antigen-binding fragment as provided herein can, in some embodiments, comprise a further SARS-CoV-2 binding domain, and/or can comprise a binding domain that binds to a different antigen or pathogen altogether.
- the antibody or antigen-binding fragment can be multispecific; e.g., bispecific, trispecific, or the like.
- the antibody or antigen-binding fragment comprises a Fc polypeptide, or a fragment thereof.
- the "Fc” fragment or Fc polypeptide comprises the carboxy-terminal portions (i.e., the CH2 and CH3 domains of IgG) of both antibody H chains held together by disulfides.
- Antibody effector functions refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.
- modifications may be made to an Fc domain in order to modify (e.g., improve, reduce, or ablate) one or more functionality of an Fc-containing polypeptide (e.g., an antibody of the present disclosure).
- Fc-containing polypeptide e.g., an antibody of the present disclosure.
- Such functions include, for example, Fc receptor (FcR) binding, antibody half-life modulation (e.g., by binding to FcRn), ADCC function, protein A binding, protein G binding, and complement binding.
- Amino acid modifications that modify (e.g., improve, reduce, or ablate) Fc functionalities include, for example, the T250Q/M428L, M252Y/S254T/T256E, H433K/N434F, M428L/N434S, E233P/L234V/L235A/G236 + A327G/A330S/P331S, E333A, S239D/A330L/I332E, P257I/Q311, K326W/E333S, S239D/I332E/G236A, N297Q, K322A, S228P, L235E + E318A/K320A/K322A, L234A/L235A (also referred to herein as “LALA”), and L234A/L235A/P329G mutations, which mutations are summarized and annotated in "Engineered Fc Regions", published by InvivoGen (2011) and available
- the C1q protein complex can bind to at least two molecules of IgG1 or one molecule of IgM when the immunoglobulin molecule(s) is attached to the antigenic target (Ward, E. S., and Ghetie, V., Ther. Immunol.2 (1995) 77-94).
- Burton, D. R. described (Mol. Immunol. 22 (1985) 161-206) that the heavy chain region comprising amino acid residues 318 to 337 is involved in complement fixation.
- FcR binding can be mediated by the interaction of the Fc moiety (of an antibody) with Fc receptors (FcRs), which are specialized cell surface receptors on cells including hematopoietic cells.
- Fc receptors belong to the immunoglobulin superfamily, and shown to mediate both the removal of antibody-coated pathogens by phagocytosis of immune complexes, and the lysis of erythrocytes and various other cellular targets (e.g. tumor cells) coated with the corresponding antibody, via antibody dependent cell mediated cytotoxicity (ADCC; Van de Winkel, J. G., and Anderson, C. L., J. Leukoc. Biol.49 (1991) 511-524).
- ADCC antibody dependent cell mediated cytotoxicity
- FcRs are defined by their specificity for immunoglobulin classes; Fc receptors for IgG antibodies are referred to as Fc ⁇ R, for IgE as Fc ⁇ R, for IgA as Fc ⁇ R and so on and neonatal Fc receptors are referred to as FcRn. Fc receptor binding is described for example in Ravetch, J. V., and Kinet, J. P., Annu. Rev. Immunol.9 (1991) 457-492; Capel, P. J., et al., Immunomethods 4 (1994) 25-34; de Haas, M., et al., J Lab. Clin. Med.126 (1995) 330-341; and Gessner, J.
- Fc ⁇ R Fc domain of native IgG antibodies
- Fc ⁇ R In humans, three classes of Fc ⁇ R have been characterized to-date, which are: (i) Fc ⁇ RI (CD64), which binds monomeric IgG with high affinity and is expressed on macrophages, monocytes, neutrophils and eosinophils; (ii) Fc ⁇ RII (CD32), which binds complexed IgG with medium to low affinity, is widely expressed, in particular on leukocytes, is believed to be a central player in antibody-mediated immunity, and which can be divided into Fc ⁇ RIIA, Fc ⁇ RIIB and Fc ⁇ RIIC, which perform different functions in the immune system, but bind with similar low affinity to the IgG-Fc, and the ectodomains of these receptors are highly homologuous; and (iii) Fc ⁇ RIII (CD16), which binds IgG with medium to low affinity and has been found in two forms: Fc ⁇ RIIIA, which has been found on NK cells, macrophages,
- Fc ⁇ RIIA is found on many cells involved in killing (e.g. macrophages, monocytes, neutrophils) and seems able to activate the killing process.
- Fc ⁇ RIIB seems to play a role in inhibitory processes and is found on B-cells, macrophages and on mast cells and eosinophils. Importantly, it has been shown that 75% of all Fc ⁇ RIIB is found in the liver (Ganesan, L. P. et al., 2012: “Fc ⁇ RIIb on liver sinusoidal endothelium clears small immune complexes,” Journal of Immunology 189: 4981–4988).
- Fc ⁇ RIIB is abundantly expressed on Liver Sinusoidal Endothelium, called LSEC, and in Kupffer cells in the liver and LSEC are the major site of small immune complexes clearance (Ganesan, L. P. et al., 2012: Fc ⁇ RIIb on liver sinusoidal endothelium clears small immune complexes. Journal of Immunology 189: 4981–4988).
- the antibodies disclosed herein and the antigen-binding fragments thereof comprise an Fc polypeptide or fragment thereof for binding to Fc ⁇ RIIb, in particular an Fc region, such as, for example IgG-type antibodies.
- the antibodies of the present disclosure comprise an engineered Fc moiety with the mutations S267E and L328F, in particular as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies.
- Fc ⁇ RIIB may function to suppress further immunoglobulin production and isotype switching to, for example, the IgE class.
- Fc ⁇ RIIB On macrophages, Fc ⁇ RIIB is thought to inhibit phagocytosis as mediated through Fc ⁇ RIIA. On eosinophils and mast cells, the B form may help to suppress activation of these cells through IgE binding to its separate receptor. Regarding Fc ⁇ RI binding, modification in native IgG of at least one of E233- G236, P238, D265, N297, A327 and P329 reduces binding to Fc ⁇ RI.
- Fc ⁇ RII binding reduced binding for Fc ⁇ RIIA is found, e.g., for IgG mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, R292 and K414.
- Fc ⁇ RIIA Two allelic forms of human Fc ⁇ RIIA are the "H131" variant, which binds to IgG1 Fc with high affinity, and the "R131" variant, which binds to IgG1 Fc with low affinity. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009).
- Fc ⁇ RIII binding reduced binding to Fc ⁇ RIIIA is found, e.g., for mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, S239, E269, E293, Y296, V303, A327, K338 and D376.
- two regions of native IgG Fc appear to be involved in interactions between Fc ⁇ RIIs and IgGs, namely (i) the lower hinge site of IgG Fc, in particular amino acid residues L, L, G, G (234 – 237, EU numbering), and (ii) the adjacent region of the CH2 domain of IgG Fc, in particular a loop and strands in the upper CH2 domain adjacent to the lower hinge region, e.g. in a region of P331 (Wines, B.D., et al., J. Immunol.2000; 164: 5313 – 5318).
- Fc ⁇ RI appears to bind to the same site on IgG Fc
- FcRn and Protein A bind to a different site on IgG Fc, which appears to be at the CH2-CH3 interface
- mutations that increase binding affinity of an Fc polypeptide or fragment thereof of the present disclosure to a (i.e., one or more) Fc ⁇ receptor (e.g., as compared to a reference Fc polypeptide or fragment thereof or containing the same that does not comprise the mutation(s)).
- an antibody or antigen-binding fragment can comprise a Fc polypeptide or fragment thereof comprising a mutation selected from G236A; S239D; A330L; and I332E; or a combination comprising any two or more of the same; e.g., S239D/I332E; S239D/A330L/I332E; G236A/S239D/I332E; G236A/A330L/I332E (also referred to herein as "GAALIE"); or G236A/S239D/A330L/I332E.
- the Fc polypeptide or fragment thereof does not comprise S239D.
- the Fc polypeptide or fragment thereof may comprise or consist of at least a portion of an Fc polypeptide or fragment thereof that is involved in binding to FcRn binding.
- the Fc polypeptide or fragment thereof comprises one or more amino acid modifications that improve binding affinity for (e.g., enhance binding to) FcRn (e.g., at a pH of about 6.0) and, in some embodiments, thereby extend in vivo half-life of a molecule comprising the Fc polypeptide or fragment thereof (e.g., as compared to a reference Fc polypeptide or fragment thereof or antibody that is otherwise the same but does not comprise the modification(s)).
- the Fc polypeptide or fragment thereof comprises or is derived from a IgG Fc and a half-life-extending mutation comprises any one or more of: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I Q311I; D376V; T307A; E380A (EU numbering).
- a half-life-extending mutation comprises M428L/N434S (also referred to herein as "MLNS").
- a half-life-extending mutation comprises M252Y/S254T/T256E.
- a half-life-extending mutation comprises T250Q/M428L. In certain embodiments, a half-life-extending mutation comprises P257I/Q311I. In certain embodiments, a half-life-extending mutation comprises P257I/N434H. In certain embodiments, a half-life-extending mutation comprises D376V/N434H. In certain embodiments, a half-life-extending mutation comprises T307A/E380A/N434A. In some embodiments, an antibody or antigen-binding fragment includes a Fc moiety that comprises the substitution mtuations M428L/N434S.
- an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mtuations G236A/A330L/I332E.
- an antibody or antigen-binding fragment includes a (e.g., IgG) Fc moiety that comprises a G236A mutation, an A330L mutation, and a I332E mutation (GAALIE), and does not comprise a S239D mutation (e.g., comprises a native S at position 239).
- an antibody or antigen-binding fragment includes an Fc polypeptide or fragment thereof that comprises the substitution mutations: M428L/N434S and G236A/A330L/I332E, and optionally does not comprise S239D.
- an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mutations: M428L/N434S and G236A/S239D/A330L/I332E.
- the antibody or antigen-binding fragment comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or the antibody or antigen-binding fragment is partially or fully aglycosylated and/or is partially or fully afucosylated.
- Host cell lines and methods of making partially or fully aglycosylated or partially or fully afucosylated antibodies and antigen-binding fragments are known (see, e.g., PCT Publication No. WO 2016/181357; Suzuki et al. Clin. Cancer Res.13(6):1875-82 (2007); Huang et al. MAbs 6:1-12 (2018)).
- the antibody or antigen-binding fragment is capable of eliciting continued protection in vivo in a subject even once no detectable levels of the antibody or antigen-binding fragment can be found in the subject (i.e., when the antibody or antigen-binding fragment has been cleared from the subject following administration). Such protection is referred to herein as a vaccinal effect. Without wishing to be bound by theory, it is believed that dendritic cells can internalize complexes of antibody and antigen and thereafter induce or contribute to an endogenous immune response against antigen.
- an antibody or antigen- binding fragment comprises one or more modifications, such as, for example, mutations in the Fc comprising G236A, A330L, and I332E, that are capable of activating dendritic cells that may induce, e.g., T cell immunity to the antigen.
- the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof, including a CH2 (or a fragment thereof, a CH3 (or a fragment thereof), or a CH2 and a CH3, wherein the CH2, the CH3, or both can be of any isotype and may contain amino acid substitutions or other modifications as compared to a corresponding wild-type CH2 or CH3, respectively.
- a Fc polypeptide of the present disclosure comprises two CH2-CH3 polypeptides that associate to form a dimer.
- the antibody or antigen-binding fragment can be monoclonal.
- the term "monoclonal antibody” (mAb) as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present, in some cases in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site.
- each monoclonal antibody is directed against a single epitope of the antigen.
- the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies.
- the term "monoclonal” is not to be construed as requiring production of the antibody by any particular method.
- monoclonal antibodies useful in the present invention may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256:495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal, or plant cells (see, e.g., U.S. Pat.
- Monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example. Monoclonal antibodies may also be obtained using methods disclosed in PCT Publication No. WO 2004/076677A2.
- Antibodies and antigen-binding fragments of the present disclosure include "chimeric antibodies" in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see, U.S. Pat. Nos.4,816,567; 5,530,101 and 7,498,415; and Morrison et al., Proc. Natl. Acad. Sci. USA, 81:6851-6855 (1984)).
- chimeric antibodies may comprise human and non-human residues.
- chimeric antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. For further details, see Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323- 329 (1988); and Presta, Curr. Op. Struct. Biol.2:593-596 (1992).
- Chimeric antibodies also include primatized and humanized antibodies.
- a "humanized antibody” is generally considered to be a human antibody that has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are typically taken from a variable domain.
- Humanization may be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Reichmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting non-human variable sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Pat. Nos.4,816,567; 5,530,101 and 7,498,415) wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species.
- a “humanized” antibody is one which is produced by a non-human cell or animal and comprises human sequences, e.g., H C domains.
- a "human antibody” is an antibody containing only sequences that are present in an antibody that is produced by a human.
- human antibodies may comprise residues or modifications not found in a naturally occurring human antibody (e.g., an antibody that is isolated from a human), including those modifications and variant sequences described herein. These are typically made to further refine or enhance antibody performance.
- human antibodies are produced by transgenic animals. For example, see U.S. Pat. Nos.5,770,429; 6,596,541 and 7,049,426.
- an antibody or antigen-binding fragment of the present disclosure is chimeric, humanized, or human.
- Presently disclosed antibodies and antigen-binding fragments can be obtained by, for example, introducing into a host (e.g., a mouse, a rabbit, a camelid, or a human) a SARS-CoV-2 spike protein or an immunogenic polypeptide as provided herein, and, in accordance with known methods, identifying from the host antibodies that bind to a presently disclosed epitope or epitope portion.
- Antigen-binding fragments can be produced from an antibody using known means.
- Presently disclosed antibodies can also be obtained by screening B cells, plasma cells, or sera from a subject that is or has been infected with a SARS-CoV-2 and identifying antibodies that bind to a presently disclosed epitope or epitope portion.
- Techniques for determining epitope-binding can include, for example, X-ray crystallography, alanine scanning mutagenesis, and cryo- electron microscopy.
- Immunogenic Polypeptides and Compositions In another aspect, the present disclosure provides immunogenic polypeptides comprising all or a portion of a presently disclosed RBD epitope or target region, and related compositions.
- An immunogenic polypeptide is a polypeptide that comprises an antibody epitope or portion thereof (e.g., the RBD epitope recognized by antibody S309, or a portion of the epitope) and is capable of inducing a host immune response against the polypeptide that may involve, for example, production of antibodies, activation of specific immunologically-competent cells, production of inflammatory cytokines, activation of complement, antibody dependent cytotoxicity, or any combination thereof.
- an immunogenic polypeptide can comprise an amino acid sequence containing an epitope residue or residues, wherein the amino acid sequence is the same as an amino acid sequence within SEQ ID NO.:165 (or within a naturally occurring variant of SEQ ID NO.:165), or is that is not the same as as an amino acid sequence within SEQ ID NO.:165 (or within a naturally occurring variant of SEQ ID NO.:165).
- an epitope residue or residues may be present in a recombinant or engineered sequence that is not found within SEQ ID NO.:165.
- Such recombinant or engineered sequences, or fragments of SEQ ID NO.:165 will maintain a conformation of the epitope residue or residues that is the same, or that is substantially the same, as a conformation of the epitope residue or residues in native SARS-CoV-2 RBD.
- any one two or more immunogenic amino acid sequences each comprising all or a portion of a presently disclosed epitope or target region can be present in, for example, an isolated fragment of a SARS-CoV-2 RBD, as fusion protein (e.g., fused to a different portion, sequence or fragment of SARS-CoV-2 RBD, or as a Fc fusion or antibody fusoni protein), as a recombinant protein, or the like.
- Two or more immunogenic polypeptides each comprising all or a portion of a presently disclosed epitope or target region can also be present as separate molecules in a composition.
- a host e.g., mouse, primate, rabbit, or human
- an immunogenic composition comprises: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-con
- the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. In certain embodiments, the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein.
- any one of amino acids 333, 335, 337, 339, 341, 343, 346, 354, 356, 361, 440, 441, 444, and 509 according to SEQ ID NO.:165 if present in the polypeptide, is a terminal amino acid of the polypeptide or shares a peptide bond with an amino acid that is not the same as the amino acid at the equivalent residue position in SEQ ID NO.:165.
- a polypeptide of an immunogenic composition can comprise amino acids 333-346 of SEQ ID NO.:165, and amino acid 333, which is not a terminal amino acid in SEQ ID NO.:165 and shares a N-terminal bond with an isoleucine in SEQ ID NO.:165, is a terminal amino acid of the polypeptide or shares a N-terminal bond with an amino acid other than isoleucine.
- a polypeptide comprises an engineered or recombinant amino acid sequence, or an isolated fragment of SEQ ID NO.:165.
- the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168.
- the immunogenic composition further comprises an adjuvant.
- adjuvants include, for example, poly-ICLC, poly I:C, GLA, CpG, GM-CSF, alum, Delta Inulin, aluminum hydroxide, alhydrogel, aluminum phosphate, MF59, AS03, TLR agonists, resiquimod, and saponins.
- an immunogenic polypeptide is provided with a carrier, such as, for example, a further polypeptide (e.g., an antibody or an antibody Fc that is conjugated to or fused to the immunogenic polyeptide), a liposome, a polysaccharide, a polylactic acid, a polyglycolic acid, polymeric amino acids, an amino acid copolymer, an inactive virus particle, a microbead, a nanobead, or the like.
- a carrier such as, for example, a further polypeptide (e.g., an antibody or an antibody Fc that is conjugated to or fused to the immunogenic polyeptide), a liposome, a polysaccharide, a polylactic acid, a polyglycolic acid, polymeric amino acids, an amino acid copolymer, an inactive virus particle, a microbead, a nanobead, or the like.
- polynucleotides that encode any of the presently disclosed antibodies, antigen-binding fragments, portions thereof (e.g., a CDR, a VH, a VL, a heavy chain, or a light chain), or immunogenic polypeptides or portions thereof.
- the polynucleotide is codon- optimized for expression in a host cell. Once a coding sequence is known or identified, codon optimization can be performed using known techniques and tools, e.g., using the GenScript® OptimiumGene TM tool; see also Scholten et al., Clin. Immunol.119:135, 2006).
- Codon-optimized sequences include sequences that are partially codon- optimized (i.e., one or more codon is optimized for expression in the host cell) and those that are fully codon-optimized. It will also be appreciated that polynucleotides encoding antibodies and antigen- binding fragments of the present disclosure may possess different nucleotide sequences while still encoding a same antibody or antigen-binding fragment or immunogenic polypeptide due to, for example, the degeneracy of the genetic code, splicing, and the like. In any of the presently disclosed embodiments, the polynucleotide can comprise deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
- DNA deoxyribonucleic acid
- RNA ribonucleic acid
- the RNA comprises messenger RNA (mRNA).
- mRNA messenger RNA
- Vectors are also provided, wherein the vectors comprise or contain a polynucleotide as disclosed herein (e.g., a polynucleotide that encodes an antibody or antigen-binding fragment that binds to a Wuhan coronavirus).
- a vector can comprise any one or more of the vectors disclosed herein.
- a vector comprises a DNA plasmid construct encoding the antibody or antigen- binding fragment, or a portion thereof (e.g., so-called "DMAb”; see, e.g., Muthumani et al., J Infect Dis.214(3):369-378 (2016); Muthumani et al., Hum Vaccin Immunother 9:2253-2262 (2013)); Flingai et al., Sci Rep.5:12616 (2015); and Elliott et al., NPJ Vaccines 18 (2017), which antibody-coding DNA constructs and related methods of use, including administration of the same, are incorporated herein by reference).
- DMAb DNA plasmid construct encoding the antibody or antigen- binding fragment, or a portion thereof
- a DNA plasmid construct comprises a single open reading frame encoding a heavy chain and a light chain (or a VH and a VL) of the antibody or antigen- binding fragment, wherein the sequence encoding the heavy chain and the sequence encoding the light chain are optionally separated by polynucleotide encoding a protease cleavage site and/or by a polynucleotide encoding a self-cleaving peptide.
- the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in a single plasmid.
- the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in two or more plasmids (e.g., a first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL).
- a single plasmid comprises a polynucleotide encoding a heavy chain and/or a light chain from two or more antibodies or antigen-binding fragments of the present disclosure.
- An exemplary expression vector is pVax1, available from Invitrogen®.
- a DNA plasmid of the present disclosure can be delivered to a subject by, for example, electroporation (e.g., intramuscular electroporation), or with an appropriate formulation (e.g., hyaluronidase).
- an isolated polynucleotide encodes: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or
- the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. In certain embodiments, the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein.
- the encoded polypeptide of (i), (ii), (iii), (iv), and/or (v) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168.
- the present disclosure also provides a host cell expressing an antibody, antigen-binding fragment, or immunogenic polypeptide according to the present disclosure; or comprising or containing a vector or polynucleotide according the present disclosure. Examples of such cells include but are not limited to, eukaryotic cells, e.g., yeast cells, animal cells, insect cells, plant cells; and prokaryotic cells, including E. coli.
- the cells are mammalian cells.
- the cells are a mammalian cell line such as CHO cells (e.g., DHFR-CHO cells (Urlaub et al., PNAS 77:4216 (1980)), human embryonic kidney cells (e.g., HEK293T cells), PER.C6 cells, Y0 cells, Sp2/0 cells.
- CHO cells e.g., DHFR-CHO cells (Urlaub et al., PNAS 77:4216 (1980)
- human embryonic kidney cells e.g., HEK293T cells
- PER.C6 cells e.g., HEK293T cells
- Y0 cells e.g., HEK293T cells
- PER.C6 cells e.g., HEK293T cells
- NS0 cells human liver cells, e.g. Hepa RG cells, myeloma cells or hybridoma cells.
- mammalian host cell lines include mouse sertoli cells (e.g., TM4 cells); monkey kidney CV1 line transformed by SV40 (COS-7); baby hamster kidney cells (BHK); African green monkey kidney cells (VERO-76); monkey kidney cells (CV1); human cervical carcinoma cells (HELA); human lung cells (W138); human liver cells (Hep G2); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); mouse mammary tumor (MMT 060562); TRI cells; MRC 5 cells; and FS4 cells.
- Mammalian host cell lines suitable for antibody production also include those described in, for example, Yazaki and Wu, Methods in Molecular Biology, Vol.248 (B. K. C.
- a host cell is a prokaryotic cell, such as an E. coli.
- the expression of peptides in prokaryotic cells such as E. coli is well established (see, e.g., Pluckthun, A. Bio/Technology 9:545-551 (1991).
- antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed.
- the cell may be transfected with a vector according to the present description with an expression vector.
- transfection refers to the introduction of nucleic acid molecules, such as DNA or RNA (e.g. mRNA) molecules, into cells, such as into eukaryotic cells.
- RNA e.g. mRNA
- transfection encompasses any method known to the skilled person for introducing nucleic acid molecules into cells, such as into eukaryotic cells, including into mammalian cells.
- Such methods encompass, for example, electroporation, lipofection, e.g., based on cationic lipids and/or liposomes, calcium phosphate precipitation, nanoparticle based transfection, virus based transfection, or transfection based on cationic polymers, such as DEAE-dextran or polyethylenimine, etc.
- the introduction is non-viral.
- host cells of the present disclosure may be transfected stably or transiently with a vector according to the present disclosure, e.g. for expressing an antibody, or an antigen-binding fragment thereof, according to the present disclosure. In such embodiments, the cells may be stably transfected with the vector as described herein.
- cells may be transiently transfected with a vector according to the present disclosure encoding an antibody or antigen-binding fragment or immunogenic composition as disclosed herein.
- a polynucleotide may be heterologous to the host cell.
- the present disclosure also provides recombinant host cells that heterologously express an antibody or antigen-binding fragment or immunogenic polypeptide of the present disclosure.
- the cell may be of a species that is different to the species from which the antibody was fully or partially obtained (e.g., CHO cells expressing a human antibody or an engineered human antibody).
- the cell type of the host cell does not express the antibody or antigen- binding fragment in nature.
- the host cell may impart a post-translational modification (PTM; e.g., glysocylation or fucosylation) on the antibody or antigen- binding fragment or immunogenic composition that is not present in a native state of the antibody or antigen-binding fragment (or in a native state of a parent antibody from which the antibody or antigen binding fragment was engineered or derived).
- PTM post-translational modification
- Such a PTM may result in a functional difference (e.g., reduced immunogenicity).
- an antibody or antigen-binding fragment or immunogenic polypeptide of the present disclosure that is produced by a host cell as disclosed herein may include one or more post-translational modification that is distinct from the antibody (or parent antibody) or amino acid sequence in its native state (e.g., a human antibody produced by a CHO cell can comprise a more post-translational modification that is distinct from the antibody when isolated from the human and/or produced by the native human B cell or plasma cell).
- Insect cells useful expressing a protein of interest include, for example, Spodoptera frugipera Sf9 cells, Trichoplusia ni BTI-TN5B1-4 cells, and Spodoptera frugipera SfSWT01 “Mimic TM ” cells. See, e.g., Palmberger et al., J. Biotechnol.153(3-4):160-166 (2011). Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells.
- Eukaryotic microbes such as filamentous fungi or yeast are also suitable hosts for cloning or expressing protein-encoding vectors, and include fungi and yeast strains with "humanized” glycosylation pathways, resulting in the production of an antibody or other protein with a partially or fully human glycosylation pattern. See Gerngross, Nat. Biotech.22:1409-1414 (2004); Li et al., Nat. Biotech.24:210-215 (2006). Plant cells can also be utilized as hosts for expressing a polypeptide, antibody, or antigen-binding fragment of the present disclosure. For example, PLANTIBODIESTM technology (described in, for example, U.S. Pat.
- the host cell comprises a mammalian cell.
- the host cell is a CHO cell, a HEK293 cell, a PER.C6 cell, a Y0 cell, a Sp2/0 cell, a NS0 cell, a human liver cell, a myeloma cell, or a hybridoma cell.
- the present disclosure provides methods for producing an antibody, antigen-binding fragment, or immunogenic composition, wherein the methods comprise culturing a host cell of the present disclosure under conditions and for a time sufficient to produce the antibody, or the antigen-binding fragment.
- Methods useful for isolating and purifying recombinantly produced proteins may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant antibody into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin.
- One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide. These purification methods may also be employed when isolating an immunogen from its natural environment. Methods for large scale production of one or more of the isolated/recombinant antibody, antigen-binding fragment, or polypeptide described herein include batch cell culture, which is monitored and controlled to maintain appropriate culture conditions. Purification of soluble proteins may be performed according to methods described herein and known in the art and that comport with laws and guidelines of domestic and foreign regulatory agencies.
- compositions that comprise any one or more of the presently disclosed antibodies, antigen-binding fragments, immunogenic polypeptides, polynucleotides, vectors, or host cells, singly or in any combination, can further comprise a pharmaceutically acceptable carrier, excipient, or diluent. Carriers, excipients, and diluents are discussed in further detail herein.
- a composition comprises a first vector comprising a first plasmid, and a second vector comprising a second plasmid, wherein the first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL of the antibody or antigen-binding fragment thereof, or encoding an immunogenic polypeptide.
- a composition comprises a polynucleotide (e.g., mRNA) coupled to a suitable delivery vehicle or carrier.
- Exemplary vehicles or carriers for administration to a human subject include a lipid or lipid-derived delivery vehicle, such as a liposome, solid lipid nanoparticle, oily suspension, submicron lipid emulsion, lipid microbubble, inverse lipid micelle, cochlear liposome, lipid microtubule, lipid microcylinder, or lipid nanoparticle (LNP) or a nanoscale platform (see, e.g., Li et al. Wilery Interdiscip Rev. Nanomed Nanobiotechnol.11(2):e1530 (2019)). Principles, reagents, and techniques for designing appropriate mRNA and and formulating mRNA-LNP and delivering the same are described in, for example, Pardi et al.
- lipid nanoparticles e.g., ionizable cationic lipid/phosphatidylcholine/cholesterol/PEG-lipid; ionizable lipid:distearoyl PC:cholesterol:polyethylene glycol lipid
- subcutaneous, intramuscular, intradermal, intravenous, intraperitoneal, and intratracheal administration of the same, are incorporated herein by reference.
- Methods and Uses are also provided herein are methods for use of an antibody or antigen-binding fragment, nucleic acid, vector, cell, or composition of the present disclosure in the diagnosis of SARS coronavirus (e.g., in a human subject, or in a sample obtained from a human subject).
- Methods of diagnosis may include contacting an antibody, antibody fragment (e.g., antigen binding fragment) with a sample.
- Such samples may be isolated from a subject, for example an isolated tissue sample taken from, for example, nasal passages, sinus cavities, salivary glands, lung, liver, pancreas, kidney, ear, eye, placenta, alimentary tract, heart, ovaries, pituitary, adrenals, thyroid, brain, skin or blood.
- the methods of diagnosis may also include the detection of an antigen/antibody complex, in particular following the contacting of an antibody or antibody fragment with a sample. Such a detection step can be performed at the bench, i.e. without any contact to the human or animal body.
- detection methods are well-known to the person skilled in the art and include, e.g., ELISA (enzyme-linked immunosorbent assay), including direct, indirect, and sandwich ELISA.
- methods of treating a subject using an antibody or antigen-binding fragment, nucleic acid, vector, cell, immunogenic polypeptide, or composition wherein the subject has, is believed to have, or is at risk for having an infection by a SARS coronavirus.
- Treatment refers to medical management of a disease, disorder, or condition of a subject (e.g., a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat).
- an appropriate dose or treatment regimen comprising an antibody or composition of the present disclosure is administered in an amount sufficient to elicit a therapeutic or prophylactic benefit.
- Therapeutic or prophylactic/preventive benefit includes improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay or prevention of disease progression; remission; survival; prolonged survival; or any combination thereof.
- prophylactic/preventative benefit includes induction of a host immune response (e.g., production of antibodies, activation of immunologically competent cells, production of pro-inflammatory cytokines, or the like) against a SARS coronavirus surface glycoprotein or RBD thereof.
- therapeutic or prophylactic/preventive benefit includes reduction or prevention of hospitalization for treatment of a SARS-CoV-2 infection (i.e., in a statistically significant manner).
- therapeutic or prophylactic/preventive benefit includes a reduced duration of hospitalization for treatment of a SARS-CoV-2 infection (i.e., in a statistically significant manner).
- therapeutic or prophylactic/preventive benefit includes a reduced or abrogated need for respiratory intervention, such as intubation and/or the use of a respirator device.
- therapeutic or prophylactic/preventive benefit includes reversing a late-stage disease pathology and/or reducing mortality.
- a "therapeutically effective amount” or “effective amount” of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition of this disclosure refers to an amount of the composition or molecule sufficient to result in a therapeutic effect, including protection from infection by a SARS coronavirus; improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay of disease progression; remission; survival; or prolonged survival in a statistically significant manner.
- a therapeutically effective amount refers to the effects of that ingredient or cell expressing that ingredient alone.
- a therapeutically effective amount refers to the combined amounts of active ingredients or combined adjunctive active ingredient with a cell expressing an active ingredient that results in a therapeutic effect, whether administered serially, sequentially, or simultaneously.
- methods are provided for treating a SARS coronavirus infection in a subject, wherein the methods comprise administering to the subject an effective amount of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition as disclosed herein.
- a presently disclosed antibody or antigen-binding fragment can be administered with an immunogenic polypepide or immunogenic composition (e.g., concurrently, or in a sequence, or simultaneously, optionally from 1 to 5 minutes apart, or up to 4 hours apart, or up to 12 hours apart, or up to 1 day apart, or up to 7 days apart, or up to one month apart).
- immunogenic polypepide or immunogenic composition e.g., concurrently, or in a sequence, or simultaneously, optionally from 1 to 5 minutes apart, or up to 4 hours apart, or up to 12 hours apart, or up to 1 day apart, or up to 7 days apart, or up to one month apart.
- Subjects that can be treated by the present disclosure are, in general, human and other primate subjects, such as monkeys and apes for veterinary medicine purposes. Other model organisms, such as mice and rats, may also be treated according to the present disclosure. In any of the aforementioned embodiments, the subject may be a human subject.
- the subjects can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects.
- a number of criteria are believed to contribute to high risk for severe symptoms or death associated with a SARS CoV-2 infection. These include, but are not limited to, age, occupation, general health, pre-existing health conditions, and lifestyle habits.
- a subject treated according to the present disclosure comprises one or more risk factors.
- a human subject treated according to the present disclosure is an infant, a child, a young adult, an adult of middle age, or an elderly person.
- a human subject treated according to the present disclosure is less than 1 year old, or is 1 to 5 years old, or is between 5 and 125 years old (e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 125 years old, including any and all ages therein or therebetween).
- a human subject treated according to the present disclosure is 0- 19 years old, 20-44 years old, 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older. Persons of middle, and especially of elderly age are believed to be at particular risk.
- the human subject is 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older.
- the human subject is male.
- the human subject is female.
- a human subject treated according to the present disclosure is a resident of a nursing home or a long-term care facility, is a hospice care worker, is a healthcare provider or healthcare worker, is a first responder, is a family member or other close contact of a subject diagnosed with or suspected of having a SARS-CoV-2 infection, is overweight or clinically obese, is or has been a smoker, has or had chronic obstructive pulmonary disease (COPD), is asthmatic (e.g., having moderate to severe asthma), has an autoimmune disease or condition (e.g., diabetes), and/or has a compromised or depleted immune system (e.g., due to AIDS/HIV infection, a cancer such as a blood cancer, a lymphodepleting therapy
- COPD chronic obstructive pulmonary disease
- a subject treated according to the present disclosure has received a vaccine for SARS-CoV-2 and the vaccine is determined to be ineffective, e.g., by post-vaccine infection or symptoms in the subject, by clinical diagnosis or scientific or regulatory criteria.
- treatment is administered as peri-exposure prophylaxis.
- treatment is administered to a subject with mild-to-moderate disease, which may be in an outpatient setting.
- treatment is administered to a subject with moderate-to-severe disease, such as requiring hospitalization.
- Typical routes of administering the presently disclosed compositions thus include, without limitation, oral, topical, transdermal, inhalation, parenteral, sublingual, buccal, rectal, vaginal, and intranasal.
- parenteral includes subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques.
- administering comprises administering by a route that is selected from oral, intravenous, parenteral, intragastric, intrapleural, intrapulmonary, intrarectal, intradermal, intraperitoneal, intratumoral, subcutaneous, topical, transdermal, intracisternal, intrathecal, intranasal, and intramuscular.
- a method comprises orally administering the antibody, antigen- binding fragment, polynucleotide, vector, host cell, or composition to the subject.
- Pharmaceutical compositions according to certain embodiments of the present invention are formulated so as to allow the active ingredients contained therein to be bioavailable upon administration of the composition to a patient.
- Compositions that will be administered to a subject or patient may take the form of one or more dosage units, where for example, a tablet may be a single dosage unit, and a container of a herein described an antibody or antigen-binding in aerosol form may hold a plurality of dosage units.
- compositions to be administered will, in any event, contain an effective amount of an antibody or antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition of the present disclosure, for treatment of a disease or condition of interest in accordance with teachings herein.
- a composition may be in the form of a solid or liquid.
- the carrier(s) are particulate, so that the compositions are, for example, in tablet or powder form.
- the carrier(s) may be liquid, with the compositions being, for example, an oral oil, injectable liquid or an aerosol, which is useful in, for example, inhalatory administration.
- the pharmaceutical composition is preferably in either solid or liquid form, where semi solid, semi liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid.
- the pharmaceutical composition may be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like. Such a solid composition will typically contain one or more inert diluents or edible carriers.
- binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, gum tragacanth or gelatin; excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, corn starch and the like; lubricants such as magnesium stearate or Sterotex; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; a flavoring agent such as peppermint, methyl salicylate or orange flavoring; and a coloring agent.
- excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, corn starch and the like
- lubricants such as magnesium stearate or Sterotex
- glidants such as colloidal silicon dioxide
- sweetening agents such as sucrose or saccharin
- a flavoring agent such as peppermint, methyl sal
- compositions When the composition is in the form of a capsule, for example, a gelatin capsule, it may contain, in addition to materials of the above type, a liquid carrier such as polyethylene glycol or oil.
- a liquid carrier such as polyethylene glycol or oil.
- the composition may be in the form of a liquid, for example, an elixir, syrup, solution, emulsion or suspension.
- the liquid may be for oral administration or for delivery by injection, as two examples.
- preferred compositions contain, in addition to the present compounds, one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer.
- a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent may be included.
- Liquid pharmaceutical compositions may include one or more of the following adjuvants: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer’s solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose.
- sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer’s solution, isotonic sodium chloride
- fixed oils such as synthetic mono or diglycerides which may serve as
- the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
- Physiological saline is a preferred adjuvant.
- An injectable pharmaceutical composition is preferably sterile.
- a liquid composition intended for either parenteral or oral administration should contain an amount of an antibody or antigen-binding fragment as herein disclosed such that a suitable dosage will be obtained. Typically, this amount is at least 0.01% of the antibody or antigen-binding fragment in the composition. When intended for oral administration, this amount may be varied to be between 0.1 and about 70% of the weight of the composition. Certain oral pharmaceutical compositions contain between about 4% and about 75% of the antibody or antigen-binding fragment.
- compositions and preparations according to the present invention are prepared so that a parenteral dosage unit contains between 0.01 to 10% by weight of antibody or antigen-binding fragment prior to dilution.
- the composition may be intended for topical administration, in which case the carrier may suitably comprise a solution, emulsion, ointment or gel base.
- the base may comprise one or more of the following: petrolatum, lanolin, polyethylene glycols, bee wax, mineral oil, diluents such as water and alcohol, and emulsifiers and stabilizers.
- Thickening agents may be present in a composition for topical administration. If intended for transdermal administration, the composition may include a transdermal patch or iontophoresis device.
- the pharmaceutical composition may be intended for rectal administration, in the form, for example, of a suppository, which will melt in the rectum and release the drug.
- the composition for rectal administration may contain an oleaginous base as a suitable nonirritating excipient.
- bases include, without limitation, lanolin, cocoa butter and polyethylene glycol.
- a composition may include various materials which modify the physical form of a solid or liquid dosage unit.
- the composition may include materials that form a coating shell around the active ingredients.
- the materials that form the coating shell are typically inert, and may be selected from, for example, sugar, shellac, and other enteric coating agents.
- the active ingredients may be encased in a gelatin capsule.
- the composition in solid or liquid form may include an agent that binds to the antibody or antigen-binding fragment of the disclosure and thereby assists in the delivery of the compound.
- Suitable agents that may act in this capacity include monoclonal or polyclonal antibodies, one or more proteins or a liposome.
- the composition may consist essentially of dosage units that can be administered as an aerosol.
- aerosol is used to denote a variety of systems ranging from those of colloidal nature to systems consisting of pressurized packages. Delivery may be by a liquefied or compressed gas or by a suitable pump system that dispenses the active ingredients. Aerosols may be delivered in single phase, bi phasic, or tri phasic systems in order to deliver the active ingredient(s).
- compositions of the present disclosure also encompass carrier molecules for polynucleotides, as described herein (e.g., lipid nanoparticles, nanoscale delivery platforms, and the like).
- carrier molecules for polynucleotides as described herein (e.g., lipid nanoparticles, nanoscale delivery platforms, and the like).
- the pharmaceutical compositions may be prepared by methodology well known in the pharmaceutical art.
- a composition intended to be administered by injection can be prepared by combining a composition that comprises an antibody, antigen-binding fragment thereof, or immunogenic polypeptide as described herein and optionally, one or more of salts, buffers and/or stabilizers, with sterile, distilled water so as to form a solution.
- a surfactant may be added to facilitate the formation of a homogeneous solution or suspension.
- Surfactants are compounds that non-covalently interact with the peptide composition so as to facilitate dissolution or homogeneous suspension of the antibody or antigen-binding fragment thereof or immunogenic polypeptide in the aqueous delivery system.
- an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome (e.g., a decrease in frequency, duration, or severity of diarrhea or associated dehydration, or inflammation, or longer disease-free and/or overall survival, or a lessening of symptom severity).
- a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder.
- compositions administered according to the methods described herein can be determined by performing pre-clinical (including in vitro and in vivo animal studies) and clinical studies and analyzing data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques, all of which can readily be practiced by a person skilled in the art.
- Compositions are administered in an effective amount (e.g., to treat a SARS coronavirus infection), which will vary depending upon a variety of factors including the activity of the specific compound employed; the metabolic stability and length of action of the compound; the age, body weight, general health, sex, and diet of the subject; the mode and time of administration; the rate of excretion; the drug combination; the severity of the particular disorder or condition; and the subject undergoing therapy.
- test subjects will exhibit about a 10% up to about a 99% reduction in one or more symptoms associated with the disease or disorder being treated as compared to placebo-treated or other suitable control subjects.
- a therapeutically effective daily dose of an antibody or antigen binding fragment is (for a 70 kg mammal) from about 0.001 mg/kg (i.e., 0.07 mg) to about 100 mg/kg (i.e., 7.0 g); preferably a therapeutically effective dose is (for a 70 kg mammal) from about 0.01 mg/kg (i.e., 0.7 mg) to about 50 mg/kg (i.e., 3.5 g); more preferably a therapeutically effective dose is (for a 70 kg mammal) from about 1 mg/kg (i.e., 70 mg) to about 25 mg/kg (i.e., 1.75 g).
- a therapeutically effective dose may be different than for an antibody or antigen-binding fragment.
- a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition to the subject at 2, 3, 4, 5, 6, 7, 8, 9, 10 times, or more.
- a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition to the subject a plurality of times, wherein a second or successive administration is performed at about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 24, about 48, about 74, about 96 hours, or more, following a first or prior administration, respectively.
- a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition at least one time prior to the subject being infected by the Wuhan coronavirus.
- compositions comprising an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or immunogenic polypeptide of the present disclosure may also be administered simultaneously with, prior to, or after administration of one or more other therapeutic agents.
- combination therapy may include administration of a single pharmaceutical dosage formulation which contains a compound of the invention and one or more additional active agents, as well as administration of compositions comprising an antibody or antigen-binding fragment or immunogenic polypeptide of the disclosure and each active agent in its own separate dosage formulation.
- an antibody or antigen-binding fragment thereof or immunogenic polypeptide as described herein and the other active agent can be administered to the patient together in a single oral dosage composition such as a tablet or capsule, or each agent administered in separate oral dosage formulations.
- an antibody or antigen-binding fragment or immunogenic polypeptide as described herein and the other active agent can be administered to the subject together in a single parenteral dosage composition such as in a saline solution or other physiologically acceptable solution, or each agent administered in separate parenteral dosage formulations.
- a single parenteral dosage composition such as in a saline solution or other physiologically acceptable solution, or each agent administered in separate parenteral dosage formulations.
- the compositions comprising an antibody or antigen-binding fragment or immunogenic polypeptide and one or more additional active agents can be administered at essentially the same time, i.e., concurrently, or at separately staggered times, i.e., sequentially and in any order; combination therapy is understood to include all these regimens.
- a combination therapy comprises any two or more compositions (antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition) of the present disclosure.
- uses of the presently disclosed antibodies, antigen-binding fragments, vectors, host cells, immunogenic polypeptides, and compositions are provided.
- an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition is provided for use in a method of treating a SARS coronavirus infection in a subject.
- an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition is provided for use in a method of manufacturing or preparing a medicament for treating a SARS coronavirus infection in a subject.
- the present disclosure also provides the following Embodiments.
- Embodiment 1. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD) when the RBD is in an open conformation and/or when the RBD is in a closed conformation.
- RBD SARS-CoV-2 surface glycoprotein receptor binding domain
- Embodiment 1 The antibody or antigen-binding fragment of Embodiment 1, wherein the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein RBD is in an open conformation, and when the RBD is in a closed conformation.
- Embodiment 3 The antibody or antigen-binding fragment of Embodiment 1 or 2, wherein the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein is comprised in a trimer thereof, wherein, optionally, each surface glycoprotein of the trimer can be simultaneously bound to a separate antibody or antigen-binding fragment of Embodiment 1 or Embodiment 2.
- Embodiment 5. The antibody or antigen-binding fragment of any one of Embodiments 1-4, wherein the SARS-CoV-2 surface glycoprotein is in prefusion conformation.
- RBD SARS-CoV-2 surface glycoprotein receptor binding domain
- Embodiment 6 wherein binding of the antibody or antigen-binding fragment to the RBD does not comprise contacting an RBD amino acid residue that contacts a human ACE2 when the surface glycoprotein is bound to the human ACE2.
- Embodiment 9 Embodiment 9.
- binding of the antibody or antigen-binding fragment to the RBD comprises contacting amino acid N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated.
- binding of the antibody or antigen-binding fragment to the RBD comprises contacting amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, D442, and R509, and, optionally, one or both of C336 and K444, according to SEQ ID NO.:165.
- Embodiment 13 The antibody or antigen-binding fragment of Embodiment 12, wherein the glycosylation of the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 comprises a fucose.
- Embodiment 14 The antibody or antigen-binding fragment of any one of Embodiments 11-13, wherein the asparagine amino acid residue (N) that is or that corresponds to N343 of SEQ ID NO.:165 is comprised in an amino acid sequence N-X- T, X being any amino acid except for P, and preferably being A.
- Embodiment 14 wherein the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence (SEQ ID NO.:234), or a variant thereof having one, two, three, four or five amino acid substitutions, provided that the sequence N-X-T is present, X being any amino acid except for P, and preferably being A.
- SEQ ID NO.:234 amino acid sequence
- X any amino acid except for P, and preferably being A.
- Embodiment 14 or 15 wherein the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence (SEQ ID NO.:235), or is comprised in a variant sequence of SEQ ID NO.:235 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions relative to SEQ ID NO.:235, provided that the amino acid sequence N-X-T is present, X being any amino acid except for P, and preferably being A, wherein optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:235 independently comprises a conservative substitution or a non-conservative substitution.
- SARS coronavirus e.g., SARS-CoV-2
- the target region comprises any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8,
- Embodiment 17 wherein the target region comprises amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- Embodiment 20 comprises amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
- Embodiment 20 Embodiment 20.
- Embodiment 17 wherein the target region comprises amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165.
- Embodiment 21 The antibody or antigen-binding fragment of any one of Embodiments 17-20, wherein the target region comprises amino acids T333-C361, according to SEQ ID NO.:165.
- Embodiment 22 is described in any one of Embodiments 17-20, wherein the target region comprises amino acids T333-C361, according to SEQ ID NO.:165.
- the antibody or antigen-binding fragment of Embodiment 21, wherin the target region further comprises amino acids N440-K444, according to SEQ ID NO.:165.
- Embodiment 23 The antibody or antigen-binding fragment of Embodiment 21 or 22, wherin the target region further comprises amino acid R509, according to SEQ ID NO.:165.
- Embodiment 24 The antibody or antigen-binding fragment of Embodiment 21, wherin the target region further comprises amino acids N440-K444, according to SEQ ID NO.:165.
- Embodiment 25 Embodiment 25.
- the antibody or antigen-binding fragment of any one of Embodiments 1-24 which is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2 that comprises any one or more of the following mutations in RBD relative to SEQ ID NO.:165: N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q; E340D; L335S; L441F; L441I; L
- Embodiment 26 The antibody or antigen-binding fragment of Embodiment 24 or Embodiment 25, wherein the antibody or antigen-binding fragment is capable of neutralizing the SARS-CoV-2 infection with a potency that is less than 3-fold reduced as compared to the potency with which the antibody or antigen-binding fragment neutralizes infection by a SARS-CoV-2 that comprises the amino acid sequence of SEQ ID NO.:165.
- Embodiment 27 The antibody or antigen-binding fragment of any one of Embodiments 1-26, which is a IgG, IgA, IgM, IgE, or IgD isotype.
- Embodiment 28 The antibody or antigen-binding fragment of any one of Embodiments 1-26, which is a IgG, IgA, IgM, IgE, or IgD isotype.
- Embodiment 29 The antibody or antigen-binding fragment of any one of Embodiments 1-28, which is human, humanized, or chimeric.
- Embodiment 30 The antibody or antigen-binding fragment of any one of Embodiments 1-27, which is an IgG isotype selected from IgG1, IgG2, IgG3, and IgG4.
- Embodiment 31. The antibody or antigen-binding fragment of any one of Embodiments 1-30, wherein the antibody or antigen-binding fragment is a multi-specific antibody or antigen binding fragment.
- Embodiment 32 is a multi-specific antibody or antigen binding fragment.
- Embodiment 31 The antibody or antigen-binding fragment of Embodiment 31, wherein the antibody or antigen binding fragment is a bispecific antibody or antigen-binding fragment.
- Embodiment 33 The antibody or antigen-binding fragment of any one of Embodiments 1-32, wherein the antibody or antigen-binding fragment further comprises a Fc polypeptide or a fragment thereof.
- Embodiment 34 The antibody or antigen-binding fragment of any one of Embodiments 1-32, wherein the antibody or antigen-binding fragment further comprises a Fc polypeptide or a fragment thereof.
- the antibody or antigen-binding fragment of Embodiment 33 wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to a FcRn as compared to a reference Fc polypeptide that does not comprise the mutation; and/or (ii) a mutation that enhances binding to a Fc ⁇ R as compared to a reference Fc polypeptide that does not comprise the mutation.
- Embodiment 35 wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to a FcRn as compared to a reference Fc polypeptide that does not comprise the mutation; and/or (ii) a mutation that enhances binding to a Fc ⁇ R as compared to a reference Fc polypeptide that does not comprise the mutation.
- Embodiment 27 wherein the mutation that enhances binding to a FcRn comprises: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I; Q311I; D376V; T307A; E380A; or any combination thereof.
- Embodiment 36 Embodiment 36.
- the antibody or antigen-binding fragment of Embodiment 34 or 35, wherein the mutation that enhances binding to FcRn comprises: (i) M428L/N434S; (ii) M252Y/S254T/T256E; (iii) T250Q/M428L; (iv) P257I/Q311I; (v) P257I/N434H; (vi) D376V/N434H; (vii) T307A/E380A/N434A; or (viii) any combination of (i)-(vii).
- Embodiment 37 comprises: (i) M428L/N434S; (ii) M252Y/S254T/T256E; (iii) T250Q/M428L; (iv) P257I/Q311I; (v) P257I/N434H; (vi) D376V/N434H; (vii) T307A/E380
- Embodiment 34-36 The antibody or antigen-binding fragment of any one of Embodiments 34-36, wherein the mutation that enhances binding to FcRn comprises M428L/N434S.
- Embodiment 38. The antibody or antigen-binding fragment of any one of Embodiments 34-37, wherein the mutation that enhances binding to a Fc ⁇ R comprises S239D; I332E; A330L; G236A; or any combination thereof.
- the antibody or antigen-binding fragment of any one of Embodiments 34-38, wherein the mutation that enhances binding to a Fc ⁇ R comprises: (i) S239D/I332E; (ii) S239D/A330L/I332E; (iii) G236A/S239D/I332E; or (iv) G236A/A330L/I332E.
- Embodiment 40 Embodiment 40.
- Embodiment 41 The antibody or antigen-binding fragment of any one of Embodiments 1-40, comprising a L234A mutation, a L235A mutation, or both.
- Embodiment 42 The antibody or antigen-binding fragment of any one of Embodiments 1-40, comprising a L234A mutation, a L235A mutation, or both.
- Embodiment 43. The isolated polynucleotide of Embodiment 42, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA).
- Embodiment 44. The isolated polynucleotide of Embodiment 42 or 43, which is codon-optimized for expression in a host cell.
- a recombinant vector comprising the polynucleotide of any one of Embodiments 42-44.
- Embodiment 46 A host cell comprising the polynucleotide of any one of Embodiments 42-44 and/or the vector of Embodiment 45, wherein the polynucleotide is heterologous to the host cell.
- Embodiment 47 A human B cell comprising the polynucleotide of any one of Embodiments 42-44, wherein polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized.
- Embodiment 48 A recombinant vector comprising the polynucleotide of any one of Embodiments 42-44.
- a composition comprising: (i) the antibody or antigen-binding fragment of any one of Embodiments 1- 41; (ii) the polynucleotide of any one of Embodiments 42-44; (iii) the recombinant vector of Embodiment 45; (iv) the host cell of Embodiment 46; and/or (v) the human B cell of Embodiment 47, and a pharmaceutically acceptable excipient, carrier, or diluent.
- Embodiment 49 Embodiment 49.
- a method of treating a sarbecovirus infection in a subject comprising administering to the subject an effective amount of: (i) the antibody or antigen-binding fragment of any one of Embodiments 1- 41; (ii) the polynucleotide of any one of Embodiments 42-44; (iii) the recombinant vector of Embodiment 45; (iv) the host cell of Embodiment 46; (v) the human B cell of Embodiment 47; and/or (vi) the composition of Embodiment 48.
- Embodiment 50 The method of Embodiment 49, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both.
- a method for in vitro diagnosis of a sarbecovirus infection comprising: (i) contacting a sample from a subject with an antibody or antigen-binding fragment of any one of Embodiments 1-41; and (ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigen binding fragment, wherein, optionally, the sarbecovirus comprises SARS-CoV-2, SARS-CoV, or both.
- Embodiment 52 The method of Embodiment 51, wherein the sample comprises blood isolated from the subject.
- Embodiment 53 The method of Embodiment 51, wherein the sample comprises blood isolated from the subject.
- Embodiment 54 The antibody or antigen-binding fragment of any one of Embodiments 1-41, the polynucleotide of any one of Embodiments 42-44, the recombinant vector of Embodiment 45, the host cell of Embodiment 46, the human B cell of Embodiment 47, and/or the composition of Embodiment 48, for use in a method of treating or diagnosing a sarbecovirus infection in a subject.
- Embodiment 54 Embodiment 54.
- Embodiment 55 The antibody or antigen-binding fragment of any one of Embodiments 1-41, the polynucleotide of any one of Embodiments 42-44, the recombinant vector of Embodiment 45, the host cell of Embodiment 46, the human B cell of Embodiment 47, and/or the composition of Embodiment 48, for use in the manufacture of a medicament for treating a sarbecovirus infection in a subject.
- Embodiment 55 Embodiment 55.
- Embodiment 56 The antibody or antigen-binding fragment of any one of Embodiments 1-41, the polynucleotide of any one of Embodiments 42-44, the recombinant vector of Embodiment 45, the host cell of Embodiment 46, the human B cell of Embodiment 47, and/or the composition of Embodiment 48 for use of Embodiment 53 or 54, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both.
- Embodiment 56 Embodiment 56.
- An immunogenic composition comprising: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (i
- Embodiment 57 The immunogenic composition of Embodiment 56, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein.
- Embodiment 58 The immunogenic compostion of Embodiment 56 or 57, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full- length SARS-CoV-2 surface glycoprotein.
- Embodiment 59 Embodiment 59.
- Embodiment 60 The immunogenic composition of any one of Embodiments 56-59, further comprising an adjuvant.
- An isolated polynucleotide that encodes: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-con
- Embodiment 62 The polynucleotide of Embodiment 61, wherein the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein.
- Embodiment 63 The polynucleotide of Embodiment 61 or 62, wherein the encoded polypeptide of (i), (ii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein.
- Embodiment 64 Embodiment 64.
- Embodiment 65 The polynucleotide of any one of Embodiments 61-64, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA).
- Embodiment 66 Embodiment 66.
- a composition comprising the polynucleotide of any one of Embodiments 42-49 or 61-65 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform.
- Embodiment 67 A recombinant vector comprising the polynucleotide of any one of Embodiments 61-65.
- Embodiment 68 A host cell comprising the polynucleotide of any one of Embodiments 61-65 and/or the vector of Embodiment 67.
- Embodiment 69 A composition comprising the polynucleotide of any one of Embodiments 61-65, the vector of Embodiment 67, and/or the host cell of Embodiment 68, and a pharmaceutically acceptable carrier, excipient, or diluent.
- Embodiment 70 Embodiment 70.
- a method of inducing an immune response in a subject against a sarbecovirus surface glycoprotein comprising administering to the subject an effective amount of (i) the immunogenic composition of any one of Embodiments 56-60, (ii) the polynucleotide of any one of Embodiments 61-65, (iii) the vector of Embodiment 67, (iv) the host cell of Embodiment 68, and/or the composition of Embodiment 66 or 69.
- Embodiment 71 The method of Embodiment 70, wherein the sarbecovirus comprises SARS-CoV-2, SARS, or both.
- Embodiment 73 Embodiment 73.
- Embodiment 74 Embodiment 74.
- Table 2 Sequences
- EXAMPLE 1 HUMAN MONOCLONAL ANTIBODIES THAT BIND SPIKE PROTEIN OF SARS-COV-2
- B cells from a donor with previous SARS-CoV infection were sorted and immortalized with EBV and screened in 384-well plates (method described in European patent EP1597280B1, which method is incorporated herein by reference).
- S SARS-CoV-2 Spike
- ExpiCHO cells were transfected with S protein of SARS-CoV-2 (strain BetaCoV/Wuhan-Hu-1/2019), or with an empty plasmid as a negative control.
- Binding data for SARS-CoV-2 S300 through SARS-CoV-2 S310 are shown in Figures 4A and 4B (in these figures, the antibodies are identified as "S300"-"S310", respectively). Graphs showing positive binding are indicated with boxes.
- the heavy chain complementarity determining region (CDR)3 and light chain (L)CDR3 amino acid sequences of certain of these antibodies, along with the percent identity of the variable region gene sequences to germline (IMGT; imgt.org), are provided in Table 3.
- EXAMPLE 2 BINDING OF ANTIBODIES TO RBD OF SARS-COV-2 USING OCTET Strepavidin biosensors (Pall ForteBio) were used to immobilize anti-Strep Tag II antibody at 3ug/ml (clone 5A9F9, Biotin, LabForce AG, Muttenz CH), after a hydration step for 10 minutes with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002 ⁇ Tween-20, 0.005% NaN3 in PBS). SARS-CoV-2 RBD with a Strep Tag II (produced in-house) was then loaded for 6 min at a concentration of 4 ⁇ g/ml in KB.
- the "S303" mAb comprises the S303-v1 VH and VL amino acid sequences provided in Table 2 (SEQ ID NOs.:63 and 67, respectively).
- the "S309” mAb comprises the S309-v1 VH and S309-v13 VL amino acid sequences provided in Table 2 (SEQ ID NOs.: 105 and 168, respectively).
- the alleles encoding SEQ ID NOs.:109 and 147-150 from S309 B cell were determined to be non-productive; SEQ ID NO.:168 was the productive allele.
- Binding affinity of three SARS-CoV/SARS-CoV-2 cross-reactive recombinant antibodies (S303 rIgG1, S304 rIgG1, S309 rIgG1) and two SARS-CoV-1 specific antibodies (S109 rIgG1, S230 rIgG1) was tested by biolayer interferometry (BLI) using Octet. Affinity was measured by immobilizing the antibody on sensors and dipping the sensors into wells containing different concentrations of RBD. Kinetics of antibody binding to RBD were recorded during the association phase, after which the sensors were dipped into buffer without antibody to observe kinetics of antibody detaching from the RBD during the dissociation phase.
- protein A biosensors (Pall ForteBio) were used to immobilize recombinant antibodies at 2.7ug/ml for 1 minute, after a hydration step for 10 minutes with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002 ⁇ Tween-20, 0.005% NaN3 in PBS). Association curves were recorded for 5 minutes by incubating the antibody-coated sensors with different concentrations of SARS-CoV-1 RBD (Sino Biological) or SARS-CoV-2 RBD (produced in house in Expi-CHO cells; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947).
- Binding of S303 rIgG1, S304 rIgG1, and S309 rIGg1 to SARS-CoV-2 RBD was in the nanomolar to sub-picomolar range, with S309 rIgG1 showing the highest affinity.
- EXAMPLE 4 NEUTRALIZATION OF SARS-COV-2 INFECTION Replication-incompetent viruses pseudotyped with the SARS-CoV-2 S gene (isolate BetaCoV/Wuhan-Hu-1/2019; accession number MN908947) were produced using methods as previously described (Temperton NJ, et al. (2005) Longitudinally profiling neutralizing antibody response to SARS coronavirus with pseudotypes. Emerg Infect Dis 11(3):411–416). Briefly, HEK293T/17 cells were cotransfected with a SARS-CoV-2 S-expressing plasmid (phCMV1, Genlantis) and with a complementing viral–genome reporter gene vector, pNL4-3.
- phCMV1, Genlantis a complementing viral–genome reporter gene vector
- Luc+.E-R+ A single-cycle infectivity assay was used to measure the neutralization of luciferase-encoding virions pseudotyped with the SARS-CoV-2 S protein, as previously described (Temperton NJ, et al. (2007) A sensitive retroviral pseudotype assay for influenza H5N1-neutralizing antibodies. Influenza Other Respi Viruses 1(3):105–112.). Briefly, appropriate dilutions of the virion-containing culture supernatants were preincubated at 37°C for 1 h with antibodies at various concentrations, and the virus–mAb mixtures were then added to Vero E6 cells that had been seeded the day before infection.
- Antibodies S300-v1 (VH: SEQ ID NO.:1; VL: SEQ ID NO.:5), S301, S302, S303-v1 (VH SEQ ID NO.:63; VL SEQ ID NO.:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S307 (VH SEQ ID NO.:239; VL SEQ ID NO.:243), S308-v1, S309 (comprising the S309-v1 VH sequence set forth in SEQ ID NO: 105 and the S309-v13 VL sequence set forth in SEQ ID NO: 168), and S310 were tested for neutralization function (Table 4, Figure 2A).
- Antibodies SARS-CoV-2 S300-v1 and SARS-CoV-2 S309 neutralized SARS-CoV-2 infection ( Figures 2A and 2B). Table 4. Percent neutralization of infection by antibodies (titration series) Additional neutralization assays were carried out using plasma from SARS CoV-1 survivors and antibodies SARS-CoV-2 S309, S311, S312, S303-v1 (rIgG1), S304 (rIgG1), S306 (rIgG1), S310 (rIgG1), and S315 ( Figure 3A-3I).
- Figure 3A shows neutralizing activity of SARS-CoV donor plasma.
- DBT cells stably transfected with ACE2 were used as target cells.
- Figure 34 shows neutralizing activity against SARS-CoV-1 pseudotyped MLV by these antibodies at various concentrations. Additional neutralization data for S304, S309, S304 + S309, S315, and S315 + S309 are shown in Figures 36 and 37.
- EXAMPLE 5 NEUTRALIZATION OF SARS-COV-2 INFECTION Neutralizing activity of two SARS-CoV-1 and SARS-CoV-2 cross-neutralizing antibodies, S304 rIgG1 and S309 (VH: SEQ ID NO.:105; VL: SEQ ID NO.:168) rIgG1, against SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pp) was assessed.
- Murine leukemia virus (MLV) pseudotyped with SARS-CoV-2 Spike protein (SARS-CoV-2pp) was used.
- DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells.
- SARS-CoV-2pp was activated with trypsin TPCK at 10 ⁇ g/ml. Activated SARS-CoV-2pp was added to a dilution series of antibodies (starting with 50 ⁇ g/ml final concentration per antibody, 3-fold dilution). Antibodies were tested at concentrations from 50 ⁇ g/ml to 0.02 ⁇ g/ml. For the combination of S304 rIgG1 and S309 rIgG1, starting concentrations were 50 ⁇ g/ml for each antibody, i.e. the total starting antibody concentration was 100 ⁇ g/ml. DBT-ACE2 cells were added to the antibody-virus mixtures and incubated for 48 hours.
- Luminescence was measured after aspirating cell culture supernatant and adding steady-GLO substrate (Promega).
- S309 rIgG1 exhibited a neutralization of infection IC50 of 0.37 ⁇ g/ml
- S304 rIgG1 exhibited an IC50 of approximately 17 ⁇ g/ml.
- a combination of these two antibodies exhibited an IC50 of 0.077 ⁇ g/ml. See Figure 7 and Table 5.
- Table 5. IC50 ( ⁇ g/ml) of antibodies Further neutralization assays were carried out using the same procedure for recombinant monoclonal antibodies S309 and S315, singly and in combination.
- 96-well plates were coated with recombinant SARS-CoV-2 Spike S1 Subunit Protein (Sino Biological), SARS-CoV-2 RBD (Sino Biological or produced in house; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947), recombinant SARS-CoV Spike S1 Subunit Protein (Sino Biological), or SARS-CoV RBD (Sino Biological).
- Wells were washed and blocked with PBS+1%BSA for 1 hour at room temperature, and were then incubated with serially diluted mAbs for 1 hour at room temperature.
- Bound mAbs were detected by incubating alkaline phosphatase- conjugated goat anti-human IgG (Southern Biotechnology: 2040-04) for 1 hour at room temperature, and were developed by 1 mg/ml p-nitrophenylphosphate substrate in 0.1 M glycine buffer (pH 10.4) for 30 min at room temperature.
- Optical density (OD) values were measured at a wavelength of 405 nm in an ELISA reader (Powerwave 340/96 spectrophotometer, BioTek). Results are shown in Figure 5A (SARS-CoV-2 S311) and Figure 5B (SARS- CoV-2 S312).
- Antibody "S300 V4-rIgG1," as shown in Figure 38C, comprises a VH comprising the amino acid sequence of SEQ ID NO.:1 and a VL (V ⁇ ) comprising the amino acid sequence of SEQ ID NO.:234.
- Antibody "S307 V3-rIgG1," as shown in Figure 38D, comprises a VH comprising the amino acid sequence of SEQ ID NO.: 239 and a VL(V ⁇ ) comprising the amino acid sequence of SEQ ID NO.:243.
- EXAMPLE 7 NEUTRALIZATION OF SARS-COV-2 INFECTION BY S309 AND S315 Neutralizing activity of recombinant antibodies S309 (VH: SEQ ID NO.:105; VL SEQ ID NO.:168) rIgG1-MLNS and S315 rIgG1-MLNS against SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pp) was determined.
- M428L and N434S mutations in the Fc domain included M428L and N434S mutations in the Fc domain (see, e.g., Zalevsky et al., Nat. Biotechnol.28(2):157-159 (2010); this combination of Fc mutations is also referred-to as "MLNS” or “LS” in the present disclosure, including in the drawings).
- Murine leukemia virus (MLV) pseudotyped with SARS-CoV-2 Spike protein (SARS-CoV-2pp) was used.
- DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells.
- SARS-CoV-2pp was activated with trypsin TPCK at 10 ⁇ g/ml.
- Activated SARS-CoV-2pp was added to a dilution series of the tested antibody.
- DBT-ACE2 cells were added to the antibody-virus mixtures and incubated for 48 hours.
- Luminescence was measured after aspirating cell culture supernatant and adding steady-GLO substrate (Promega). Luciferase signal of infected cells was used to calculate the percentage of neutralization relative to a no-antibody control.
- 384-well shallow ELISA plates were coated with stabilized prefusion Spike protein trimer of SARS-CoV-1, SARS-CoV-2, OC43, or MERS at 1 ⁇ g/ml, or with SARS-CoV-2 RBD (produced in house; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947) at 10 ⁇ g/ml, or SARS- CoV-1 RBD (Sino Biological) at 1 ⁇ g/ml. Wells were washed and blocked with PBS+1% BSA for 1 hour at room temperature, and were then incubated with serially diluted antibody for 1-2 hours at room temperature.
- Antibodies were tested at a concentration range of 5 to 0.00028 ⁇ g/ml. Plates were washed and bound antibodies were detected by incubating alkaline phosphatase-conjugated goat anti-human IgG (Southern Biotechnology: 2040-04) for 1 hour at room temperature followed by color development using 1 mg/ml p- nitrophenylphosphate substrate (Sigma-Aldrich 71768) in 0.1 M glycine buffer (pH 10.4) for 30 min at room temperature. The optical density (OD) values were measured at a wavelength of 405 nm in an ELISA reader (Powerwave 340/96 spectrophotometer, BioTek). The ELISA assay results are shown in Figures 8A-8K and 18A-18J.
- Recombinant antibodies some bearing MLNS Fc mutations, are indicated with rIgG1.
- EXAMPLE 9 BINDING OF ANTIBODIES TO SPIKE PROTEIN OF SARS-COV-1 AND SARS- COV-2 ExpiCHO cells were transfected with phCMV1- SARS-CoV-2-S, SARS- spike_pcDNA.3 (strain SARS), or empty phCMV1 using Expifectamine CHO Enhancer. Two days after transfection, cells were collected for immunostaining with antibody. An Alexa647-labelled secondary antibody anti-human IgG Fc was used for detection.
- Binding of monoclonal antibody to transfected cells was analyzed by flow cytometry using a ZE5 Cell Analyzer (Biorard) and FlowJo software (TreeStar). Positive binding was defined by differential staining of CoV-S transfectants versus mock transfectants.
- Antibody S309 VH of SEQ ID NO.:105; VL of SEQ ID NO.:168
- Results are shown in Figure 11. Binding of monoclonal antibodies S303, S304, S306, S309, S310, S315, S110, S124, S230, and S109 (all expressed as rIgG1) to SARS-CoV-1 S protein and SARS- CoV-2 S protein was measured by flow cytometry. Results are shown in Figures 12A, 12B, 40A, and 40B. Eight of the tested antibodies exhibited EC50 values ranging between 1.4 ng/ml and 6,100 ng/ml for SARS-CoV-2 S protein binding and between 0.8 ng/ml and 254 ng/ml for SARS-CoV-1 S protein binding.
- Results are shown in Figures 33A and 44A (binding to SARS- CoV-2 S protein), and 33B and 44B (binding to SARS-CoV-1 S protein).
- MFI mean fluorescence intensity as measured by flow cytometry. The same assay was performed using recombinant antibodies S300 and S307.
- EXAMPLE 10 BINDING OF ANTIBODIES S309, S303, S304, AND S315 TO RBD OF SARS-COV- 2 AND SARS-COV-1 Affinity of recombinant antibodies S309, S303, S304, and S315 for RBD of CoV-1 and CoV-2 was tested using biolayer interferometry (BLI; Octet).
- His- tagged RBD of SARS-CoV-1 or SARS-CoV-2 was loaded at 3 ⁇ g/ml in kinetics buffer (KB) for 15 minutes onto anti-HIS (HIS2) biosensors (Molecular Devices, ForteBio). Association of full-length antibodies was performed in KB at 15 ⁇ g/ml for 5 minutes. Association of Fab fragments was performed in KB at 5 ⁇ g/mL for 5 minutes. Dissociation in KB was measured for 10 minutes. Affinities, represented by KD values, were calculated using a global fit model (Octet). Octet Red96 (ForteBio) equipment was used.
- Figures 14A-14D show association and dissociation curves for S309, S303, S304, and S315, respectively. Each of these antibodies bound to SARS-CoV-2 and SARS-CoV-1 RBD with nanomolar to sub-picomolar affinity.
- Figures 20A and 20B show association and dissociation curves for S309 IgG and S309 Fab, respectively. In these figures, the switch from antibody (or Fab) solution to buffer is indicated with a vertical dashed line.
- EXAMPLE 11 BINDING OF S309 IGG AND S309 FAB TO SARS-COV-2 S PROTEIN ECTODOMAIN TRIMER AND RBD Affinity and avidity determination of IgG1 and Fab fragment: biotinylated RBD of SARS-CoV-2 (produced in-house; amino acid residues 331-550 of spike protein from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947, biotinylated with EZ-Link NHS-PEG4-Biotin from ThermoFisher) and biotinylated SARS-CoV-22P S avi-tagged were loaded at 7.5 ⁇ g/ml in Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002% Tween-20, 0.005% NaN3 in PBS) for 8 minutes onto Streptavidin biosensors (Molecular Devices, ForteBio).
- Kinetics Buffer KB; 0.01% endotoxin-free BSA
- EXAMPLE 12 COMPETITIVE BINDING OF ANTIBODIES TO RBD OF SARS-COV-1 OR SARS-COV-2 Competitive binding of pairs of monoclonal antibodies to SARS-CoV-1 RBD or SARS-CoV-2 RBD was measured to identify respective binding sites of the antibodies.
- Strepavidin biosensors (Pall ForteBio) were used to immobilize anti-Strep Tag II antibody at 3ug/ml (clone 5A9F9, Biotin, LabForce AG, Muttenz CH), after a hydration step for 10 min with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002 ⁇ Tween-20, 0.005% NaN3 in PBS).
- FIG. 15A shows competition of antibody pairs for binding to the RBD of SARS-CoV-1.
- Figure 15B shows competition of antibody pairs for binding to the RBD of SARS-CoV-2.
- the dashed vertical lines in Figures 15A and 15B indicate the switch from the first antibody, indicated on the left of the matrix, to the second antibody, indicated on top of the matrix.
- ACE2-His Bio-Techne AG was loaded for 30 minutes at 5 ⁇ g/ml in kinetics buffer (KB) onto anti-HIS (HIS2) biosensors (molecular Devices-ForteBio) SARS-CoV-1 RBD-rabbit Fc or SARS-CoV-2 RBD-mouse Fc (Sino Biological Europe GmbH) at 1 ⁇ g/ml was associated for 15 mintues, after a preincubation with or without antibody at 30 ⁇ g/ml for 30 minutes. Dissociation was monitored for 5 minutes.
- Figure 16 shows data obtained using antibody S309 or S230.
- FIGS 19A and 19B show data obtained using antibodies S304, S303, or S230 ( Figure 19A), or RBD and antibody S315 ( Figure 19B).
- the vertical dashed line in each of Figures 16, 19A, and 19B indicates the start of the loading of RBD with or without antibody.
- EXAMPLE 14 EFFECTOR FUNCTION OF ANTIBODIES
- Natural killer (NK)-mediated antibody-dependent cell cytotoxicity (ADCC) can contribute to viral control by killing infected cells displaying viral protein on their surface.
- ADCC was interrogated in vitro using human NK cells (isolated from fresh blood of healthy donors using the MACSxpress NK Isolation Kit (Miltenyi Biotec, Cat.
- Target cells were incubated with different amounts of antibody and after 10 minutes were incubated with primary human NK cells as effector cells at a target:effector ratio of 9:1.
- Antibody-dependent cell killing was measured using a LDH release assay (Cytotoxicity Detection Kit (LDH) (Roche; Cat. Nr.: 11644793001)) after 4 hours of incubation at 37°C.
- LDH Low Dendritic Cell-mediated antibody-dependent cellular phagocytosis
- ADCP can also contribute to viral control by clearing infected cells and by potentially stimulating T cell response with viral antigen presentation.
- ADCP was tested using peripheral blood mononuclear cells as phagocytes and ExpiCHO transfected with SARS-CoV-2 S fluorescently labeled with PKH67 Fluorescent Cell Linker Kits (Sigma Aldrich, Cat. Nr.: MINI67) as target cells.
- Target cells were incubated with different amounts of antibody for 10 minutes, followed by incubation with human PBMCs isolated from healthy donors that were fluorescently labeled with Cell Trace Violet (Invitrogen, Cat. Nr.: C34557) at an effector:target ratio of 20:1. After an overnight incubation at 37°C, cells were stained with anti-human CD14-APC antibody (BD Pharmingen, Cat.
- FIG 17B shows ADCP function of antibodies using PBMCs as phagocytic cells and PKF67-labelled SARS-CoV-2 S-expressing ExpiCHO as target cells. Symbols show means ⁇ SD of duplicate measurements.
- Fc variants of S309 were tested for ADCC.
- S309-LS includes the M428L and N434S Fc mutations.
- S309-GRLR includes the G236R/L328R Fc mutation, which exhibits minimal binding to Fc ⁇ Rs.
- S309-LS-GAALIE includes the MLNS and GAALIE (G236A/A330L/I332E) Fc mutations. Results are shown in Figure 45.
- Figure 24A shows ADCC of antibodies using primary NK effector cells and SARS-CoV- or SARS-CoV-2 S- expressing ExpiCHO as target cells.
- the graph in Figure 24A shows the % killing determined for one representative donor homozygous for the high affinity Fc ⁇ RIIIa (symbols show mean ⁇ SD).
- Figure 24B shows area under the curve (AUC) for the responses of cells from donors homozygous for the high affinity Fc ⁇ RIIIa variant 158V (VV), compared to cells from donors heterozygous for 158V (FV) or homozygous for the low affinity variant 158F (FF) (mean ⁇ SD).
- Figure 25A shows ADCP using PBMCs as phagocytic cells and PKH67-labelled SARS-CoV-2 S-expressing ExpiCHO as target cells, for one representative donor. % ADCP indicates the percentage of monocytes positive for PKH67.
- Figure 25B shows the area under the curve (AUC) for the responses from multiple donors.
- EXAMPLE 15 REACTIVITY OF ANTIBODIES TO CELL LYSATE OF SARS-COV-2-INFECTED CELLS Reactivity of antibodies S304, S306, S309, and S310 against cell lysate of SARS-CoV-2-infected VeroE6 cells was measured.
- Figure 21A shows reactivity of the antibodies, as measured by indirect ELISA S against TX100-extracted lysate of SARS- CoV-2-infected VeroE6 cells.
- Figure 21B shows reactivity of the antibodies, as measured by indirect ELISA S against SDS extracted (denatured) lysate of SARS-CoV- 2-infected VeroE6 cells.
- Figure 21C shows reactivity of human SARS-CoV-1 convalescent serum, as measured by indirect ELISA S against TX100-extracted or SDS-extracted lysate of SARS-CoV-2-infected VeroE6 cells.
- EXAMPLE 16 NEUTRALIZATION OF SARS-COV-2 INFECTION BY ANTIBODIES S304 AND S309, ALONE OR IN COMBINATION Neutralization of SARS-CoV-2 infection by monoclonal antibodies S304 and S309 was assessed using a SARS-CoV-2 live virus assay.
- the live virus neutralization assay quantifies the number of infected cells by staining for viral nucleoprotein (NP) with an NP-specific polyclonal rabbit serum.
- NP viral nucleoprotein
- S309-11 comprises the wild-type VH sequence (SEQ ID NO: 105) and the wild-type VL sequence (SEQ ID NO: 168) of S309.
- S309-12 comprises an N55Q mutation in CDRH2, providing a VH variant sequence (SEQ ID NO: 113) and the wild- type VL sequence (SEQ ID NO: 168) of S309.
- S309-13 comprises a W50F mutation in VH (SEQ ID NO: 129) and the wild-type VL sequence (SEQ ID NO: 168) of S309.
- S309-14 comprises a W105F VH variant sequence (SEQ ID NO: 119) and the wild- type VL sequence (SEQ ID NO: 168) of S309.
- S309-15 comprises a W50F/G56A/W105F VH variant (SEQ ID NO: 172) and the wild-type VL sequence of S309 (SEQ ID NO: 168).
- S309 recombinant antibody (S309-11) and each of the four variants S309-12 – S309-15 were produced by transient transfection and expression of a plasmid vector encoding the recombinant antibody in HD 293F cells (GenScript). This signal peptide provided superior antibody production as compared to other signal peptides tested. Data not shown. Cells were harvested on day 4 and IgG expression was validated by Western blot and protein A titer analysis.
- EXAMPLE 18 BINDING OF S309 RIGG AND VARIANTS TO SARS-COV-2 RBD Binding of recombinant monoclonal antibody S309 and the four S309 variants described in Example 17 (S309-12 – S309-15) to RBD was measured using surface plasmon resonance (SPR). SPR experiments were carried out with a Biacore T200 instrument using a single-cycle kinetics approach. Antibody expressed as IgG was captured on the surface and increasing concentrations of purified SARS-CoV-2 RBD, either glycosylated or deglycosylated form, were injected. SPR was conducted using a sensor chip with anti-human Fc covalently immobilized (GE).
- GE anti-human Fc covalently immobilized
- Buffer used was 10 mM HEPES pH 7.4, 150 mM NaCl, 3mM EDTA, and 0.05% P20 detergent. Assays were conducted at 25°C. Recombinant antibodies were diluted from supernatant to approximately 2 ⁇ g/ml. RBD concentrations were 0.8 nM, 3.1 nM, 12.5 nM, 50 nM, and 200 nM. Glycosylated RBD was obtained by expression in HEK293 cells and purified using one-step Ni affinity purification.
- Deglycosylated RBD was obtained by expression in-house in Expi293 cells grown in the presence of kifunensine, purification using one-step Ni affinity purification, and treatment with endoglycosidase H. Single- cycle kinetics assays were carried out with 3 minute injections and 20 minute dissociation periods. Association and dissociation kinetics were monitored and fit to a binding model to determine affinity. Results are shown in Figures 30A-30F and Table 8. Table 8. Binding to deglycosylated RBD was measured in two different SPR assays using different parameters. Experiment 1 used 10-minute injections and an RBD concentration series of 4-fold dilutions from 100 nM.
- Experiment 2 used 3-minute injections and a concentration series of 4-fold dilutions from 200 nM, as described above. Results are shown in Table 9. Results of Experiment 1 for S309-15 are also shown in Figure 30F, top two panels. Table 9. Binding of recombinant antibody S309 and the four engineered variants to RBD was measured by surface plasmon resonance (SPR) using the same procedure described above, except using purified recombinant antibodies rather than cell culture supernatant. Resuts are shown in Table 10. Table 10.
- ExpiCHO cells were transiently transfected with SARS-CoV-2 S (BetaCoV/Wuhan- Hu-1/2019), and incubated with titrated concentrations of antibody for 10 minutes. ExpiCHO cells were then incubated with Jurkat cells expressing Fc ⁇ RIIIa or Fc ⁇ RIIa on their surface and stably transfected with NFAT-driven luciferase gene (Promega, Cat. Nr.: G9798 and G7018) at an effector to target ratio of 6:1 for Fc ⁇ RIIIa and 5:1 for Fc ⁇ RIIa. Activation of human Fc ⁇ Rs in this bioassay results in the NFAT-mediated expression of the luciferase reporter gene.
- Luminescence was measured after 21 hours of incubation at 37°C with 5% CO2, using the Bio-Glo-TM Luciferase Assay Reagent according to the manufacturer’s instructions.
- Antibodies S303, S304, S306, S309, S315, and a combination of S309 and S315 were assayed, along with comparator antibody S230. Results are shown in Figures 31 and 32.
- FIG 35A shows Spike protein variants occurring with a frequency of n>1 as spheres mapped onto the closed and open form of the full trimeric Spike ectodomain.
- Figure 35B shows the prevalence of variants in Spike glycoprotein by amino acid. Each dot is a distinct variant. The locations of Domain A and RBD are shown. Variants passing a frequency threshold of 0.1% are as indicated.
- Figure 43 shows variants supported by at least two sequences (prevalence greater than 0.01%) rendered as indicated spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. Each dot is a distinct variant.
- Figure 43 shows Spike protein variants supported by at least two sequences as indicated spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. The RBD and other Spike protein domains are shown in the colors indicated. 171 variants (out of 11,839 total Spike protein sequences analyzed) are shown.
- Variants are labeled if their prevalence is greater than 1% (D614G only) or if they are located within the RBD. The location of conserved N343 is also indicated.
- EXAMPLE 22 Neutralization of MLV-S Protein Pseudovirus by Monoclonal Antibody S309 Neutralization of SARS-CoV-2-MLV, SARS-CoV-1-MLV bearing S Protein from various isolates, and other sarbecovirus isolates by monoclonal antibody S309 was assayed.
- HEK293T cells were co-transfected with a SARS-CoV, SARS-CoV-2, CUHK, GZ02, or WiV1 S encoding-plasmid, an MLV Gag-Pol packaging construct and the MLV transfer vector encoding a luciferase reporter using the Lipofectamine 2000 transfection reagent (Life Technologies) according to the manufacturer’s instructions.
- Cells were incubated for 5 hours at 37°C with 8% CO2 with OPTIMEM transfection medium.
- DMEM containing 10% FBS was added for 72 hours.
- VeroE6 cells or DBT cells transfected with human ACE2 were cultured in DMEM containing 10% FBS, 1% PenStrep and plated into 96 well plates for 16-24 hours.
- DMEM Concentrated pseudovirus with or without serial dilution of antibodies was incubated for 1 hour and then added to the wells after washing 3X with DMEM. After 2-3 hours DMEM containing 20% FBS and 2% PenStrep was added to the cells for 48 hours. Following 48 hours of infection, One-Glo-EX (Promega) was added to the cells and incubated in the dark for 5-10 minutes prior to reading on a Varioskan LUX plate reader (ThermoFisher). Measurements were done in duplicate and relative luciferase units (RLU) were converted to percent neutralization and plotted with a non-linear regression curve fit in PRISM. Results are shown in Figure 38.
- RLU relative luciferase units
- S309 was shown to neutralize SARS-CoV-MLVs from isolates of the three phases of the 2002-2003 epidemic with IC50 values of between 120 ng/ml and 180 ng/ml, and to partially neutralize SARSr- CoV 39 WIV-1.
- EXAMPLE 23 Characterization of the Structure of SARS-CoV-2 S Glycoprotein in Complex with the S309 Neutralizing Antibody Fab Fragment The structure of the complex between the S309 Fab fragment and a prefusion stabilized SARS-CoV-2 S Protein ectodomain trimer was characterized using single- particle cryoEM.
- the epitope is accessible in both the open and closed S states, explaining the stoichiometric binding of S309 Fab fragment to the S trimer.
- the S309 paratope is composed of all six CDR loops and buries a surface area of ⁇ 1,050 ⁇ 2 at the interface with S B (RBD) through electrostatic interactions and hydrophobic contacts.
- the 20-residue long CDRH3 sits atop the S B (RBD) helix comprising residues 337-344 and also contacts the edge of the S B (RBD) five-stranded ⁇ -sheet (residues 356-361), overall accounting for ⁇ 50% of the buried surface area.
- CDRL1 and CDRL2 extend the epitope by interacting with the helix spanning residues 440-444 that is located near the S 3-fold molecular axis.
- CDRH3 and CDRL2 sandwich the SARS-CoV-2 S glycan at position N343 through contacts with the core fucose moiety (in agreement with the detection of SARS-CoV-2 N343 core- fucosylated peptides by mass-spectrometry) and to a lesser extent with the core N- acetyl-glucosamine. These latter interactions bury an average surface of ⁇ 170 ⁇ 2 and stabilize the N343 oligosaccharide which is resolved to a much larger extent than in the apo SARS-CoV-2 S structures.
- the 20-residue long CDRH3 sits atop the S B (RBD) helix comprising residues 337-344 and also contacts the edge of the S B (RBD) five-stranded ⁇ -sheet (residues 356-361), overall accounting for ⁇ 50% of the buried surface area.
- CDRL1 and CDRL2 extend the epitope by interacting with the helix spanning residues 440-444 that is located near the S 3-fold molecular axis.
- CDRH3 and CDRL2 sandwich the SARS-CoV-2 S glycan at position N343 through contacts with the core fucose moiety (in agreement with the detection of SARS-CoV-2 N343 core-fucosylated peptides by mass-spectrometry) and to a lesser extent with the core N-acetyl-glucosamine. These latter interactions were shown to bury an average surface of ⁇ 300 ⁇ 2 and stabilize the N343 oligosaccharide which is resolved to a much larger extent than in the apo SARS-CoV-2 S structures. Table 14.
- the oligosaccharide at position N343 is also conserved in both viruses and corresponds to SARS-CoV N330, for which core-fucosylated glycopeptides were detected by mass spectrometry, and would allow for similar interactions with the S309 Fab fragment.
- EXAMPLE 24 BINDING OF MONOCLONAL ANTIBODIES TO DISULFIDE STABILIZED SPIKE PROTEIN Structural changes in the SARS-CoV-1 and SARS-CoV-2 Spike proteins, from a closed to an open conformation, have been reported to enable exposure of the receptor-binding motif, which mediates interaction with ACE2. SARS-CoV-1 and SARS-CoV-2 Spike were engineered to be stabilized in the prefusion closed conformation.
- SARS-CoV-2 Spike protein that comprised the amino acid substitutions R682S, R683G and R685G, K986P and V987P, an inter-molecular disulfide bond was created by substituting cysteines in place of S383 and D985.
- This engineered Spike protein was recombinantly expressed, and is referred to as SARS-CoV-2 DS Spike or SARS-CoV-2 DS S.
- Recombinant S proteins (wild-type or disulfide-stabilized) were produced in 500 mL cultures using FreeStyle 293 expression medium (Life Technologies) at 37°C in a humidified 8% CO2 incubator rotating at 130 r.p.m; The culture was transfected using 293fectin (ThermoFisher Scientific) with cells grown to a density of 10 6 cells per mL and cultivated for three days. The supernatant was harvested and cells were resuspended for another three days, yielding two harvests. Clarified supernatants were purified using a 5 mL Cobalt affinity column (Takara).
- Purified protein was concentrated and flash frozen in a buffer containing 50 mM Tris pH 8.0 and 150 mM NaCl prior to cryoEM analysis. Electron microscopy confirmed proper folding of the engineered protein (data not shown). Similarly, a disulfide-stabilized SARS-CoV-1 Spike protein was engineered by substituting cysteines in place of S370 and D969, forming SARS-CoV-1 DS S. Electron microscopy confirmed proper folding of this engineered protein as well (data not shown).
- the monoclonal antibodies were then tested by flow-cytometry at 10 ⁇ g/ml for their ability to stain ExpiCHO cells expressing the S protein of 2019-nCoV, SARS-CoV, MERS-CoV or Mock cell transfectants.
- Transient expression of recombinant SARS-CoV-2 protein The full-length S gene of SARS-CoV-2 strain (2019-nCoV-S) isolate BetaCoV/Wuhan-Hu-1/2019 (accession number MN908947) was codon optimized for human cell expression and cloned into the phCMV1 expression vector (Genlantis).
- Expi-CHO cells were transiently transfected with phCMV1-SARS-CoV-2-S, phCMV1- MERS-CoV-S (London1/2012), SARS-spike_pcDNA.3 (strain SARS) or the empty phCMV1 (Mock) using Expifectamine CHO Enhancer. Two days after transfection, cells were collected, fixed, or fixed and permeabilized with saponin for immunostaining with a panel of monoclonal antibodies reactive to SARS-CoV Receptor Binding Domain (RBD). An Alexa647-labelled secondary antibody anti-human IgG Fc was used for detection.
- RBD SARS-CoV Receptor Binding Domain
- Binding of antibodies to transfected cells was analyzed by flow- cytometry using a ZE5 Cell Analyzer (Biorard) and FlowJo software (TreeStar). Positive binding was defined by differential staining of CoV-S-transfectants versus mock-transfectants. Competition experiments using Octet (BLI, biolayer interferometry) Unless otherwise indicated herein, anti-His sensors (BIOSENSOR ANTI- PENTA-HIS (HIS1K)) were used to immobilize the S1 subunit protein of SARS-CoV (Sino Biological Europe GmbH).
- Dissociation was recorded for 9min by moving the sensors to wells containing KB. K D values were calculated using a global fit model (Octet). Octet Red96 (ForteBio) equipment was used. For K D determination of full-length antibodies compared to Fab fragments, His- tagged RBD of SARS-CoV-1 or SARS-CoV-2 were loaded at 3 ⁇ g/ml in KB for 15 minutes onto anti-HIS (HIS2) biosensors (Molecular Devices, ForteBio). Association of full-length antibody and Fab was performed in KB at 15 ug/ml and 5 ug/ml respectively for 5 minutes. Dissociation in KB was measured for 10min.
- ELISA binding The reactivities of mAbs with SARS-CoV Spike S1 Subunit Protein (strain WH20) protein were determined by enzyme-linked immunosorbent assays (ELISA). Briefly, 96-well plates were coated with 3 ⁇ g/ml of recombinant SARS-CoV Spike S1 Subunit Protein (Sino. Biological). Wells were washed and blocked with PBS+1%BSA for 1 h at room temperature and were then incubated with serially diluted mAbs for 1 h at room temperature.
- Bound mAbs were detected by incubating alkaline phosphatase- conjugated goat anti-human IgG (Southern Biotechnology: 2040-04) for 1 h at room temperature and were developed by 1 mg/ml p-nitrophenylphosphate substrate in 0.1 M glycine buffer (pH 10.4) for 30 min at room temperature.
- the optical density (OD) values were measured at a wavelength of 405 nm in an ELISA reader (Powerwave 340/96 spectrophotometer, BioTek).
- Murine leukemia virus (MLV) pseudotyped with SARS-CoV-2 Spike protein (SARS-CoV-2pp) or SARS-CoV-1 Spike protein (SARS- CoV-1pp) were used.
- DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells.
- SARS-CoV-2pp or SARS-CoV-1pp was activated with trypsin TPCK at 10ug/ml.
- Activated SARS-CoV-2pp or SARS-CoV-1pp was added to a dilution series of antibodies (starting 50ug/ml final concentration per antibody, 3-fold dilution).
- DBT- ACE2 cells were added to the antibody-virus mixtures and incubated for 48h. Luminescence was measured after aspirating cell culture supernatant and adding steady- GLO substrate (Promega). Unless otherwise indicated, pseudoparticle neutralization assays use a VSV- based luciferase reporter pseudotyping system (Kerafast). VSV pseudoparticles and antibody are mixed in DMEM and allowed to incubate for 30 minutes at 37C. The infection mixture is then allowed to incubate with Vero E6 cells for 1h at 37C, followed by the addition of DMEM with Pen-Strep and 10% FBS (infection mixture is not removed). The cells are incubated at 37C for 18-24 hours.
- Luciferase is measured using an Ensight Plate Reader (Perkin Elmer) after the addition of Bio-Glo reagent (Promega).
- SPR single-cycle kinetics SPR experiments were carried out with a Biacore T200 instrument using a single-cycle kinetics approach. S309 IgG was captured on the surface and increasing concentrations of purified SARS-CoV-2 RBD, either glycosylated or deglycosylated, were injected. Association and dissociation kinetics were monitored and fit to a binding model to determine affinity. Expression of recombinant antibodies Recombinant antibodies were expressed in ExpiCHO cells transiently co- transfected with plasmids expressing the heavy and light chain as previously described. (Stettler et al.
- Bat and pangolin sequences were removed to yield human-only sequences.
- Sourced SARS-CoV genome sequences comprised all the major published strains, such as Urbani, Tor2, TW1, P2, Frankfurt1, among others.
- Pangolin sequences as shown by Tsan-Yuk Lam et al were sourced from GISAID.
- Bat sequences from the three clades of Sarbecoviruses as shown by Lu et al (Lancet 2020) were sourced from Genbank.
- Civet and racoon dog sequences were similarly sourced from Genbank.
- two rounds of reference-free 2D classification were performed using cryoSPARC 48 to select well-defined particle images.
- two rounds of 3D classification with 50 iterations each (angular sampling 7.5 ⁇ for 25 iterations and 1.8 ⁇ with local search for 25 iterations), using our previously reported closed SARS- CoV-2 S structure as initial model, were carried out using Relion 49 without imposing symmetry to separate distinct SARS-CoV-2 S conformations.
- Glycan refinement relied on a dedicated Rosetta protocol, which uses physically realistic geometries based on prior knowledge of saccharide chemical properties, and was aided by using both sharpened and unsharpened maps. Models were analyzed using MolProbity, EMringer, Phenix and privateer to validate the stereochemistry of both the protein and glycan components. Figures were generated using UCSF ChimeraX.
- Crystallization and X-ray structure determination of Fab S309 Fab S309 crystals were grown in hanging drop set up with a mosquito at 20°C using 150 nL protein solution in Tris HCl pH 8.0, 150 mM NaCl and 150nL mother liquor solution containing 1.1 M Sodium Malonate, 0.1 M HEPES, pH 7.0 and 0.5% (w/v) Jeffamine ED-2001. Crystals were cryo-protected using the mother liquor solution supplemented with 30% glycerol. The dataset was collected at ALS beamline 5.0.2 and processed to 3.3 ⁇ resolution in space group P4 1 2 1 2 using mosflm and Aimless.
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Abstract
The present disclosure provides a conserved target region of a SARS coronavirus receptor binding domain (RBD). Also provided are antibodies and antigen-binding fragments thereof that are capable of bind in a target region, in certain embodiments, are capable of neutralizing a SARS-CoV-2 infection. Also provided are immunogenic compositions derived from a target region, and methods of using the same to, for example, treat or prevent a sarbecovirus infection.
Description
IMMUNOTHERAPY TARGETING A CONSERVED REGION IN SARS CORONAVIRUSES STATEMENT REGARDING SEQUENCE LISTING The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 930585_404WO_SEQUENCE_LISTING.txt. The text file is 304 KB, was created on April 2, 2021, and is being submitted electronically via EFS-Web. BACKGROUND A novel betacoronavirus emerged in Wuhan, China, in late 2019. As of March 24, 2021, approximately 124 million cases of infection by this virus (termed, among other names, SARS-CoV-2) had occurred worldwide, resulting in over 2.7 million deaths. Therapies for infection by SARS-CoV-2 and other sarbecoviruses are needed. BRIEF DESCRIPTION OF THE DRAWINGS Figures 1A and 1B Figures 1A and 1B show binding by antibodies (1A) S303 (VH SEQ ID NO.:63; VL SEQ ID NO.:67) and (1B) S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) to recombinant SARS-CoV-2 RBD. Figures 2A and 2B shows the SARS-CoV-2 neutralization capacity of certain antibodies. Figures 3A-3I show SARS-CoV-2 neutralization of infection. Figure 3A shows neutralization by donor plasma from SARS-CoV-1 survivors. Figures 3B-3D and 3I show neutralization by supernatant from B cells expressing certain antibodies. Figures 3E-3H show neutralization by certain recombinant IgG1 antibodies. Figures 4A and 4B show binding of antibody-containing B cell supernatant to SARS-CoV-2 S protein expressed on ExpiCHO cells. Graphs showing binding profiles of antibodies S300-S310 are indicated with boxes.
Figures 5A and 5B show binding of antibodies S311 and S312 in the supernatant of cultured B cells to SARS-CoV-1 and SARS-CoV-2. Antibody concentrations are estimates. SARS S1 Sino: protein from Sino Biological. RBD2: RBD of SARS-CoV-2 produced in-house. Figures 6A-6E show (top) binding curves of certain antibodies for SARS-CoV- 1 (SARS1) RBD and SARS-CoV-2 (SARS2) RBD, as measured by Octet, and (bottom) KD values. KD values for antibodies (e.g., <1.0x10-12M) with very strong binding and slow dissociation are estimates. Figure 7 shows neutralization of infection by S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83) and S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) antibodies, alone or in combination, against SARS-CoV-2 pseudotyped virus. Figures 8A-8K show binding curves of certain antibodies for RBD of SARS- CoV-1, RBD of SARS-CoV-2, and ectodomains of various coronaviruses, as measured by ELISA. Figure 9 shows neutralization of infection by S309 rIgG1 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) and S315 rIgG1 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) against SARS-CoV-2 pseudotyped virus. Figure 10 shows neutralization of infection by S309 full-length rIgG1 and S309 rFab (both of which comprise a VH of SEQ ID NO.:105 and a VL of SEQ ID NO.:168) against SARS-CoV-2 pseudotyped virus. Figure 11 shows binding of antibody S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) to SARS-CoV-1 and SARS-CoV-2 spike protein expressed on ExpiCHO cells. Stacked histograms of flow cytometry graphs show antibody dose-dependent binding of S309 to SARS-CoV and SARS-CoV-2. Figure 12A and 12B show concentration-dependent binding measured by flow cytometry for certain antibodies. Figure 12A shows binding to SARS-CoV-2. Figure 12B shows binding to SARS-CoV-1. Figure 13 shows neutralization of infection by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID
NO.:168), S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) against SARS-CoV-2 pseudotyped virus. Figure 14A-14D show binding affinity/avidity of antibodies S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) to RBD of SARS-CoV-1 (right panels) and SARS-CoV-2 (left panels). Figure 15A and 15B show competition of pairs of antibodies for binding to the RBD of SARS-CoV-1 (Figure 15A) and SARS-CoV-2 (Figure 15B). For each graph, the x-axis shows time (0 to 1000 seconds), and the y-axis shows the binding to RBD as measured by BLI (0 to 3 nm). The first antibody is indicated on the left of the matrix and the second antibody is indicated on the top of the matrix. The dashed vertical lines in Figure 15B show the switch from the first antibodyto the second antibody. At right ("I"-"IV" in Figure 15A, "II" and "IV" in Figure 15B) are antigenic sites as determined by structural information, escape mutant analysis, and BLI-based epitope binning. Figure 16 shows the ability of S309 to interfere with RBD of SARS-CoV-1 (left) or SARS-CoV-2 (right) binding to human ACE2 (hACE2). hACE2 was loaded onto BLI sensors, followed by incubation of the sensors with RBD alone or RBD in combination with antibody. The vertical dashed line indicates the start of the association of RBD with or without antibody. In the graph at left, antibody S230 was used as a positive control of inhibition of SARS-CoV-1 RBD binding to ACE2 based on previous studies (see. Walls et al., Cell 176(5):1023-1039.e15 (2019)). Figure 17A and 17B show antibody-dependent effects of certain antibodies against model infected cells. Figure 17A shows antibody-dependent cytotoxicity using primary NK effector cells and SARS-CoV-2-expressing ExpiCHO cells as target cells. Bar graph at right shows ADCC for the indicated antibody(ies), calculated as area under the curve (AUC). Figure 17B shows antibody-dependent cellular phagocytosis using PBMCs as phagocytic cells and PKF67-labelled SARS-CoV-2-expressing ExpiCHO as target cells. Line graphs show mean fluorescence intensity (MFI) of PBMCs after incubation with target cells and antibodies, determined for one representative donor with high affinity FcγRIIIa (symbols show means ± SD of duplicates).
Figure 18A-18J show binding curves of certain recombinant antibodies for RBD of SARS-CoV-1, RBD of SARS-CoV-2, and ectodomains of various coronavirus strains, as measured by ELISA. Recombinant mAbs were tested by ELISA at a concentration range of 5 to 0.00028mg/ml. RBD2: Receptor binding domain of SARS- CoV-2. RBD1: Receptor binding domain of SARS-CoV (also referred-to herein as SARS-CoV-1). Spike: stabilized prefusion trimer of the indicated coronavirus. Some antibodies were recombinantly expressed as IgG1 (rIgG1), and some antibodies were recombinantly expressed as IgG1 with the MLNS mutation (M428L and N434S (EU numbering)) in the Fc (rIgG1-LS). Figure 19A and 19B show ability of certain antibodies to interfere with RBD binding to human ACE2. Human ACE2 (hACE2) was loaded onto BLI sensors, followed by incubation of the sensors with RBD alone or RBD in combination with recombinant antibody. The vertical dashed line indicates the start of the loading of RBD with or without antibody. RBD: Receptor binding domain. Figure 19A shows SARS-CoV-1 RBD binding to ACE2. Figure 19B shows SARS-CoV-2 RBD binding to ACE2. Figure 20A and 20B show binding affinity and avidity of antibody S309 IgG (Figure 20A) versus S309 Fab (Figure 20B) for SARS-CoV-1 RBD (bottom of each figure) and SARS-CoV-2 RBD (top of each figure). For both the IgG and the Fab: VH SEQ ID NO.:105; VL SEQ ID NO.:168. RBD was loaded to BLI pins and association of different concentrations of S309-IgG-MLNS or S309 Fab was measured. Vertical dashed lines indicate the start of the dissociation phase when BLI pins were switched to buffer. Figure 21A-21C show reactivity of S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), and S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159) antibodies against SARS-CoV-2. Figure 21A shows reactivity of S304, S306, S309, and S310 antibodies against TX100 extracted lysate of SARS-CoV-2 infected Vero E6 cells. Figure 21B shows reactivity of the same antibodies against SDS extracted lysate of SARS-CoV-2 infected Vero E6 cells. Figure 21C shows
reactivity of human SARS-CoV-1 convalescent serum against TX100 extracted or SDS extracted lysate of SARS-CoV-2 infected Vero E6 cells. Figures 21A and 21B also show data for comparator antibody LCA57, which is specific for spike protein of MERS-CoV (Corti et al. PNAS 112(33):10473-10478 (2015). Figure 22A-22D show neutralization of SARS-CoV-2 infection by antibodies as assessed by inhibition of nucleoprotein (NP) expression at 24 and 45 hours post infection. Figure 22A shows neutralization of SARS-CoV-2 infection by S304 S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83). Figure 22B shows neutralization of SARS- CoV-2 infection by S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168. Figure 22C shows neutralization of SARS-CoV-2 infection by the combination of S304 and S309. Figure 22D shows control neutralization of SARS-CoV-2 infection by comparator antibody LCA57, which is specific for spike protein of MERS-CoV (Corti et al. PNAS 112(33):10473-10478 (2015)). Figure 23 shows neutralization of infection by antibodies S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182), alone or in combination, against SARS-CoV-2 pseudotyped virus. Figure 24A and 24B show antibody-dependent effects of certain antibodies against model infected cells. Figure 24A shows antibody-dependent cell-mediated cytotoxicity (ADCC) using primary NK effector cells and SARS-CoV-2-expressing ExpiCHO cells as target cells. The graph shows the % killing of target cells after incubation with antibody or combination of antibodies shown in the legend. Figure 24B shows ADCC for the indicated antibody(ies), calculated as area under the curve (AUC). Left panel: AUC determined using cells with VV FcγRIIIa genotype; right panel: AUC determined for cells with FF or FV FcγRIIIa genotype. Figures 25A and 25B show further antibody-dependent effects of certain antibodies. Figure 25A shows antibody-dependent cellular phagocytosis (ADCP) using PBMCs as phagocytic cells and PKF67-labelled SARS-CoV-2-expressing ExpiCHO cells as target cells. The graph shows mean fluorescence intensity (MFI) of PBMCs after incubation with target cells and antibodies, determined for one representative donor with high affinity FcγRIIIa (symbols show means ± SD of duplicates). Figure
25B shows ADCP for the indicated antibody(ies), calculated as area under the curve (AUC). Figure 26 shows antibody binding as measured by flow cytometry. Binding of antibody S309 to SARS-CoV-2 Spike protein expressed in Expi-CHO cells was detected with a fluorescently labeled secondary antibody. Figure 27 shows binding of antibody S309 (labeled as "11" in the figure key) and four engineered variants of S309 (labeled as "12" through "15", respectively) to S protein, as measured by flow cytometry. The four engineered variant antibodies are as follows: S309 N55Q comprises an N55Q mutation in CDRH2, resulting in a variant VH sequence (SEQ ID NO:.113), and the wild-type VL sequence (SEQ ID NO.:168) of S309; S309 W50F comprises a W50F variant VH sequence (SEQ ID NO: 129) and the wild-type VL sequence (SEQ ID NO.:168) of S309; S309 W105F comprises a W105F variant VH sequence (SEQ ID NO: 119) and the wild-type VL sequence (SEQ ID NO.:168) of S309; and S309 W50F/G56A/W105F comprises a W50F/G56A/W105F variant VH sequence (SEQ ID NO.:172) and the wild-type VL sequence of S309. In Figure 27, S309 N55Q is labeled as "12," S309 W50F is labeled as "13," S309 W105F is labeled as "14," and S309 W50F-G56A-W105F is labeled as "15." Antibody binding to SARS-CoV-2 Spike protein expressed on Expi-CHO cells was detected with a fluorescently labeled secondary antibody. Data from two experiments are shown. Figure 28 shows neutralization of infection by antibody S309 (referred to in the figure as "Variant-11 (wt)") and four S309 variant antibodies against SARS-CoV-2 pseudotyped viruses. In Figure 28, S309 N55Q is labeled as "Variant-12," S309 W50F is labeled as "Variant-13," S309 W105F is labeled as "Variant-14," and S309 W50F- G56A-W105F is labeled as "Variant-15." Pseudotyped viruses are VSV pseudotyped with SARS-CoV-2 Spike protein. Figure 29 shows a summary of results from binding and pseudovirus neutralization assays for antibody S309 ("S309-WT") and four engineered variants of S309 ("N55Q"; "W50F"; "W105F"; "W50F/G56A/W105F"). The dashed horizontal line shows change of function of engineered variant versus S309-WT baseline. Differently hatched bars show binding to glycosylated RBD as measured by SPR,
binding to deglycosylated RBD as measured by SPR, binding to antigen-expressing cells, as measured by FACS, and neutralization as measured using SARS-CoV-2 pseudoviruses. Figures 30A-30F show binding kinetics of certain monoclonal antibodies to SARS-CoV-2 glycosylated or deglycosylated RBD as measured by SPR. Figure 30A shows binding kinetics of S309 wild type antibody (2 replicate experiments). Figure 30B shows binding kinetics of S309 variant N55Q (bottom), as compared to S309 wild type antibody (top). Figure 30C shows binding kinetics of S309 variant W50F (bottom) as compared to S309 wild type antibody (top). Figure 30D shows binding kinetics of S309 variant W105F (bottom) as compared to S309 wild type antibody (top). Figure 30E shows binding of S309 variant W50F/G56A/W105F (bottom) as compared to S309 wild type antibody (top). Figure 30F shows binding of S309 variant W50F/G56A/W105F using 10 minute injection period (top panel) or 3 minute injection period (bottom panel). Figure 31 shows activation of high affinity (158V) FcγRIIIa (left panel) or low affinity (158F) FcγRIIIa (right panel) by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), and a combination of S309 and S315, along with comparator antibody S230. Activation was measured using SARS-CoV-2 S-expressing ExpiCHO cells as target cells and Jurkat reporter cells stably transfected with NFAT-driven luciferase reporter gene. Activation of FcγRIIIa results in NFAT-mediated expression of the luciferase reporter gene. Results are from one experiment, one or two measurements per mAb. Figure 32 shows activation of FcγRIIa by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO.:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), and a combination of S309 and S315, along with comparator monoclonal antibody S230. Activation was measured using SARS-CoV-2 S-expressing ExpiCHO cells as target cells and Jurkat reporter cells stably transfected with NFAT-driven
luciferase reporter gene. Activation of FcγRIIa results in NFAT-mediated expression of the luciferase reporter gene. Figures 33A and 33B show binding of antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182), along with comparator antibodies S110, S230, and S109, to S protein expressed on a cell surface. Figure 33A shows binding to ExpiCHO cells transfected with SARS-CoV-2 S protein. Figure 33B shows binding to ExpiCHO cells transfected with SARS-CoV-1 S protein. Mean fluorescence intensity was measured by flow cytometry for each antibody. Antibody concentrations tested are indicated in the x-axis. Figure 34 shows neutralization of infection by antibodies S303 (VH SEQ ID NO.:63; VL SEQ ID NO:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S310 (VH SEQ ID NO.:155; VL SEQ ID NO.:159), and S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) against SARS-CoV-1 pseudotyped virus. Figure 35A and 35B show conservation of Spike protein residues. Figure 35A shows Spike protein variants occurring with a frequency of n>1 as spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. The RBD and other Spike protein domains are shown as indicated. 40 mutations (out of 2229 total) are shown. Only residue 367 (n=8) is highlighted in the RBD, and residues 476 (n=7) and 483 (n=17) are not. Figure 35B shows the prevalence of variants in Spike glycoprotein by amino acid. Each dot is a distinct variant. The locations of Domain A and RBD are shown. Variants passing a frequency threshold of 0.1% are as indicated. Figure 36 shows neutralization of SARS-CoV-2-MLV by antibody S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) combined with an equimolar amount of antibody S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83). For antibody cocktails, the concentration shown on the x axis is that of the individual antibodies.
Figure 37 shows neutralization of SARS-CoV2-MLV by S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168) combined with an equimolar amount of antibody S315 (VH SEQ ID NO.:178; VL SEQ ID NO.:182) antibodies. For antibody cocktails, the concentration shown on the x axis is that of the individual antibodies. Figure 38 shows neutralization of SARS-CoV-2-MLV, SARS-CoV-MLV (bearing S from various isolates) and other sarbecovirus isolates by mAb S309. Figures 39A-39C show structures of SARS-CoV-2 S glycoprotein in complex with the S309 antibody Fab fragment, as determined by cryoEM. For these data, resolution was 4.2 Å (Fab bound to open SARS-CoV-2 S protein trimer) and 3.6 Å (Fab bound to closed SARS-CoV-2 S protein trimer) resolution. Figure 39A shows a ribbon diagram of the partially open SARS-CoV-2 S protein trimer with one RBD (SB) domain open, bound to three S309 Fab fragments (left) and the closed SARS-CoV-2 S protein trimer bound to three S309 Fab fragments shown in two orthogonal orientations (center and right). Figure 39B shows close-up views of the S309 epitope (as determined using cryoEM at the above resolution) showing the contacts formed with the core fucose (labeled with a star) and the core N-acetyl-glucosamine of the oligosaccharide at position N343 (left) and the 20-residue long CDRH3 sitting atop the RBD (SB) helix comprising residues 337-344 (right). The oligosaccharide at position N343 is omitted for clarity. Figures 39A and 39B show selected residues involved in interactions between S309 and SARS-CoV-2 S protein. Figure 39C shows a molecular surface representation of the SARS-CoV-2 S protein trimer, showing the S309 footprint indicated by residue conservation (conserved amino acid residue or conservative substitution) on one protomer among SARS-CoV-2 and SARS-CoV-1 S glycoproteins. Data were refined at higher resolution (3.7 Å for open trimer, and 3.1 Å for closed trimer; see Figures 47A-48C; in Figure 48B, R509 should be indicated part of the S309 epitope). Figures 40 shows ribbon diagrams of S309 and ACE2 bound to SARS-CoV-2 S protein RBD (SB). The composite model was generated using the SARS-CoV-2 S/S309 cryoEM structure and a crystal structure of SARS-CoV-2 S protein bound to ACE2.
Figures 41A-41C show conservation of Spike and RBD residues in relation to the binding footprints of ACE2 and S309. Figure 41A shows the ACE2 and S309 footprints mapped onto the structure of the SARS-CoV-2 RBD (PDB ID: 6M0J). The ACE2 footprint was defined by residues being within 5Å of the receptor in 6M0J. The highly conserved NAT glycosylation motif is indicated in the left-most image, the SARS-CoV-1 and SARS-CoV-2 differences within the S309 footprint are indicated in the second image from left, and the three high frequency RBD variants are indicated in the image at far right. Figure 41B shows alignments of the full RBD sequences of multiple sarbecoviruses. The ACE2 and S309 footprints are indicated; subsequent analysis determined that D442 was not in the S309 footprint (epitope). The three high frequency variant residues are indicated. Figure 41C shows conservation analysis of spike glycoprotein residues making contact with S309 across clades of sarbecoviruses. Residue coordinates for both SARS-CoV-2 and SARS-CoV-1 are shown. The NAT motif enabling glycosylation of N343 is indicated. The SARS-CoV-1 and SARS-CoV- 2 sequence differences are indicated. The column labeled “n” indicates the number of sequences used for this analysis. The IC50 is the half maximal neutralizing concentration of S309 against SARS-CoV-1-MLV or SARS-CoV-2-MLV. Figure 42 shows competition of antibodies with RBD for binding to ACE2. SARS-CoV-2 S protein ectodomain was loaded onto BLI sensors, followed by incubation of the sensors with hACE2 or S309 IgG (left panel) or Fab (right panel). In a third step, sensors were incubated with hACE2 or S309 IgG/Fab as indicated. Figures 43A-43D show cryoEM data processing and validation of the SARS- CoV-2 S protein structure. Figure 43A shows a representative electron micrograph (top panel) and class averages (bottom panel) of SARS-CoV-2 S protein embedded in vitreous ice. Scale bar: 100nm. Figure 43B shows gold-standard Fourier shell correlation curves for the closed and partially open trimers. The 0.143 cutoff is indicated by horizontal dashed lines. Figure 43C shows a local resolution map calculated using cryoSPARC for the closed reconstruction. Figure 43D shows the atomic model fit into the cryoEM density.
Figures 44A and 44B show binding of certain antibodies to S glycoproteins of SARS-CoV-2 (Figure 44A) or SARS-CoV-1 (Figure 44B) expressed at the surface of ExpiCHO cells. Symbols are means of duplicates from one experiment. Figures 45A and 45B show binding affinity and avidity of S309 IgG (Figure 45A) and S309 Fab (Figure 45B) for SARS-CoV-2 RBD (top panel) or SARS-CoV-2 Spike protein (bottom panel). For both IgG and Fab: VH SEQ ID NO.:105 and VL SEQ ID NO.:168. Biotinylated RBD of SARS-CoV-2 or biotinylated SARS-CoV-2 prefusion S ectodomain trimer were loaded onto Streptavidin biosensors, and association of different concentrations of S309-IgG-MLNS (comprising M428L and N434S Fc mutations (EU numbering)) or S309 Fab was measured. Vertical dashed lines indicate the start of the dissociation phase when biosensors were switched to buffer. Figures 46A and 46B show binding of antibodies S303, S304, S306, S309, S310, and S315, along with comparator antibodies S110, S124, S230, and S109, to S protein expressed on a cell surface. Figure 42A shows binding to ExpiCHO cells transfected with SARS-CoV-2 S protein. Figure 42B shows binding to ExpiCHO cells transfected with SARS-CoV-1 S protein. Mean fluorescence intensity was measured by flow cytometry for each antibody. Antibody concentrations tested are indicated in the x axis. Figures 47A-47D show cryoEM data processing and validation of the SARS- CoV-2 S protein structure. Figure 47A shows a representative electron micrograph (top panel) and class averages (bottom panel) of SARS-CoV-2 S protein embedded in virtreous ice. Scale bar: 100nm. Figure 47B shows gold-standard (solid line) and map/model (dashed line) Fourier shell correlation curves for the closed and partially open trimers. The 0.143 and 0.5 cutoffs are indicated by horizontal dashed lines. Figures 47C and 47D show local resolution maps calculated using cryoSPARC for the closed state (Figure 47C) and open state (Figure 47D) reconstructions. Figures 48A-48C show conservation of Spike and RBD residues in relation to the binding footprints of ACE2 and S309 at the higher resolution (as determined by cryo-EM at 3.7 Å for open trimer, and 3.1 Å for closed trimer). Figure 48A shows the ACE2 and S309 footprints mapped onto the structure of the SARS-CoV-2 RBD (PDB
ID: 6M0J). The ACE2 footprint was defined by residues being within 5Å of the receptor in 6M0J. The highly conserved NAT glycosylation motif is shown in in the top image, the SARS-CoV-1 and SARS-CoV-2 differences are shown in the bottom two images (identified specifically in the bottom right miage), and the differences within the S309 footprint are indicated in the bottom right image. Figure 48B shows alignments of the full RBD sequences of multiple sarbecoviruses. The ACE2 and S309 footprints also indicated; R509, not shown in Figure 48B, is part of the S309 antibody footprint (epitope). Dashed boxes indicate glycosylation sites and asterisks indicate the N343 glycosylation site. The three high frequency variant residues are indicated. Figure 48C shows conservation analysis of spike glycoprotein residues making contact with S309 across clades of sarbecoviruses. Residue coordinates for both SARS-CoV-2 and SARS-CoV-1 are shown. The NAT motif enabling glycosylation of N343 is indicated. The SARS-CoV-1 and SARS-CoV-2 sequence differences are indicated. Dashes indicate identity to SARS-CoV-2 consensus residues. Blanks indicate deletions. When multiple variants are found, they are listed in order of prevalence (high to low). For SARS-CoV-2, where more than 10,000 sequences were analyzed, variants found in a single sequence are not shown and variants found in only two sequences are parenthesized. For the 21 sequences of analyzed for Clade 3 “Other Bat CoVs,” at most the top three variants at each position are shown. The column labeled “n” indicates the number of sequences used for this analysis. The IC50 is the half maximal neutralizing concentration of S309 against SARS-CoV-1-MLV or SARS- CoV-2-MLV. Figures 49A and 49B show conservation of Spike protein residues. Figure 49A shows Spike protein variants supported by at least two sequences as spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. The RBD and other Spike protein domains are shown in the colors indicated. 171 variants (out of 11,839 total Spike protein sequences analyzed) are shown. Figure 49B shows the prevalence of variants in Spike glycoprotein by amino acid position. Each dot is a distinct variant. The location of the RBD is shown. Location within the RBD, RBM, or S309 epitope is indicated. Variants are labeled if their prevalence is greater than 1%
(D614G only) or if they are located within the RBD or S309 epitope. The location of conserved N343 is also indicated. Figures 50A and 50B show binding of various concentrations of monoclonal antibodies to immobilized SARS-CoV-2 DS Spike protein (green curve) or SARS- CoV-2 wild-type ("WT") Spike protein (black curve). The "DS" Spike protein comprises the following mutations and is stabilized in a prefusion "closed" conformation: S383C, R682S, R683G, R685G, D985C, K986P, V987P (numbering in reference to SEQ ID NO.:165). Figure 50A shows binding of antibody S309. Figure 50B shows binding of antibody S304. Calculated IC50 values are shown above each graph. Figure 51 shows binding of various concentrations of monoclonal antibody S309 to immobilized SARS-CoV-1 DS Spike protein or SARS-CoV-1 Spike protein. Calculated IC50 values are shown above the graph. Figure 52 shows conservation of the S309 N55Q (VH: SEQ ID NO.:113; VL: SEQ ID NO.:168) MLNS epitope in SARS-CoV-2, based on analysis of SARS-CoV-2 variants as of March 12, 2021 (GISAID (human spike protein seqs; <10% Xs; >1018 aa (80% full length)). Epitope residues in accordance with SEQ ID NO.:165 (surface glycoprotein [Wuhan seafood market pneumonia virus]; GenBank: QHD43416.1; January 23, 2020), are shown along the x-axis. The bars in the graph show (1) variant amino acid residues (substitution mutants) that have been identified at each of the epitope residue positions along the x-axis , (2) whether SARS-CoV-2 having the indicated amino acid variation(s) has a greater than 3-fold or less than 3-fold reduction in neutralization potency by antibody S309 N55Q MLNS, as compared to SARS-CoV-2 having the surface glycoprotein amino acid sequence shown in SEQ ID NO.:165, (3) the number of identified counts of variants (y-axis, left hand side of graph) at the indicated epitope residue position, and (4) conservation of the epitope residue shown on the x-axis, expressed as percentage of SARS-CoV-2 sequences comprising the epitope residue shown on the x-axis.
DETAILED DESCRIPTION The present disclosure provides, in part, antibodies and antigen-binding fragments that recognize a novel target region present in SARS CoV-2 surface glycoprotein receptor binding domain (RBD, also referred to as "SB"), which target region is highly conserved in other SARS coronaviruses, such as SARS-CoV (e.g., Urbani, CHUK-1, GZ02, HC_SZ_61_03, A031G, WIV1 SARS-like bat). The target region can include amino acid residues that are distinct from those RBD amino acid residues that interact with human ACE2. In some embodiments, antibodies and antigen-binding fragments can bind to and optionally neutralize a SARS-CoV-2 variant comprising one or more amino acid substitution mutation within the target region. In some embodiments, the target region comprises or consists of epitope amino acid residues contacted (e.g., as determined by X-ray crystallography, cryo-electron microscopy, or the like) by certain antibodies or antigen-binding fragments of the present disclosure, such as an antibody or antigen-binding fragment comprising a VH having the amino acid sequence set forth in SEQ ID NO.:105 and a VL having the amino acid sequence set forth in SEQ ID NO.:168. In some embodiments, the target region or epitope comprises any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, R509, C336, and K444, according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike") glycoprotein). In some embodiments, the target region or epitope comprises any one or more of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike") glycoprotein). In some embodiments, the target region or epitope comprises any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509,
according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike") glycoprotein). In certain embodiments, the target region further comprses D442 according to SEQ ID NO.:165 (Wuhan-Hu-1 CoV-2 surface ("S" or "spike") glycoprotein). In some embodiments, the target region or epitope comprises amino acid residue N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated. Also provided are antibodies and antigen-binding fragments that can bind to SARS-CoV-2 S protein RBD when the SARS-CoV-2 S protein RBD is in an open confirmation, in a closed conformation, or both. Also provided are immunogenic compositions that comprise a polypeptide or polypeptides that comprise(s) all or a portion of a target region or epitope. Also provided are polynucleotides that encode an antibody or antigen-binding fragment, and/or that encode a polypeptide or polypeptides that comprise(s) all or a portion of a target region or epitope. Also provided are vectors that comprise a polynucleotide, host cells that comprise a polynucleotide and/or a vector, compositions, and uses of the same to, for example, treat a SARS coronavirus infection in a subject and/or to induce an immune response against a SARS coronavirus infection in a subject. Prior to setting forth this disclosure in more detail, it may be helpful to an understanding thereof to provide definitions of certain terms to be used herein. Additional definitions are set forth throughout this disclosure. As used herein, " SARS-CoV-2 ", also referred to herein as "Wuhan coronavirus", or "Wuhan seafood market pneumonia virus", or "Wuhan CoV", or "novel CoV", or "nCoV", or "2019 nCoV", or "Wuhan nCoV" is a betacoronavirus believed to be of lineage B (sarbecovirus). SARS-CoV-2 was first identified in Wuhan, Hubei province, China, in late 2019 and spread within China and to other parts of the world by early 2020. Symptoms of SARS-CoV-2 include fever, dry cough, and dyspnea.
The genomic sequence of SARS-CoV-2 isolate Wuhan-Hu-1 is provided in SEQ ID NO.:163 (see also GenBank MN908947.3, January 23, 2020), and the amino acid translation of the genome is provided in SEQ ID NO.:164 (see also GenBank QHD43416.1, January 23, 2020). Like other coronaviruses (e.g., SARS CoV), SARS- CoV-2 comprises a "spike" or surface ("S") type I transmembrane glycoprotein containing a receptor binding domain (RBD). RBD is believed to mediate entry of the lineage B SARS coronavirus to respiratory epithelial cells by binding to the cell surface receptor angiotensin-converting enzyme 2 (ACE2). In particular, a receptor binding motif (RBM) in the virus RBD is believed to interact with ACE2. The amino acid sequence of the SARS-CoV-2 Wuhan-Hu-1 surface glycoprotein (S) is provided in SEQ ID NO.:165. The amino acid sequence of SARS-CoV-2 Wuhan-Hu-1 RBD is provided in SEQ ID NO.:166. SARS-CoV-2 Wuhan-Hu-1 S protein has approximately 73% amino acid sequence identity with SARS-CoV S protein. The amino acid sequence of SARS- CoV-2 Wuhan-Hu-1 RBM is provided in SEQ ID NO.:167. SARS-CoV-2 RBD has approximately 75% to 77% amino acid sequence similarity to SARS coronavirus RBD, and SARS-CoV-2 Wuhan Hu-1RBM has approximately 50% amino acid sequence similarity to SARS coronavirus RBM. Unless otherwise indicated herein, SARS-CoV-2 Wuhan Hu-1 refers to a virus comprising the amino acid sequence set forth in any one or more of SEQ ID NOs.:164, 165, and 166, optionally with the genomic sequence set forth in SEQ ID NO.:163. There have been a number of emerging SARS-CoV-2 variants. Some SARS- CoV-2 variants contain an N439K mutation, which has enhanced binding affinity to the human ACE2 receptor (Thomson, E.C., et al., The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. bioRxiv, 2020). Some SARS-CoV-2 variants contain an N501Y mutation, which is associated with increased transmissibility, including the lineages B.1.1.7 (also known as 20I/501Y.V1 and VOC 202012/01; (del69-70, del144, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H mutations)) and B.1.351 (also known as 20H/501Y.V2; L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and
A701V mutations), which were discovered in the United Kingdom and South Africa, respectively (Tegally, H., et al., Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv, 2020: p.2020.12.21.20248640; Leung, K., et al., Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. medRxiv, 2020: p.2020.12.20.20248581). B.1.351 also include two other mutations in the RBD domain of SARS-CoV2 spike protein, K417N and E484K (Tegally, H., et al., Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv, 2020: p.2020.12.21.20248640). Other SARS-CoV-2 variants include the Lineage B.1.1.28, which was first reported in Brazil; the Variant P.1, lineage B.1.1.28 (also known as 20J/501Y.V3), which was first reported in Japan; Variant L452R, which was first reported in California in the United States (Pan American Health Organization, Epidemiological update: Occurrence of variants of SARS-CoV-2 in the Americas, January 20, 2021, available at reliefweb.int/sites/reliefweb.int/files/resources/2021-jan-20-phe-epi-update-SARS- CoV-2.pdf). Other SARS-CoV-2 variants include a SARS CoV-2 of clade 19A; SARS CoV-2 of clade 19B; a SARS CoV-2 of clade 20A; a SARS CoV-2 of clade 20B; a SARS CoV-2 of clade 20C; a SARS CoV-2 of clade 20D; a SARS CoV-2 of clade 20E (EU1); a SARS CoV-2 of clade 20F; a SARS CoV-2 of clade 20G; and SARS CoV-2 B1.1.207; and other SARS CoV-2 lineages described in Rambaut, A., et al., A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 5, 1403–1407 (2020). SARS-CoV-2 variants also include: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K; N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q; E340D; L335S; L441F; L441I; L441R; L441V; T345S; T345I;
T345N; T333I; T333K; N334D; N334Y; N260S; N360A; N360Y; I332V; R509K; R509T; C336S. The foregoing SARS-CoV-2 variants, and the amino acid and nucleotide sequences thereof, are incorporated herein by reference. In the present description, any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated. Also, any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness, are to be understood to include any integer within the recited range, unless otherwise indicated. As used herein, the term "about" means ± 20% of the indicated range, value, or structure, unless otherwise indicated. It should be understood that the terms "a" and "an" as used herein refer to "one or more" of the enumerated components. The use of the alternative (e.g., "or") should be understood to mean either one, both, or any combination thereof of the alternatives. As used herein, the terms "include," "have," and "comprise" are used synonymously, which terms and variants thereof are intended to be construed as non-limiting. "Optional" or "optionally" means that the subsequently described element, component, event, or circumstance may or may not occur, and that the description includes instances in which the element, component, event, or circumstance occurs and instances in which they do not. In addition, it should be understood that the individual constructs, or groups of constructs, derived from the various combinations of the structures and subunits described herein, are disclosed by the present application to the same extent as if each construct or group of constructs was set forth individually. Thus, selection of particular structures or particular subunits is within the scope of the present disclosure. The term "consisting essentially of" is not equivalent to "comprising" and refers to the specified materials or steps of a claim, or to those that do not materially affect the basic characteristics of a claimed subject matter. For example, a protein domain, region, or module (e.g., a binding domain) or a protein "consists essentially of" a
particular amino acid sequence when the amino acid sequence of a domain, region, module, or protein includes extensions, deletions, mutations, or a combination thereof (e.g., amino acids at the amino- or carboxy-terminus or between domains) that, in combination, contribute to at most 20% (e.g., at most 15%, 10%, 8%, 6%, 5%, 4%, 3%, 2% or 1%) of the length of a domain, region, module, or protein and do not substantially affect (i.e., do not reduce the activity by more than 50%, such as no more than 40%, 30%, 25%, 20%, 15%, 10%, 5%, or 1%) the activity of the domain(s), region(s), module(s), or protein (e.g., the target binding affinity of a binding protein). As used herein, "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an α-carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid. As used herein, "mutation" refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively. A mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s). A "conservative substitution" refers to amino acid substitutions that do not significantly affect or alter binding characteristics of a particular protein. Generally, conservative substitutions are ones in which a substituted amino acid residue is replaced with an amino acid residue having a similar side chain. Conservative substitutions
include a substitution found in one of the following groups: Group 1: Alanine (Ala or A), Glycine (Gly or G), Serine (Ser or S), Threonine (Thr or T); Group 2: Aspartic acid (Asp or D), Glutamic acid (Glu or Z); Group 3: Asparagine (Asn or N), Glutamine (Gln or Q); Group 4: Arginine (Arg or R), Lysine (Lys or K), Histidine (His or H); Group 5: Isoleucine (Ile or I), Leucine (Leu or L), Methionine (Met or M), Valine (Val or V); and Group 6: Phenylalanine (Phe or F), Tyrosine (Tyr or Y), Tryptophan (Trp or W). Additionally or alternatively, amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing). For example, an aliphatic grouping may include, for purposes of substitution, Gly, Ala, Val, Leu, and Ile. Other conservative substitutions groups include: sulfur-containing: Met and Cysteine (Cys or C); acidic: Asp, Glu, Asn, and Gln; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gln; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, Ile, Val, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information can be found in Creighton (1984) Proteins, W.H. Freeman and Company. As used herein, "protein" or "polypeptide" refers to a polymer of amino acid residues. Proteins apply to naturally occurring amino acid polymers, as well as to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, and non-naturally occurring amino acid polymers. Variants of proteins, peptides, and polypeptides of this disclosure are also contemplated. In certain embodiments, variant proteins, peptides, and polypeptides comprise or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.9% identical to an amino acid sequence of a defined or reference amino acid sequence as described herein. "Nucleic acid molecule" or "polynucleotide" or "polynucleic acid" refers to a polymeric compound including covalently linked nucleotides, which can be made up of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g.,
morpholine ring). Purine bases include adenine, guanine, hypoxanthine, and xanthine, and pyrimidine bases include uracil, thymine, and cytosine. Nucleic acid molecules include polyribonucleic acid (RNA), which includes mRNA, microRNA, siRNA, viral genomic RNA, and synthetic RNA, and polydeoxyribonucleic acid (DNA), which includes cDNA, genomic DNA, and synthetic DNA, either of which may be single or double stranded. If single-stranded, the nucleic acid molecule may be the coding strand or non-coding (anti-sense) strand. A nucleic acid molecule encoding an amino acid sequence includes all nucleotide sequences that encode the same amino acid sequence. Some versions of the nucleotide sequences may also include intron(s) to the extent that the intron(s) would be removed through co- or post-transcriptional mechanisms. In other words, different nucleotide sequences may encode the same amino acid sequence as the result of the redundancy or degeneracy of the genetic code, or by splicing. Variants of nucleic acid molecules of this disclosure are also contemplated. Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and are preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical a nucleic acid molecule of a defined or reference polynucleotide as described herein, or that hybridize to a polynucleotide under stringent hybridization conditions of 0.015M sodium chloride, 0.0015M sodium citrate at about 65-68ºC or 0.015M sodium chloride, 0.0015M sodium citrate, and 50% formamide at about 42ºC. Nucleic acid molecule variants retain the capacity to encode a binding domain thereof having a functionality described herein, such as binding a target molecule. "Percent sequence identity" refers to a relationship between two or more sequences, as determined by comparing the sequences. Preferred methods to determine sequence identity are designed to give the best match between the sequences being compared. For example, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment). Further, non-homologous sequences may be disregarded for comparison purposes. The percent sequence identity referenced herein is calculated over the length of the reference sequence, unless indicated otherwise. Methods to determine sequence identity and similarity can be found in publicly
available computer programs. Sequence alignments and percent identity calculations may be performed using a BLAST program (e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX). The mathematical algorithm used in the BLAST programs can be found in Altschul et al., Nucleic Acids Res.25:3389-3402, 1997. Within the context of this disclosure, it will be understood that where sequence analysis software is used for analysis, the results of the analysis are based on the "default values" of the program referenced. "Default values" mean any set of values or parameters which originally load with the software when first initialized. The term "isolated" means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated. Such nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide. "Isolated" can, in some embodiments, also describe an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition that is outside of a human body. The term "gene" means the segment of DNA or RNA involved in producing a polypeptide chain; in certain contexts, it includes regions preceding and following the coding region (e.g., 5’ untranslated region (UTR) and 3’ UTR) as well as intervening sequences (introns) between individual coding segments (exons). A "functional variant" refers to a polypeptide or polynucleotide that is structurally similar or substantially structurally similar to a parent or reference compound of this disclosure, but differs slightly in composition (e.g., one base, atom or functional group is different, added, or removed), such that the polypeptide or encoded polypeptide is capable of performing at least one function of the parent polypeptide with at least 50% efficiency, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide. In other words, a functional variant of a polypeptide or encoded polypeptide of this
disclosure has "similar binding," "similar affinity" or "similar activity" when the functional variant displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide, such as an assay for measuring binding affinity (e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (KD) constant). As used herein, a "functional portion" or "functional fragment" refers to a polypeptide or polynucleotide that comprises only a domain, portion or fragment of a parent or reference compound, and the polypeptide or encoded polypeptide retains at least 50% activity associated with the domain, portion or fragment of the parent or reference compound, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide, or provides a biological benefit (e.g., effector function). A "functional portion" or "functional fragment" of a polypeptide or encoded polypeptide of this disclosure has "similar binding" or "similar activity" when the functional portion or fragment displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide (preferably no more than 20% or 10%, or no more than a log difference as compared to the parent or reference with regard to affinity). As used herein, the term "engineered," "recombinant," or "non-natural" refers to an organism, microorganism, cell, nucleic acid molecule, or vector that includes at least one genetic alteration or has been modified by introduction of an exogenous or heterologous nucleic acid molecule, wherein such alterations or modifications are introduced by genetic engineering (i.e., human intervention). Genetic alterations include, for example, modifications introducing expressible nucleic acid molecules encoding functional RNA, proteins, fusion proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of a cell’s genetic material. Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a polynucleotide, gene, or operon. As used herein, "heterologous" or "non-endogenous" or "exogenous" refers to any gene, protein, compound, nucleic acid molecule, or activity that is not native to a
host cell or a subject, or any gene, protein, compound, nucleic acid molecule, or activity native to a host cell or a subject that has been altered. Heterologous, non-endogenous, or exogenous includes genes, proteins, compounds, or nucleic acid molecules that have been mutated or otherwise altered such that the structure, activity, or both is different as between the native and altered genes, proteins, compounds, or nucleic acid molecules. In certain embodiments, heterologous, non-endogenous, or exogenous genes, proteins, or nucleic acid molecules (e.g., receptors, ligands, etc.) may not be endogenous to a host cell or a subject, but instead nucleic acids encoding such genes, proteins, or nucleic acid molecules may have been added to a host cell by conjugation, transformation, transfection, electroporation, or the like, wherein the added nucleic acid molecule may integrate into a host cell genome or can exist as extra-chromosomal genetic material (e.g., as a plasmid or other self-replicating vector). The term "homologous" or "homolog" refers to a gene, protein, compound, nucleic acid molecule, or activity found in or derived from a host cell, species, or strain. For example, a heterologous or exogenous polynucleotide or gene encoding a polypeptide may be homologous to a native polynucleotide or gene and encode a homologous polypeptide or activity, but the polynucleotide or polypeptide may have an altered structure, sequence, expression level, or any combination thereof. A non-endogenous polynucleotide or gene, as well as the encoded polypeptide or activity, may be from the same species, a different species, or a combination thereof. In certain embodiments, a nucleic acid molecule or portion thereof native to a host cell will be considered heterologous to the host cell if it has been altered or mutated, or a nucleic acid molecule native to a host cell may be considered heterologous if it has been altered with a heterologous expression control sequence or has been altered with an endogenous expression control sequence not normally associated with the nucleic acid molecule native to a host cell. In addition, the term "heterologous" can refer to a biological activity that is different, altered, or not endogenous to a host cell. As described herein, more than one heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a
single nucleic acid molecule encoding an antibody or antigen-binding fragment (or other polypeptide), or any combination thereof. As used herein, the term "endogenous" or "native" refers to a polynucleotide, gene, protein, compound, molecule, or activity that is normally present in a host cell or a subject. The term "expression", as used herein, refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene. The process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post- translational modification, or any combination thereof. An expressed nucleic acid molecule is typically operably linked to an expression control sequence (e.g., a promoter). The term "operably linked" refers to the association of two or more nucleic acid molecules on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter). "Unlinked" means that the associated genetic elements are not closely associated with one another and the function of one does not affect the other. As described herein, more than one heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a protein (e.g., a heavy chain of an antibody), or any combination thereof. When two or more heterologous nucleic acid molecules are introduced into a host cell, it is understood that the two or more heterologous nucleic acid molecules can be introduced as a single nucleic acid molecule (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof. The number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic
acid molecules or the number of protein activities, not the number of separate nucleic acid molecules introduced into a host cell. The term "construct" refers to any polynucleotide that contains a recombinant nucleic acid molecule (or, when the context clearly indicates, a fusion protein of the present disclosure). A (polynucleotide) construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome. A "vector" is a nucleic acid molecule that is capable of transporting another nucleic acid molecule. Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules. Vectors of the present disclosure also include transposon systems (e.g., Sleeping Beauty, see, e.g., Geurts et al., Mol. Ther.8:108, 2003: Mátés et al., Nat. Genet.41:753, 2009). Exemplary vectors are those capable of autonomous replication (episomal vector), capable of delivering a polynucleotide to a cell genome (e.g., viral vector), or capable of expressing nucleic acid molecules to which they are linked (expression vectors). As used herein, "expression vector" or "vector" refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host. Such control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation. The vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself or deliver the polynucleotide contained in the vector into the genome without the vector sequence. In the present specification, "plasmid," "expression plasmid," "virus," and "vector" are often used interchangeably. The term "introduced" in the context of inserting a nucleic acid molecule into a cell, means "transfection", "transformation," or "transduction" and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell
wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA). In certain embodiments, polynucleotides of the present disclosure may be operatively linked to certain elements of a vector. For example, polynucleotide sequences that are needed to effect the expression and processing of coding sequences to which they are ligated may be operatively linked. Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion. Expression control sequences may be operatively linked if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest. In certain embodiments, the vector comprises a plasmid vector or a viral vector (e.g., a lentiviral vector or a γ-retroviral vector). Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as ortho-myxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox, and canarypox). Other viruses include, for example, Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus. Examples of retroviruses include avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
"Retroviruses" are viruses having an RNA genome, which is reverse-transcribed into DNA using a reverse transcriptase enzyme, the reverse-transcribed DNA is then incorporated into the host cell genome. "Gammaretrovirus" refers to a genus of the retroviridae family. Examples of gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses. "Lentiviral vectors" include HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope, and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells. In certain embodiments, the viral vector can be a gammaretrovirus, e.g., Moloney murine leukemia virus (MLV)-derived vectors. In other embodiments, the viral vector can be a more complex retrovirus-derived vector, e.g., a lentivirus-derived vector. HIV-1-derived vectors belong to this category. Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus). Methods of using retroviral and lentiviral viral vectors and packaging cells for transducing mammalian host cells with viral particles containing transgenes are known in the art and have been previous described, for example, in: U.S. Patent 8,119,772; Walchli et al., PLoS One 6:327930, 2011; Zhao et al., J. Immunol.174:4415, 2005; Engels et al., Hum. Gene Ther.14:1155, 2003; Frecha et al., Mol. Ther.18:1748, 2010; and Verhoeyen et al., Methods Mol. Biol.506:97, 2009. Retroviral and lentiviral vector constructs and expression systems are also commercially available. Other viral vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and
adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defective HSV and attenuated HSV (Krisky et al., Gene Ther.5:1517, 1998). Other vectors that can be used with the compositions and methods of this disclosure include those derived from baculoviruses and α-viruses. (Jolly, D J.1999. Emerging Viral Vectors. pp 209-40 in Friedmann T. ed. The Development of Human Gene Therapy. New York: Cold Spring Harbor Lab), or plasmid vectors (such as sleeping beauty or other transposon vectors). When a viral vector genome comprises a plurality of polynucleotides to be expressed in a host cell as separate transcripts, the viral vector may also comprise additional sequences between the two (or more) transcripts allowing for bicistronic or multicistronic expression. Examples of such sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide, or any combination thereof. Plasmid vectors, including DNA-based antibody or antigen-binding fragment- encoding plasmid vectors for direct administration to a subject, are described further herein. As used herein, the term "host" refers to a cell or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest (e.g., an antibody of the present disclosure). A host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids or express proteins. The term also encompasses progeny of the host cell, whether genetically or phenotypically the same or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate the vector or other material by use of a viral vector, transformation via calcium phosphate precipitation, DEAE-dextran, electroporation, microinjection, or other methods. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual 2d ed. (Cold Spring Harbor Laboratory, 1989).
In the context of a SARS-CoV-2 infection, a "host" refers to a cell or a subject (e.g., a human) infected with SARS-CoV-2. "Antigen" or "Ag", as used herein, refers to an immunogenic molecule that provokes an immune response. This immune response may involve antibody production, activation of specific immunologically-competent cells, activation of complement, antibody dependent cytotoxicicity, or any combination thereof. An antigen (immunogenic molecule) may be, for example, a peptide, glycopeptide, polypeptide, glycopolypeptide, polynucleotide, polysaccharide, lipid, or the like. It is readily apparent that an antigen can be synthesized, produced recombinantly, or derived from a biological sample. Exemplary biological samples that can contain one or more antigens include tissue samples, stool samples, cells, biological fluids, or combinations thereof. Antigens can be produced by cells that have been modified or genetically engineered to express an antigen. Antigens can also be present in a SARS-CoV-2 (e.g., a surface glycoprotein or portion thereof), such as present in a virion, or expressed or presented on the surface of a cell infected by SARS-CoV-2. The term "epitope" or "antigenic epitope" includes any molecule, structure, amino acid sequence, or protein determinant that is recognized and specifically bound by a cognate binding molecule, such as an immunoglobulin, or other binding molecule, domain, or protein. Epitopic determinants generally contain chemically active surface groupings of molecules, such as amino acids or sugar side chains, and can have specific three-dimensional structural characteristics, as well as specific charge characteristics. Where an antigen is or comprises a peptide or protein, the epitope can be comprised of consecutive amino acids (e.g., a linear epitope), or can be comprised of amino acids from different parts or regions of the protein that are brought into proximity by protein folding (e.g., a discontinuous or conformational epitope), or non-contiguous amino acids that are in close proximity irrespective of protein folding. An epitope may also be referred to herein as a "footprint" of a cognate binding molecule (e.g., antibody or antigen-binding fragment) on the molecule (e.g., RBD or S protein) bound thereby. In some contexts, an antibody or antigen-binding fragment "contacts" an epitope structure (amino acid residue or glycan) as described herein when any atom of the
antibody or antigen-binding fragment, when bound to a SARS or SARS-CoV-2 RBD, is within 5.0 Å of the epitope structure (e.g., as determined by cryo-electron microscopy (e.g., single-particle cryo-EM) at 3.7 Å resolution or at 3.1 Å resolution; and/or as determined by x-ray crystallography, at 2.65 Å resolution such as described herein). In some contexts, an antibody or antigen-binding fragment contacts an epitope structure (amino acid residue or glycan) as described herein when any atom of the antibody or antigen-binding fragment, when bound to the RBD, is within 3.7 Å of the epitope structure. In some contexts, an antibody or antigen-binding fragment contacts an epitope structure (amino acid residue or glycan) as described herein when any atom of the antibody or antigen-binding fragment, when bound to a SARS or SARS-CoV-2 RBD, is within 3.1 Å of the epitope structure. In some embodiments, contacting comprises an electrostatic interaction between the antibody or antigen-binding fragment and the epitope structure. In some embodiments, contacting comprises a hydrophobic contact or hydrophobic interaction between the antibody or antigen-binding fragment and the epitope structure. SARS-CoV-2 Target Region The present disclosure provides, in part, a target region in SARS-CoV-2 RBD that is highly conserved across other SARS coronaviruses and current SARS-CoV-2 variants. The target region comprises an epitope that is specifically recognized and bound by an antibody or antigen-binding fragment thereof, and can include additional structures (e.g. amino acids, sugar side chains) that are in proximity to and/or are between epitope residues in three-dimensional space. Accordingly, antibodies and antigen-binding fragments that are capable of binding to a SARS coronavirus (e.g., SARS-CoV-2 or a variant thereof) in a target region are provided, as well as immunogenic polypeptides that comprise amino acid residues, sequences, and/or features (e.g., helix, beta-sheet) of a target region. As disclosed herein, RBD epitope of antibody S309 (VH: SEQ ID NO.:105; VL: SEQ ID NO.:168) was determined by cryo-electron microscopy (initially at 4.2 Å resolution of the Fab in complex with open-conformation RBD and 3.6 Å resolution of the Fab in complex with closed-conformation RBD; refined at 3.7 Å resolution of the
Fab in complex with open-conformation RBD and 3.1 Å resolution of the Fab in complex with closed-conformation RBD) and by x-ray crystal studies (2.65 Å resolution, with epitope features identified as all RBD amino acid residues within 5.0 Å of any atom of the Fab of antibody S309). The cryo-electron microscopy studies at the higher resolution identified the following amino acids (numbering as in SEQ ID NO.:165) as the epitope of antibody S309: T333; N334; L335; P337; G339; E340; V341; N343 (bearing a glycan that contains a core fucose); A344; T345; R346; N354; K356; R357; I358; S359; N360; C361; N440; L441; K444; R509. At the intial, lower resolution by cryo-EM (4.2 Å resolution of the Fab in complex with open-conformation RBD and 3.6 Å resolution of the Fab in complex with closed-conformation RBD), C336 and D442 were included in the epitope. The higher resolution data are preferred. The x-ray crystal studies identified the following amino acids as the epitope of antibody S309: T333; N334; L335; C336; P337; G339; E340; V341; N343 (bearing a glycan that contains a core fucose); A344; T345; R346; N354; K356; R357; I358; S359; N360; C361; N440; L441; R509. Briefly, a non-limiting example of procedures and parameters for performing cryo-electron microscopy using SARS-CoV-2 glycoprotein and an antibody or antigen- binding fragment comprises (1)-(4) below; see also Protein Data Bank codes 6WPS (Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment; DOI: 10.2210/pdb6WPS/pdb; EMDataResource: EMD-21864) and 6WPT (Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state); DOI: 10.2210/pdb6WPT/pdbEMDataResource: EMD-21865; Deposited: 2020-04- 27 Released: 2020-05-27): (1) Recombinant S-glycoprotein ectodomain and SB production: ● Producing SARS-CoV-22P S glycoprotein (GenBank: YP_009724390.1) ectodomain in 500-ml cultures of HEK293F cells grown in suspension using FreeStyle 293 expression medium (Life
technologies) at 37 °C in a humidified 8% CO2 incubator rotating at 130 r.p.m. ● Transfecting the culture using 293fectin (ThermoFisher Scientific) with cells grown to a density of 106 cells per ml and cultivated for 3 d. ● Collecting supernatant, and resuspending cells for another three days, yielding two collections. ● Purifying clarified supernatants using a 5-ml Cobalt affinity column (Takara). ● Concentrating purified protein and concentrating flash-frozen protein in a buffer containing 20 mM Tris pH 8.0 and 150 mM NaCl before cryo- EM analysis. (2) Cryo-EM sample preparation and data collection ● Mixing three microlitres of SARS-CoV-2 S glycoprotein at 1.6 mg/ml with 0.45 μl of antibody Fab (obtained by LysC fragmentation of antibody IgG) at 7.4 mg/ml for 1 min at room temperature before application onto a freshly glow-discharged 1.2/1.3 UltraFoil grid (300 mesh). ● Plunge freezing using a vitrobot MarkIV (ThermoFisher Scientific) using a blot force of 0 and 6.5 s blot time at 100% humidity and 25 °C. ● Acquiring data using Leginon software to control an FEI Titan Krios transmission electron microscope operated at 300 kV and equipped with a Gatan K2 Summit direct detector and Gatan Quantum GIF energy filter, operated in zero-loss mode with a slit width of 20 eV. ● Performing automated data collection using Leginon at a nominal magnification of 130,000× with a pixel size of 0.525 Å with tilt angles ranging between 20° and 50°. ● Adjusting the dose rate adjusted to 8 counts per pixel per s, and acquiring data (e.g., movies) in super-resolution mode fractionated in 50 frames of 200 ms.
● Collecting micrographs with a defocus range of between −1.0 and −3.0 μm. (3) Cryo-EM data processing ● Using Warp (see Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019) to align data (e.g. align movie frames), estimate the microscope contrast-transfer function parameters, pick particles, and perform extraction. ● Extracting particle images with a box size of 800 binned to 400, yielding a pixel size of 1.05 Å. ● For each dataset, performing two rounds of reference-free 2D classification using cryoSPARC (see Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290– 296 (2017)) to select well-defined particle images. ● Performing two rounds of 3D classification with 50 iterations each (angular sampling 7.5° for 25 iterations and 1.8° with local search for 25 iterations), using a closed SARS-CoV-2 S glycoprotein structure (see, e.g., Walls, A. C. et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281–292.e6 (2020)) as initial model, using Relion (see Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018)) without imposing symmetry to separate distinct SARS- CoV-2 S glycoprotein conformations. ● Performing three-dimensional refinements using non-uniform refinement along with per-particle defocus refinement in cryoSPARC. ● Subjecting particle images to Bayesian polishing (see Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019)) before performing another round of non-uniform refinement in
cryoSPARC, followed by per-particle defocus refinement and again non- uniform refinement. ● Resolutions can be based on the gold-standard Fourier shell correlation of 0.143 criterion and Fourier shell correlation curves, and may be corrected for the effects of e.g. soft masking by high-resolution noise substitution (see Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012)). (4) Cryo-EM model building and analysis ● Using UCSF Chimera (Goddard, T. D., Huang, C. C. & Ferrin, T. E. Visualizing density maps with UCSF Chimera. J. Struct. Biol.157, 281– 287 (2007)) and Coot (Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)) fit atomic models (e.g., for SARS-CoV-2, Protein Data Bank codes (PDB) 6VXX and PDB 6VYB) into the cryo-EM maps. ● Manually building the antibody or antigen-binding fagment using Coot. Hand-building N-linked glycans into the density where visible ● Refining and relaxing models using Rosetta (see Wang, R. Y. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, e17219 (2016)). ● Refining glycan using a Rosetta protocol, which uses physically realistic geometries based on prior knowledge of saccharide chemical properties (see Frenz, B. et al. Automatically fixing errors in glycoprotein structures with Rosetta. Structure 27, 134–139.e3 (2019)), optionally using both sharpened and unsharpened maps. ● Analyzing models using MolProbity (see Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)), EMringer (see Barad, B. A. et al. EMRinger: side chain-directed model and map validation for 3D cryo- electron microscopy. Nat. Methods 12, 943–946 (2015)), Phenix (see Liebschner, D. et al. Macromolecular structure determination using X-
rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019)) and privateer (Agirre, J. et al. Privateer: software for the conformational validation of carbohydrate structures. Nat. Struct. Mol. Biol.22, 833–834 (2015)) to validate stereochemistry of both the protein and glycan components. ● Generating figures using UCSF ChimeraX (see Goddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci.27, 14–25 (2018)). Briefly, a non-limiting example of performing X-ray crystal structure analysis is described in Piccoli et al., Cell.2020 Nov 12; 183(4): 1024–1042.e21 (See also Protein Database code (PDB) 7JX3 (Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology; DOI: 10.2210/pdb7JX3/pdb; Deposited: 2020-08-26 Released: 2020-10-14). This can include: obtaining crystals of the SARS-CoV-2 RBD-antibody Fab complex at 22 ºC by sitting drop vapor diffusion; mixing a total of 200 nL complex with 200 nL mother liquor solution containing 16.2% (w/v) PEG 4000, 0.09 M sodium citrate pH 6.0, 0.18 M ammonium acetate, 0.02 M potassium acetate, 0.01 M MES pH 6.0 and 1.5% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH); collecting data, e.g., at a synchrotron facility such as, for example, the Molecular Biology Consortium beamline 4.2.2 at the Advanced Light Source synchrotron facility in Berkeley, CA; processing two individual datasets from the same crystal processed with the XDS software package (Kabsch, 2010); merging processed datasets for a final dataset at 2.65 Å in space group C2; determining the RBD-antibody complex structure by molecular replacement using Phaser (McCoy et al., 2007) and X-ray structures of the RBD and Fabs as search models; optionally performing subsequent rounds of model building and refinement using Coot (Emsley et al., 2010), Refmac5 (Murshudov et al., 2011), and MOE (www.chemcomp.com), to arrive at a final model for the ternary complex; Using the RBD-antibody complex crystal, determining binding epitopes on the RBD by identifying all RBD residues within a 5.0 Å distance from any antibody atoms using the
Molecular Operating Environment (MOE) software package from the Chemical Computing Group (www.chemcomp.com) and manually confirming the results. As disclosed in further detail herein, the epitope is accessible when the RBD is when an open conformation and when the RBD is in a closed conformation. This epitope is highly conserved across SARS coronaviruses and SARS-CoV-2 variants. In some embodiments, a target region in RBD comprises a helix that comprises amino acid residues 337-344 of SEQ ID NO.:165, a 5-stranded β-sheet (residues 356- 361 of SEQ ID NO.:165, and another helix that spans residues 440-444 of SEQ ID NO.:165 and is located near the three-fold molecular axis of an S glycoprotein trimer. This RBD epitope and portions thereof, and, in some embodiments, target region sequence that is not within the epitope but that is adjacent, is proximal to, and/or is between epitope residues or portions of the epitope, provides immunogenic polypeptides that are described in further detail in the present disclosure. In certain embodiments, an antibody or antigen-binding fragment is capable of binding in a target region comprising, or an immunogenic polypeptide comprises, any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. In some embodiments, a target region and/or an immunogenic polypeptide further comprises D442 according to SEQ ID NO.:165. In certain embodiments, an antibody or antigen-binding fragment is capable of binding in a target region comprising, or an immunogenic polypeptide comprises, any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165). In some embodiments, a target region
and/or an immunogenic polypeptide further comprises D442 according to SEQ ID NO.:165. In certain embodiments, an antibody or antigen-binding fragment is capable of binding in a target region comprising, or an immunogenic polypeptide comprises, any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165). In some embodiments, a target region and/or an immunogenic polypeptide further comprises D442 according to SEQ ID NO.:165. Table 1. shows SEQ ID NO.:165 with S309 antibody epitope residues (as determined by cryo-EM (higher-resolution settings) or X-ray studies) in bold. Table 1. Wuhan-Hu-1 CoV-2 S Glycoprotein Amino Acid Sequence (SEQ ID NO.:165) showing S309 Antibody Epitope Residues (bold) and human ACE2 Contact Residues (underlined), as Determined by X-Ray or Cryo-EM Studies
Antibodies, Antigen-Binding Fragments, and Compositions In certain embodments, the present disclosure provides an antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD) when the RBD is in an open conformation and/or when the RBD is in a closed conformation. Structure and function of antibodies and antigen-binding fragments is decribed further herein. As described herein, SARS-CoV-2 surface glycoproteins has been observed in an "open" conformation, wherein the surface glycoprotein is present in a homotrimer of surface glycoprotein monomers and the RBD of one surface glycoprotein monomer of the trimer points upward relative to the other two RBDs, away from the C-terminal end of the surface glycoprotein, and also in a "closed" confrmation, where none of the three RBDs of a surface glycoprotein trimer point upward. See, for example, Figure 39A. As used herein, "open" in the context of a surface glycoprotein conformation includes a partially open conformation and a fully open conformation. In further embodiments, the antibody or antigen-binding fragment is capable of binding to the RBD when the RBD is in an open conformation, and is capable of binding to the RBD when the RBD is in a closed conformation. In some embodiments, the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein is comprised in a trimer thereof, wherein, optionally, each surface glycoprotein of the trimer can be simultaneously bound to a separate antibody or antigen-binding fragment. In some embodiments, one RBD of the trimer is in an open conformation. In some embodiments, two or three RBDs of the trimer are in a closed conformation. In some embodiments, the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein RBD of a SARS coronavirus and/or of another sarbecovirus that is not SARS-CoV-2. In some embodiments, the SARS coronavirus
comprises Urbani, CHUK-1, GZ02, HC_SZ_61_03, A031G, WIV1 SARS-like bat, or any combination thereof. Prefusion conformation of SARS-CoV-2 and other sarbecoviruses has been reported (see, e.g., Walls et al., "Structure, function and antigenicity of the SARS-CoV- 2 spike glycoprotein" doi.org/10.1101/2020.02.19.956581, published online on Februay 20, 2020). In some embodiments, the antibody or antigen-binding fragment is capable of binding to a SARS-CoV-2 surface glycoprotein when the SARS-CoV-2 surface glycoprotein is in a prefusion conformation. Also provided herein is an antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD), wherein the binding comprises contacting one or more amino acid residues of the RBD that are different from the amino acid residues of the RBD that contact a human ACE2 when the SARS CoV-2 surface glycoprotein is bound to the human ACE2, wherein, optionally, the antibody or antigen-binding fragment does not compete with human ACE2 for binding to the RBD. Competition for binding to human ACE2 can be determined using, for example, biolayer interferometry (BLI), wherein human ACE2 is loaded onto a BLI sensor followed by incubation of RBD alone or RBD plus antibody aor antigen-binding fragment. In some embodiments, binding of the antibody or antigen-binding fragment to the RBD does not comprise contacting an RBD amino acid residue that contacts a human ACE2 when the surface glycoprotein is bound to the human ACE2. In some embodiments, RBD residues that contact human ACE2 are V445, G446, G447, Y449, Y453, L455, F456, Y473, A475, G476, E484, F486, N487, Y489, Q493, G496, F497, Q498, T500, N501, G502, and Y505 of SEQ ID NO.:165. Also provided is an antibody or antigen-binding fragment that is capable of binding to a SARS-CoV-2 epitope that comprises or consists of any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and
R509, according to SEQ ID NO.:165. In some embodiments, binding comprises contacting any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. In some embodiments, binding comprises contacting amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. In some embodiments, the antibody or antigen-binding fragment is capable of binding to a SARS-CoV-2 epitope that comprises or consists of any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. In some embodiments, binding comprises contacting any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. In some embodiments, binding comprises contacting amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. In some embodiments, the antibody or antigen-binding fragment is capable of binding to a SARS-CoV-2 epitope that comprises or consists of any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165. In some embodiments, binding comprises contacting any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any
10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, or all 22) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165. In some embodiments, binding comprises contacting amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165. In certain embodiments, binding of the antibody or antigen-binding fragment to the RBD can comprise contacting amino acid N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated, such as, for example, comprising a fucose. In certain embodiments, an antibody or antigen-binding fragment thereof is provided that is capable of binding to a target region in RBD that comprises (i) a helix that comprises amino acid residues 337-344 of SEQ ID NO.:165, (ii) a 5-stranded β- sheet (residues 356-361 of SEQ ID NO.:165, and (iii) a helix that spans residues 440- 444 of SEQ ID NO.:165 and is located near the three-fold molecular axis of an S glycoprotein trimer. Also provided is an antibody, or an antigen-binding fragment thereof, that is capable of binding to an epitope in a sarbecovirus surface glycoprotein receptor binding domain (RBD), wherein the epitope comprises an asparagine amino acid residue that is or that corresponds to amino acid residue N343 of SEQ ID NO.:165, wherein the correspondence is determined according to sequence alignment of (i) a sarbecovirus surface glycoprotein or RBD amino acid sequence containing the asparagine amino acid residue with (ii) SEQ ID NO.:165. In certain embodiments, the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 is glycosylated. In some contexts, an asparagine amino acid residue that "corresponds to" N343 of SEQ ID NO.:165 refers to an asparagine amino acid of a coronavirus, betacoronavirus, sarbecovirus, or SARS-CoV amino acid sequence that is not SEQ ID NO.:165 or is not from Wuhan-Hu-1, wherein the asparagine amino acid has an equivalent position within the amino acid sequence as compared to the position of N343 in SEQ ID No.:365 – for
example, the coronavirus, betacoronavirus, sarbecovirus, or SARS-CoV amino acid sequence that is not SEQ ID NO.:165 may be shorter or longer than the amino acid sequence comprising SEQ ID NO.:165, such that position 343 in the coronavirus, betacoronavirus, sarbecovirus, or SARS-CoV amino acid sequence that is not SEQ ID NO.:165 or from Wuhan-Hu-1 may not be the equivalent residue to N343 in SEQ ID NO.:165; in such contexts, amino acid sequence alignment can be used to determine equivalent residue positions. As a non-limiting example, viral genomic sequences can be downloaded from GISAID using the ‘complete (>29,000 bp)’ and ‘low coverage exclusion’ filters. Non-human sequences can be included or excluded. S glycoprotein ORF can be localized by aligning a reference protein sequence (e.g. YP_009724390.1) to the genomic sequence of isolates with Exonerate v.2.4.0 (-m protein2dna --refine full --minintron 999999 --percent 30 --showalignment false --showvulgar false --ryo “>%ti\n%tcs). Coding nucleotide sequences can be translated in silico using seqkit v.0.12.0. Multiple sequence alignment can be performed using MAFFT v.7.455 (-- amino–bl 80 --nomemsave --reorder --add spike_aa_sequences.fasta --keeplength reference_aa_sequence.fasta). Variants can be determined by comparison of aligned sequences to the reference sequence using the R v3.6.3/Bioconductor v.3.10 package Biostrings v.2.54.0 (function: consensusMatrix). Additionally, S glycoprotein sequences can be extracted and translated from SARS-CoV genomes sourced from ViPR (example search criteria: SARS-related coronavirus, full-length genomes, human host, deposited before December 2019 to exclude SARS-CoV-2, n = 53). In some embodiments, the glycosylation of the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 comprises a fucose. In some embodments, the asparagine amino acid residue (N) that is or that corresponds to N343 of SEQ ID NO.:165 is comprised in an amino acid sequence N-X- T, X being any amino acid except for P, and preferably being A. In some embodiments, the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence NITNCLPFGEVFNATR (SEQ ID NO.:234), or a variant thereof having one, two,
three, four or five amino acid substitutions, provided that the sequence N-X-T is present, X being any amino acid except for P, and preferably being A. In some embodiments, the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence NITNCLPFGEVFNATRFASVYAWNRKRISNCV (SEQ ID NO.:235), or is comprised in a variant sequence of SEQ ID NO.:235 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions relative to SEQ ID NO.:235, provided that the amino acid sequence N-X-T is present, X being any amino acid except for P, and preferably being A, wherein optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:235 independently comprises a conservative substitution or a non-conservative substitution. In some embodiments, the antibody or antigen-binding fragment is capable of binding to, and optionally is capable of neutralizing an infection (e.g., in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human) by, a SARS-CoV-2 that comprises any one or more of the following mutations relative to SEQ ID NO.:165: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. In some embodiments, the antibody or antigen-binding fragment is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2 that comprises any one or more of the following mutations in RBD relative to SEQ ID NO.:165: N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q; E340D; L335S; L441F; L441I; L441R; L441V; T345S; T345I; T345N; T333I; T333K; N334D; N334Y; N260S; N360A; N360Y; I332V; R509K; R509T; C336S. In some embodiments, the antibody or antigen-binding fragment is capable of neutralizing the SARS-CoV-2 infection with a potency that is less than 3-fold reduced as compared to the potency with which the antibody or antigen-binding fragment
neutralizes infection by a SARS-CoV-2 that comprises the amino acid sequence of SEQ ID NO.:165. An exemplary antibody or antigen-binding fragment according to the presently disclosed embodiments comprises the VH amino acid sequence of SEQ ID NO.:105 and the VL amino acid sequence of SEQ ID NO.:168 (e.g., antibody S309). Engineered variants of S309 that bind to SARS-CoV-2 (e.g., by SPR and/or FACS) include those having the VH amino acid sequence set forth in SEQ ID NO.:113, SEQ ID NO.:129, SEQ ID NO.:119, or SEQ ID NO.:172, and the VL amino acid sequence set forth in SEQ ID NO.:168. Terms understood by those in the art of antibody technology are each given the meaning acquired in the art, unless expressly defined differently herein. For example, the term "antibody" refers to an intact antibody comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as any antigen-binding portion or fragment of an intact antibody that has or retains the ability to bind to the antigen target molecule recognized by the intact antibody, such as an scFv, Fab, or Fab'2 fragment. Thus, the term "antibody" herein is used in the broadest sense and includes polyclonal and monoclonal antibodies, including intact antibodies and functional (antigen-binding) antibody fragments thereof, including fragment antigen binding (Fab) fragments, F(ab')2 fragments, Fab' fragments, Fv fragments, recombinant IgG (rIgG) fragments, single chain antibody fragments, including single chain variable fragments (scFv), and single domain antibodies (e.g., sdAb, sdFv, nanobody) fragments. The term encompasses genetically engineered and/or otherwise modified forms of immunoglobulins, such as intrabodies, peptibodies, chimeric antibodies, fully human antibodies, humanized antibodies, and heteroconjugate antibodies, multispecific, e.g., bispecific antibodies, diabodies, triabodies, tetrabodies, tandem di-scFv, and tandem tri-scFv. Unless otherwise stated, the term "antibody" should be understood to encompass functional antibody fragments thereof. The term also encompasses intact or full-length antibodies, including antibodies of any class or sub-class, including IgG and sub-classes thereof (IgG1, IgG2, IgG3, IgG4), IgM, IgE, IgA, and IgD.
The terms "VL" or "VL" and "VH" or "VH" refer to the variable binding region from an antibody light chain and an antibody heavy chain, respectively. In certain embodiments, a VL is a kappa (κ) class (also "VK" herein). In certain embodiments, a VL is a lambda (λ) class. The variable binding regions comprise discrete, well-defined sub-regions known as "complementarity determining regions" (CDRs) and "framework regions" (FRs). The terms "complementarity determining region," and "CDR," are synonymous with "hypervariable region" or "HVR," and refer to sequences of amino acids within antibody variable regions, which, in general, together confer the antigen specificity and/or binding affinity of the antibody, wherein consecutive CDRs (i.e., CDR1 and CDR2, CDR2 and CDR3) are separated from one another in primary amino acid sequence by a framework region. There are three CDRs in each variable region (HCDR1, HCDR2, HCDR3; LCDR1, LCDR2, LCDR3; also referred to as CDRHs and CDRLs, respectively). In certain embodiments, an antibody VH comprises four FRs and three CDRs as follows: FR1-HCDR1-FR2-HCDR2-FR3-HCDR3-FR4; and an antibody VL comprises four FRs and three CDRs as follows: FR1-LCDR1-FR2- LCDR2-FR3-LCDR3-FR4. In general, the VH and the VL together form the antigen- binding site through their respective CDRs. As used herein, a "variant" of a CDR refers to a functional variant of a CDR sequence having up to 1-3 amino acid substitutions (e.g., conservative or non- conservative substitutions), deletions, or combinations thereof. Numbering of CDR and framework regions may be according to any known method or scheme, such as the Kabat, Chothia, EU, IMGT, and AHo numbering schemes (see, e.g., Kabat et al., "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5th ed.; Chothia and Lesk, J. Mol. Biol.196:901-917 (1987)); Lefranc et al., Dev. Comp. Immunol.27:55, 2003; Honegger and Plückthun, J. Mol. Bio.309:657-670 (2001)); or the antibody numbering method developed by the Chemical Computing Group (CCG); e.g., using Molecular Operating Environment (MOE) software (www.chemcomp.com). Equivalent residue positions can be annotated and for different
molecules to be compared using Antigen receptor Numbering And Receptor Classification (ANARCI) software tool (2016, Bioinformatics 15:298-300). The term "CL" refers to an "immunoglobulin light chain constant region" or a "light chain constant region," i.e., a constant region from an antibody light chain. The term "CH" refers to an "immunoglobulin heavy chain constant region" or a "heavy chain constant region," which is further divisible, depending on the antibody isotype into CH1, CH2, and CH3 (IgA, IgD, IgG), or CH1, CH2, CH3, and CH4 domains (IgE, IgM). The Fc region of an antibody heavy chain is described further herein. In any of the presently disclosed embodiments, an antibody or antigen-binding fragment of the present disclosure comprises any one or more of CL, a CH1, a CH2, and a CH3. In certain embodiments, a CL comprises an amino acid sequence having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 975, 98%, 99%, or 100% identity to the amino acid sequence of SEQ ID NO.:174 or SEQ ID NO.: 193. In certain embodiments, a CH1-CH2-CH3 comprises an amino acid sequence having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 975, 98%, 99%, or 100% identity to the amino acid sequence of SEQ ID NO.:173 or SEQ ID NO.:175. A "Fab" (fragment antigen binding) is the part of an antibody that binds to antigens and includes the variable region and CH1 of the heavy chain linked to the light chain via an inter-chain disulfide bond. Each Fab fragment is monovalent with respect to antigen binding, i.e., it has a single antigen-binding site. Pepsin treatment of an antibody yields a single large F(ab')2 fragment that roughly corresponds to two disulfide linked Fab fragments having divalent antigen-binding activity and is still capable of cross-linking antigen. Both the Fab and F(ab’)2 are examples of "antigen- binding fragments." Fab' fragments differ from Fab fragments by having additional few residues at the carboxy terminus of the CH1 domain including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
Fab fragments may be joined, e.g., by a peptide linker, to form a single chain Fab, also referred to herein as "scFab." In these embodiments, an inter-chain disulfide bond that is present in a native Fab may not be present, and the linker serves in full or in part to link or connect the Fab fragments in a single polypeptide chain. A heavy chain- derived Fab fragment (e.g., comprising, consisting of, or consisting essentially of VH + CH1, or "Fd") and a light chain-derived Fab fragment (e.g., comprising, consisting of, or consisting essentially of VL + CL) may be linked in any arrangement to form a scFab. For example, a scFab may be arranged, in N-terminal to C-terminal direction, according to (heavy chain Fab fragment – linker – light chain Fab fragment) or (light chain Fab fragment – linker – heavy chain Fab fragment). Peptide linkers and exemplary linker sequences for use in scFabs are discussed in further detail herein. A scFab can be comprise any combination of VH and VL sequences or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein. "Fv" is a small antibody fragment that contains a complete antigen-recognition and antigen-binding site. This fragment generally consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although typically at a lower affinity than the entire binding site. "Single-chain Fv" also abbreviated as "sFv" or "scFv", are antibody fragments that comprise the VH and VL antibody domains connected into a single polypeptide chain. In some embodiments, the scFv polypeptide comprises a polypeptide linker disposed between and linking the VH and VL domains that enables the scFv to retain or form the desired structure for antigen binding. Such a peptide linker can be incorporated into a fusion polypeptide using standard techniques well known in the art. For a review of scFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol.113, Rosenburg and Moore eds., Springer-Verlag, New York, pp.269-315 (1994); Borrebaeck 1995, infra. In certain embodiments, the antibody or antigen-binding fragment comprises a scFv comprising a VH domain, a VL domain, and a peptide linker
linking the VH domain to the VL domain. In particular embodiments, a scFv comprises a VH domain linked to a VL domain by a peptide linker, which can be in a VH-linker- VL orientation or in a VL-linker-VH orientation. Any scFv of the present disclosure may be engineered so that the C-terminal end of the VL domain is linked by a short peptide sequence to the N-terminal end of the VH domain, or vice versa (i.e., (N)VL(C)-linker-(N)VH(C) or (N)VH(C)-linker-(N)VL(C). Alternatively, in some embodiments, a linker may be linked to an N-terminal portion or end of the VH domain, the VL domain, or both. Peptide linker sequences may be chosen, for example, based on: (1) their ability to adopt a flexible extended conformation; (2) their inability or lack of ability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides and/or on a target molecule; and/or (3) the lack or relative lack of hydrophobic or charged residues that might react with the polypeptides and/or target molecule. Other considerations regarding linker design (e.g., length) can include the conformation or range of conformations in which the VH and VL can form a functional antigen-binding site. In certain embodiments, peptide linker sequences contain, for example, Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala, may also be included in a linker sequence. Other amino acid sequences which may be usefully employed as linker include those disclosed in Maratea et al., Gene 40:3946 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:82588262 (1986); U.S. Pat. No. 4,935,233, and U.S. Pat. No.4,751,180. Other illustrative and non-limiting examples of linkers may include, for example, Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys- Val-Asp (SEQ ID NO: 215) (Chaudhary et al., Proc. Natl. Acad. Sci. USA 87:1066- 1070 (1990)) and Lys-Glu-Ser-Gly-Ser-Val-Ser-Ser-Glu-Gln-Leu-Ala-Gln-Phe-Arg- Ser-Leu-Asp (SEQ ID NO: 216) (Bird et al., Science 242:423-426 (1988)) and the pentamer Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 217) when present in a single iteration or repeated 1 to 5 or more times, or more; see, e.g., SEQ ID NO: 213. Any suitable linker may be used, and in general can be about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 1523, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100 amino acids in length, or less than about 200 amino acids in length, and will preferably
comprise a flexible structure (can provide flexibility and room for conformational movement between two regions, domains, motifs, fragments, or modules connected by the linker), and will preferably be biologically inert and/or have a low risk of immunogenicity in a human. Exemplary linkers include those comprising or consisting of the amino acid sequence set forth in any one or more of SEQ ID NOs: 206-217. In certain embodiments, the linker comprises or consists of an amino acid sequence having at least 75% (i.e., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in any one of SEQ ID NOs: 206-217. In some embodiments, linker sequences are not required; for example, when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference. During antibody development, DNA in the germline variable (V), joining (J), and diversity (D) gene loci may be rearranged and insertions and/or deletions of nucleotides in the coding sequence may occur. Somatic mutations may be encoded by the resultant sequence, and can be identified by reference to a corresponding known germline sequence. In some contexts, somatic mutations that are not critical to a desired property of the antibody (e.g., binding to a Wuhan coronavirus antigen), or that confer an undesirable property upon the antibody (e.g., an increased risk of immunogenicity in a subject administered the antibody), or both, may be replaced by the corresponding germline-encoded amino acid, or by a different amino acid, so that a desirable property of the antibody is improved or maintained and the undesirable property of the antibody is reduced or abrogated. Thus, in some embodiments, the antibody or antigen-binding fragment of the present disclosure comprises at least one more germline-encoded amino acid in a variable region as compared to a parent antibody or antigen-binding fragment, provided that the parent antibody or antigen binding fragment comprises one or more somatic mutations. Variable region and CDR amino acid sequences of certain antibodies that bind to SARS-CoV-2 are provided in Table 2 herein. An exemplary antibody that binds to an epitope as described herein comprises the VH amino acid sequence set forth in SEQ ID NO.:105 and the VL amino
acid sequence set forth in SEQ ID NO.:168. Engineered variants of S309 that bind to SARS-CoV-2 (e.g., by SPR and/or FACS) include those having the VH amino acid sequence set forth in SEQ ID NO.:113, SEQ ID NO.:129, SEQ ID NO.:119, or SEQ ID NO.:172, and the VL amino acid sequence set forth in SEQ ID NO.:168. In certain embodiments, an antibody or antigen-binding fragment comprises an amino acid modification (e.g., a substitution mutation) to remove an undesired risk of oxidation, deamidation, and/or isomerization. Also provided herein are variant antibodies that comprise one or more amino acid alterations in a variable region (e.g., VH, VL, framework or CDR) as compared to a presently disclosed ("parent") antibody, wherein the variant antibody is capable of binding to a Wuhan coronavirus antigen. In certain embodiments, an antibody or antigen-binding fragment of the present disclosure is monospecific (e.g., binds to a single epitope) or is multispecific (e.g., binds to multiple epitopes and/or target molecules). Antibodies and antigen binding fragments may be constructed in various formats. Exemplary antibody formats disclosed in Spiess et al., Mol. Immunol.67(2):95 (2015), and in Brinkmann and Kontermann, mAbs 9(2):182-212 (2017), which formats and methods of making the same are incorporated herein by reference and include, for example, Bispecific T cell Engagers (BiTEs), DARTs, Knobs-Into-Holes (KIH) assemblies, scFv-CH3-KIH assemblies, KIH Common Light-Chain antibodies, TandAbs, Triple Bodies, TriBi Minibodies, Fab-scFv, scFv-CH-CL-scFv, F(ab')2-scFv2, tetravalent HCabs, Intrabodies, CrossMabs, Dual Action Fabs (DAFs) (two-in-one or four-in-one), DutaMabs, DT-IgG, Charge Pairs, Fab-arm Exchange, SEEDbodies, Triomabs, LUZ-Y assemblies, Fcabs, κλ-bodies, orthogonal Fabs, DVD-Igs (e.g., US Patent No. 8,258,268, which formats are incorporated herein by reference in their entirety), IgG(H)-scFv, scFv-(H)IgG, IgG(L)-scFv, scFv-(L)IgG, IgG(L,H)-Fv, IgG(H)-V, V(H)- IgG, IgG(L)-V, V(L)-IgG, KIH IgG-scFab, 2scFv-IgG, IgG-2scFv, scFv4-Ig, Zybody, and DVI-IgG (four-in-one), as well as so-called FIT-Ig (e.g., PCT Publication No. WO 2015/103072, which formats are incorporated herein by reference in their entirety), so- called WuxiBody formats (e.g., PCT Publication No. WO 2019/057122, which formats
are incorporated herein by reference in their entirety), and so-called In-Elbow-Insert Ig formats (IEI-Ig; e.g., PCT Publication Nos. WO 2019/024979 and WO 2019/025391, which formats are incorporated herein by reference in their entirety). In certain embodiments, the antibody or antigen-binding fragment comprises two or more of VH domains, two or more VL domains, or both (i.e., two or more VH domains and two or more VL domains). In particular embodiments, an antigen-binding fragment comprises the format (N-terminal to C-terminal direction) VH-linker-VL- linker-VH-linker-VL, wherein the two VH sequences can be the same or different and the two VL sequences can be the same or different. Such linked scFvs can include any combination of VH and VL domains arranged to bind to a given target, and in formats comprising two or more VH and/or two or more VL, one, two, or more different eptiopes or antigens may be bound. It will be appreciated that formats incorporating multiple antigen-binding domains may include VH and/or VL sequences in any combination or orientation. For example, the antigen-binding fragment can comprise the format VL-linker-VH-linker-VL-linker-VH, VH-linker-VL-linker-VL-linker-VH, or VL-linker-VH-linker-VH-linker-VL. A bispecific or multispecific antibody or antigen-binding fragment may, in some embodiments, comprise one, two, or more antigen-binding domains (e.g., a VH and a VL) of the instant disclosure. Two or more binding domains may be present that bind to the same or a different SARS-CoV-2 epitope, and a bispecific or multispecific antibody or antigen-binding fragment as provided herein can, in some embodiments, comprise a further SARS-CoV-2 binding domain, and/or can comprise a binding domain that binds to a different antigen or pathogen altogether. In any of the presently disclosed embodiments, the antibody or antigen-binding fragment can be multispecific; e.g., bispecific, trispecific, or the like. In certain embodiments, the antibody or antigen-binding fragment comprises a Fc polypeptide, or a fragment thereof. The "Fc" fragment or Fc polypeptide comprises the carboxy-terminal portions (i.e., the CH2 and CH3 domains of IgG) of both antibody H chains held together by disulfides. Antibody “effector functions” refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino
acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation. As discussed herein, modifications (e.g., amino acid substitutions) may be made to an Fc domain in order to modify (e.g., improve, reduce, or ablate) one or more functionality of an Fc-containing polypeptide (e.g., an antibody of the present disclosure). Such functions include, for example, Fc receptor (FcR) binding, antibody half-life modulation (e.g., by binding to FcRn), ADCC function, protein A binding, protein G binding, and complement binding. Amino acid modifications that modify (e.g., improve, reduce, or ablate) Fc functionalities include, for example, the T250Q/M428L, M252Y/S254T/T256E, H433K/N434F, M428L/N434S, E233P/L234V/L235A/G236 + A327G/A330S/P331S, E333A, S239D/A330L/I332E, P257I/Q311, K326W/E333S, S239D/I332E/G236A, N297Q, K322A, S228P, L235E + E318A/K320A/K322A, L234A/L235A (also referred to herein as “LALA”), and L234A/L235A/P329G mutations, which mutations are summarized and annotated in "Engineered Fc Regions", published by InvivoGen (2011) and available online at invivogen.com/PDF/review/review-Engineered-Fc-Regions- invivogen.pdf?utm_source=review&utm_medium=pdf&utm_ campaign=review&utm_content=Engineered-Fc-Regions, and are incorporated herein by reference. For example, to activate the complement cascade, the C1q protein complex can bind to at least two molecules of IgG1 or one molecule of IgM when the immunoglobulin molecule(s) is attached to the antigenic target (Ward, E. S., and Ghetie, V., Ther. Immunol.2 (1995) 77-94). Burton, D. R., described (Mol. Immunol. 22 (1985) 161-206) that the heavy chain region comprising amino acid residues 318 to 337 is involved in complement fixation. Duncan, A. R., and Winter, G. (Nature 332 (1988) 738-740), using site directed mutagenesis, reported that Glu318, Lys320 and Lys322 form the binding site to C1q. The role of Glu318, Lys320 and Lys 322 residues
in the binding of C1q was confirmed by the ability of a short synthetic peptide containing these residues to inhibit complement mediated lysis. For example, FcR binding can be mediated by the interaction of the Fc moiety (of an antibody) with Fc receptors (FcRs), which are specialized cell surface receptors on cells including hematopoietic cells. Fc receptors belong to the immunoglobulin superfamily, and shown to mediate both the removal of antibody-coated pathogens by phagocytosis of immune complexes, and the lysis of erythrocytes and various other cellular targets (e.g. tumor cells) coated with the corresponding antibody, via antibody dependent cell mediated cytotoxicity (ADCC; Van de Winkel, J. G., and Anderson, C. L., J. Leukoc. Biol.49 (1991) 511-524). FcRs are defined by their specificity for immunoglobulin classes; Fc receptors for IgG antibodies are referred to as FcγR, for IgE as FcεR, for IgA as FcαR and so on and neonatal Fc receptors are referred to as FcRn. Fc receptor binding is described for example in Ravetch, J. V., and Kinet, J. P., Annu. Rev. Immunol.9 (1991) 457-492; Capel, P. J., et al., Immunomethods 4 (1994) 25-34; de Haas, M., et al., J Lab. Clin. Med.126 (1995) 330-341; and Gessner, J. E., et al., Ann. Hematol.76 (1998) 231-248. Cross-linking of receptors by the Fc domain of native IgG antibodies (FcγR) triggers a wide variety of effector functions including phagocytosis, antibody-dependent cellular cytotoxicity, and release of inflammatory mediators, as well as immune complex clearance and regulation of antibody production. Fc moieties providing cross- linking of receptors (e.g., FcγR) are contemplated herein. In humans, three classes of FcγR have been characterized to-date, which are: (i) FcγRI (CD64), which binds monomeric IgG with high affinity and is expressed on macrophages, monocytes, neutrophils and eosinophils; (ii) FcγRII (CD32), which binds complexed IgG with medium to low affinity, is widely expressed, in particular on leukocytes, is believed to be a central player in antibody-mediated immunity, and which can be divided into FcγRIIA, FcγRIIB and FcγRIIC, which perform different functions in the immune system, but bind with similar low affinity to the IgG-Fc, and the ectodomains of these receptors are highly homologuous; and (iii) FcγRIII (CD16), which binds IgG with medium to low affinity and has been found in two forms: FcγRIIIA, which has been
found on NK cells, macrophages, eosinophils, and some monocytes and T cells, and is believed to mediate ADCC; and FcγRIIIB, which is highly expressed on neutrophils. FcγRIIA is found on many cells involved in killing (e.g. macrophages, monocytes, neutrophils) and seems able to activate the killing process. FcγRIIB seems to play a role in inhibitory processes and is found on B-cells, macrophages and on mast cells and eosinophils. Importantly, it has been shown that 75% of all FcγRIIB is found in the liver (Ganesan, L. P. et al., 2012: “FcγRIIb on liver sinusoidal endothelium clears small immune complexes,” Journal of Immunology 189: 4981–4988). FcγRIIB is abundantly expressed on Liver Sinusoidal Endothelium, called LSEC, and in Kupffer cells in the liver and LSEC are the major site of small immune complexes clearance (Ganesan, L. P. et al., 2012: FcγRIIb on liver sinusoidal endothelium clears small immune complexes. Journal of Immunology 189: 4981–4988). In some embodiments, the antibodies disclosed herein and the antigen-binding fragments thereof comprise an Fc polypeptide or fragment thereof for binding to FcγRIIb, in particular an Fc region, such as, for example IgG-type antibodies. Moreover, it is possible to engineer the Fc moiety to enhance FcγRIIB binding by introducing the mutations S267E and L328F as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926–3933. Thereby, the clearance of immune complexes can be enhanced (Chu, S., et al., 2014: Accelerated Clearance of IgE In Chimpanzees Is Mediated By Xmab7195, An Fc-Engineered Antibody With Enhanced Affinity For Inhibitory Receptor FcγRIIb. Am J Respir Crit, American Thoracic Society International Conference Abstracts). In some embodiments, the antibodies of the present disclosure, or the antigen binding fragments thereof, comprise an engineered Fc moiety with the mutations S267E and L328F, in particular as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926–3933.
On B cells, FcγRIIB may function to suppress further immunoglobulin production and isotype switching to, for example, the IgE class. On macrophages, FcγRIIB is thought to inhibit phagocytosis as mediated through FcγRIIA. On eosinophils and mast cells, the B form may help to suppress activation of these cells through IgE binding to its separate receptor. Regarding FcγRI binding, modification in native IgG of at least one of E233- G236, P238, D265, N297, A327 and P329 reduces binding to FcγRI. IgG2 residues at positions 233-236, substituted into corresponding positions IgG1 and IgG4, reduces binding of IgG1 and IgG4 to FcγRI by 103-fold and eliminated the human monocyte response to antibody-sensitized red blood cells (Armour, K. L., et al. Eur. J. Immunol. 29 (1999) 2613-2624). Regarding FcγRII binding, reduced binding for FcγRIIA is found, e.g., for IgG mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, R292 and K414. Two allelic forms of human FcγRIIA are the "H131" variant, which binds to IgG1 Fc with high affinity, and the "R131" variant, which binds to IgG1 Fc with low affinity. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009). Regarding FcγRIII binding, reduced binding to FcγRIIIA is found, e.g., for mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, S239, E269, E293, Y296, V303, A327, K338 and D376. Mapping of the binding sites on human IgG1 for Fc receptors, the above-mentioned mutation sites, and methods for measuring binding to FcγRI and FcγRIIA, are described in Shields, R. L., et al., J. Biol. Chem.276 (2001) 6591-6604. Two allelic forms of human FcγRIIIA are the "F158" variant, which binds to IgG1 Fc with low affinity, and the "V158" variant, which binds to IgG1 Fc with high affinity. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009). Regarding binding to FcγRII, two regions of native IgG Fc appear to be involved in interactions between FcγRIIs and IgGs, namely (i) the lower hinge site of IgG Fc, in particular amino acid residues L, L, G, G (234 – 237, EU numbering), and (ii) the adjacent region of the CH2 domain of IgG Fc, in particular a loop and strands in
the upper CH2 domain adjacent to the lower hinge region, e.g. in a region of P331 (Wines, B.D., et al., J. Immunol.2000; 164: 5313 – 5318). Moreover, FcγRI appears to bind to the same site on IgG Fc, whereas FcRn and Protein A bind to a different site on IgG Fc, which appears to be at the CH2-CH3 interface (Wines, B.D., et al., J. Immunol. 2000; 164: 5313 – 5318). Also contemplated are mutations that increase binding affinity of an Fc polypeptide or fragment thereof of the present disclosure to a (i.e., one or more) Fcγ receptor (e.g., as compared to a reference Fc polypeptide or fragment thereof or containing the same that does not comprise the mutation(s)). See, e.g., Delillo and Ravetch, Cell 161(5):1035-1045 (2015) and Ahmed et al., J. Struc. Biol.194(1):78 (2016), the Fc mutations and techniques of which are incorporated herein by reference. In any of the herein disclosed embodiments, an antibody or antigen-binding fragment can comprise a Fc polypeptide or fragment thereof comprising a mutation selected from G236A; S239D; A330L; and I332E; or a combination comprising any two or more of the same; e.g., S239D/I332E; S239D/A330L/I332E; G236A/S239D/I332E; G236A/A330L/I332E (also referred to herein as "GAALIE"); or G236A/S239D/A330L/I332E. In some embodiments, the Fc polypeptide or fragment thereof does not comprise S239D. In certain embodiments, the Fc polypeptide or fragment thereof may comprise or consist of at least a portion of an Fc polypeptide or fragment thereof that is involved in binding to FcRn binding. In certain embodiments, the Fc polypeptide or fragment thereof comprises one or more amino acid modifications that improve binding affinity for (e.g., enhance binding to) FcRn (e.g., at a pH of about 6.0) and, in some embodiments, thereby extend in vivo half-life of a molecule comprising the Fc polypeptide or fragment thereof (e.g., as compared to a reference Fc polypeptide or fragment thereof or antibody that is otherwise the same but does not comprise the modification(s)). In certain embodiments, the Fc polypeptide or fragment thereof comprises or is derived from a IgG Fc and a half-life-extending mutation comprises any one or more of: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I Q311I; D376V; T307A; E380A (EU numbering). In certain
embodiments, a half-life-extending mutation comprises M428L/N434S (also referred to herein as "MLNS"). In certain embodiments, a half-life-extending mutation comprises M252Y/S254T/T256E. In certain embodiments, a half-life-extending mutation comprises T250Q/M428L. In certain embodiments, a half-life-extending mutation comprises P257I/Q311I. In certain embodiments, a half-life-extending mutation comprises P257I/N434H. In certain embodiments, a half-life-extending mutation comprises D376V/N434H. In certain embodiments, a half-life-extending mutation comprises T307A/E380A/N434A. In some embodiments, an antibody or antigen-binding fragment includes a Fc moiety that comprises the substitution mtuations M428L/N434S. In some embodiments, an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mtuations G236A/A330L/I332E. In certain embodiments, an antibody or antigen-binding fragment includes a (e.g., IgG) Fc moiety that comprises a G236A mutation, an A330L mutation, and a I332E mutation (GAALIE), and does not comprise a S239D mutation (e.g., comprises a native S at position 239). In particular embodiments, an antibody or antigen-binding fragment includes an Fc polypeptide or fragment thereof that comprises the substitution mutations: M428L/N434S and G236A/A330L/I332E, and optionally does not comprise S239D. In certain embodiments, an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mutations: M428L/N434S and G236A/S239D/A330L/I332E. In certain embodiments, the antibody or antigen-binding fragment comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or the antibody or antigen-binding fragment is partially or fully aglycosylated and/or is partially or fully afucosylated. Host cell lines and methods of making partially or fully aglycosylated or partially or fully afucosylated antibodies and antigen-binding fragments are known (see, e.g., PCT Publication No. WO 2016/181357; Suzuki et al. Clin. Cancer Res.13(6):1875-82 (2007); Huang et al. MAbs 6:1-12 (2018)).
In certain embodiments, the antibody or antigen-binding fragment is capable of eliciting continued protection in vivo in a subject even once no detectable levels of the antibody or antigen-binding fragment can be found in the subject (i.e., when the antibody or antigen-binding fragment has been cleared from the subject following administration). Such protection is referred to herein as a vaccinal effect. Without wishing to be bound by theory, it is believed that dendritic cells can internalize complexes of antibody and antigen and thereafter induce or contribute to an endogenous immune response against antigen. In certain embodiments, an antibody or antigen- binding fragment comprises one or more modifications, such as, for example, mutations in the Fc comprising G236A, A330L, and I332E, that are capable of activating dendritic cells that may induce, e.g., T cell immunity to the antigen. In any of the presently disclosed embodiments, the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof, including a CH2 (or a fragment thereof, a CH3 (or a fragment thereof), or a CH2 and a CH3, wherein the CH2, the CH3, or both can be of any isotype and may contain amino acid substitutions or other modifications as compared to a corresponding wild-type CH2 or CH3, respectively. In certain embodiments, a Fc polypeptide of the present disclosure comprises two CH2-CH3 polypeptides that associate to form a dimer. In any of the presently disclosed embodiments, the antibody or antigen-binding fragment can be monoclonal. The term "monoclonal antibody" (mAb) as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present, in some cases in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations that include different antibodies directed against different epitopes, each monoclonal antibody is directed against a single epitope of the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies. The term "monoclonal" is not to be construed as requiring production of the antibody by any particular method. For example,
monoclonal antibodies useful in the present invention may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256:495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal, or plant cells (see, e.g., U.S. Pat. No.4,816,567). Monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example. Monoclonal antibodies may also be obtained using methods disclosed in PCT Publication No. WO 2004/076677A2. Antibodies and antigen-binding fragments of the present disclosure include "chimeric antibodies" in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see, U.S. Pat. Nos.4,816,567; 5,530,101 and 7,498,415; and Morrison et al., Proc. Natl. Acad. Sci. USA, 81:6851-6855 (1984)). For example, chimeric antibodies may comprise human and non-human residues. Furthermore, chimeric antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. For further details, see Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323- 329 (1988); and Presta, Curr. Op. Struct. Biol.2:593-596 (1992). Chimeric antibodies also include primatized and humanized antibodies. A "humanized antibody" is generally considered to be a human antibody that has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are typically taken from a variable domain. Humanization may be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Reichmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting non-human variable sequences for the corresponding sequences of a human antibody. Accordingly,
such "humanized" antibodies are chimeric antibodies (U.S. Pat. Nos.4,816,567; 5,530,101 and 7,498,415) wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In some instances, a “humanized” antibody is one which is produced by a non-human cell or animal and comprises human sequences, e.g., HC domains. A "human antibody" is an antibody containing only sequences that are present in an antibody that is produced by a human. However, as used herein, human antibodies may comprise residues or modifications not found in a naturally occurring human antibody (e.g., an antibody that is isolated from a human), including those modifications and variant sequences described herein. These are typically made to further refine or enhance antibody performance. In some instances, human antibodies are produced by transgenic animals. For example, see U.S. Pat. Nos.5,770,429; 6,596,541 and 7,049,426. In certain embodiments, an antibody or antigen-binding fragment of the present disclosure is chimeric, humanized, or human. Presently disclosed antibodies and antigen-binding fragments can be obtained by, for example, introducing into a host (e.g., a mouse, a rabbit, a camelid, or a human) a SARS-CoV-2 spike protein or an immunogenic polypeptide as provided herein, and, in accordance with known methods, identifying from the host antibodies that bind to a presently disclosed epitope or epitope portion. Antigen-binding fragments can be produced from an antibody using known means. Presently disclosed antibodies can also be obtained by screening B cells, plasma cells, or sera from a subject that is or has been infected with a SARS-CoV-2 and identifying antibodies that bind to a presently disclosed epitope or epitope portion. Techniques for determining epitope-binding can include, for example, X-ray crystallography, alanine scanning mutagenesis, and cryo- electron microscopy. Immunogenic Polypeptides and Compositions In another aspect, the present disclosure provides immunogenic polypeptides comprising all or a portion of a presently disclosed RBD epitope or target region, and related compositions. An immunogenic polypeptide is a polypeptide that comprises an
antibody epitope or portion thereof (e.g., the RBD epitope recognized by antibody S309, or a portion of the epitope) and is capable of inducing a host immune response against the polypeptide that may involve, for example, production of antibodies, activation of specific immunologically-competent cells, production of inflammatory cytokines, activation of complement, antibody dependent cytotoxicity, or any combination thereof. It will be understood that an immunogenic polypeptide can comprise an amino acid sequence containing an epitope residue or residues, wherein the amino acid sequence is the same as an amino acid sequence within SEQ ID NO.:165 (or within a naturally occurring variant of SEQ ID NO.:165), or is that is not the same as as an amino acid sequence within SEQ ID NO.:165 (or within a naturally occurring variant of SEQ ID NO.:165). For example, an epitope residue or residues may be present in a recombinant or engineered sequence that is not found within SEQ ID NO.:165. Such recombinant or engineered sequences, or fragments of SEQ ID NO.:165 (or of a naturally occurring variant thereof) will maintain a conformation of the epitope residue or residues that is the same, or that is substantially the same, as a conformation of the epitope residue or residues in native SARS-CoV-2 RBD. It will also be understood that any one two or more immunogenic amino acid sequences each comprising all or a portion of a presently disclosed epitope or target region can be present in, for example, an isolated fragment of a SARS-CoV-2 RBD, as fusion protein (e.g., fused to a different portion, sequence or fragment of SARS-CoV-2 RBD, or as a Fc fusion or antibody fusoni protein), as a recombinant protein, or the like. Two or more immunogenic polypeptides each comprising all or a portion of a presently disclosed epitope or target region can also be present as separate molecules in a composition. Examples of amino acid sequences that can be present in an immunogenic polypeptide or composition include, but are not limited to: residues 333-346 of SEQ ID NO.:165; residues 354-361 of SEQ ID NO.:165; residues 333-361 of SEQ ID NO.:165; residues 440-444 of SEQ ID NO.:165; residues 333-509 of SEQ ID NO.:365; and variants thereof that are functional to elicit an immune response in a host (e.g., mouse,
primate, rabbit, or human), and/or that can be specifically bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168. In some embodiments, an immunogenic composition is provided that comprises: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 333-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-361 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or fifteen amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iv) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 440-444 of SEQ ID NO.:165, or a variant of residues 440-444 of SEQ ID NO.:165 comprising one or two amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (v) a polypeptide comprising or consisting essentially of, in N- to C-terminal direction (a) residues 333-361 of SEQ ID NO.:165, in sequence, (b) residues 440-444 or 440-445 of SEQ ID NO.:165, in sequence, and (c) disposed between and connecting (a) and (b),
either (1) an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of residues 362-439 of SEQ ID NO.:165 or (2) a linker amino acid sequence having a length of from four to about fifteen, from four to about twenty, or from four to about thirty amino acids; and/or (vi) a polypeptide comprising or consisting essentially of a variant amino acid sequence of residues 333-509 of SEQ ID NO.:165, the variant amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence of residues 333-509 of SEQ ID NO.:165, provided that: (a) amino acid residues 333-337, 339-341, 343-346, 354, 356-361, 440-442, 444, and 509 are as in SEQ ID NO.:165; or (b) one or more of the following amino acid mutations relative to SEQ ID NO.:165 is present in the polypeptide: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. In certain embodiments, the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. In certain embodiments, the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein. In certain embodiments, any one of amino acids 333, 335, 337, 339, 341, 343, 346, 354, 356, 361, 440, 441, 444, and 509 according to SEQ ID NO.:165, if present in the polypeptide, is a terminal amino acid of the polypeptide or shares a peptide bond with an amino acid that is not the same as the amino acid at the equivalent residue position in SEQ ID NO.:165. For example, a polypeptide of an immunogenic composition can comprise amino acids 333-346 of SEQ ID NO.:165, and amino acid 333, which is not a terminal amino acid in SEQ ID NO.:165 and shares a N-terminal bond with an isoleucine in SEQ ID NO.:165, is a terminal amino acid of the polypeptide or shares a N-terminal bond with an amino acid other than isoleucine. In other words, in certain embodiments, a polypeptide comprises an engineered or recombinant amino acid sequence, or an isolated fragment of SEQ ID NO.:165.
In certain embodiments, the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168. In certain embodiments, the immunogenic composition further comprises an adjuvant. Examples of adjuvants include, for example, poly-ICLC, poly I:C, GLA, CpG, GM-CSF, alum, Delta Inulin, aluminum hydroxide, alhydrogel, aluminum phosphate, MF59, AS03, TLR agonists, resiquimod, and saponins. In some embodiments, an immunogenic polypeptide is provided with a carrier, such as, for example, a further polypeptide (e.g., an antibody or an antibody Fc that is conjugated to or fused to the immunogenic polyeptide), a liposome, a polysaccharide, a polylactic acid, a polyglycolic acid, polymeric amino acids, an amino acid copolymer, an inactive virus particle, a microbead, a nanobead, or the like. Polynucleotides, Vectors, and Host cells In another aspect, the present disclosure provides isolated polynucleotides that encode any of the presently disclosed antibodies, antigen-binding fragments, portions thereof (e.g., a CDR, a VH, a VL, a heavy chain, or a light chain), or immunogenic polypeptides or portions thereof. In certain embodiments, the polynucleotide is codon- optimized for expression in a host cell. Once a coding sequence is known or identified, codon optimization can be performed using known techniques and tools, e.g., using the GenScript® OptimiumGeneTM tool; see also Scholten et al., Clin. Immunol.119:135, 2006). Codon-optimized sequences include sequences that are partially codon- optimized (i.e., one or more codon is optimized for expression in the host cell) and those that are fully codon-optimized. It will also be appreciated that polynucleotides encoding antibodies and antigen- binding fragments of the present disclosure may possess different nucleotide sequences while still encoding a same antibody or antigen-binding fragment or immunogenic polypeptide due to, for example, the degeneracy of the genetic code, splicing, and the like.
In any of the presently disclosed embodiments, the polynucleotide can comprise deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). In some embodiments, the RNA comprises messenger RNA (mRNA). Vectors are also provided, wherein the vectors comprise or contain a polynucleotide as disclosed herein (e.g., a polynucleotide that encodes an antibody or antigen-binding fragment that binds to a Wuhan coronavirus). A vector can comprise any one or more of the vectors disclosed herein. In particular embodiments, a vector is provided that comprises a DNA plasmid construct encoding the antibody or antigen- binding fragment, or a portion thereof (e.g., so-called "DMAb"; see, e.g., Muthumani et al., J Infect Dis.214(3):369-378 (2016); Muthumani et al., Hum Vaccin Immunother 9:2253-2262 (2013)); Flingai et al., Sci Rep.5:12616 (2015); and Elliott et al., NPJ Vaccines 18 (2017), which antibody-coding DNA constructs and related methods of use, including administration of the same, are incorporated herein by reference). In certain embodiments, a DNA plasmid construct comprises a single open reading frame encoding a heavy chain and a light chain (or a VH and a VL) of the antibody or antigen- binding fragment, wherein the sequence encoding the heavy chain and the sequence encoding the light chain are optionally separated by polynucleotide encoding a protease cleavage site and/or by a polynucleotide encoding a self-cleaving peptide. In some embodiments, the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in a single plasmid. In other embodiments, the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in two or more plasmids (e.g., a first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL). In certain embodiments, a single plasmid comprises a polynucleotide encoding a heavy chain and/or a light chain from two or more antibodies or antigen-binding fragments of the present disclosure. An exemplary expression vector is pVax1, available from Invitrogen®. A DNA plasmid of the present disclosure can be delivered to a subject by, for example, electroporation (e.g., intramuscular electroporation), or with an appropriate formulation (e.g., hyaluronidase).
In certain embodiments, an isolated polynucleotide is provided that encodes: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 333-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-361 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or fifteen amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iv) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 440-444 of SEQ ID NO.:165, or a variant of residues 440-444 of SEQ ID NO.:165 comprising one or two amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (v) a polypeptide comprising or consisting essentially of, in N- to C-terminal direction (a) residues 333-361 of SEQ ID NO.:165, in sequence, (b) residues 440-445 of SEQ ID NO.:165, in sequence, and (c) disposed between and connecting (a) and (b), either (1) an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of residues 362-439 of SEQ ID NO.:165 or (2) a linker amino acid sequence
having a length of from four to about fifteen, from four to about twenty, or from four to about thirty amino acids; and/or (vi) a polypeptide comprising or consisting essentially of a variant amino acid sequence of residues 333-509 of SEQ ID NO.:165, the variant amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence of residues 333-509 of SEQ ID NO.:165, provided that: (a) amino acid residues 333-337, 339-341, 343-346, 354, 356- 361, 440-442, 444, and 509 are as in SEQ ID NO.:165; or (b) one or more of the following amino acid mutations relative to SEQ ID NO.:165 is present in the polypeptide: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. In certain embodiments, the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. In certain embodiments, the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein. In certain embodiments, the encoded polypeptide of (i), (ii), (iii), (iv), and/or (v) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168. In a further aspect, the present disclosure also provides a host cell expressing an antibody, antigen-binding fragment, or immunogenic polypeptide according to the present disclosure; or comprising or containing a vector or polynucleotide according the present disclosure. Examples of such cells include but are not limited to, eukaryotic cells, e.g., yeast cells, animal cells, insect cells, plant cells; and prokaryotic cells, including E. coli. In some embodiments, the cells are mammalian cells. In certain such embodiments, the cells are a mammalian cell line such as CHO cells (e.g., DHFR-CHO cells (Urlaub et al., PNAS 77:4216 (1980)), human embryonic kidney cells (e.g., HEK293T cells),
PER.C6 cells, Y0 cells, Sp2/0 cells. NS0 cells, human liver cells, e.g. Hepa RG cells, myeloma cells or hybridoma cells. Other examples of mammalian host cell lines include mouse sertoli cells (e.g., TM4 cells); monkey kidney CV1 line transformed by SV40 (COS-7); baby hamster kidney cells (BHK); African green monkey kidney cells (VERO-76); monkey kidney cells (CV1); human cervical carcinoma cells (HELA); human lung cells (W138); human liver cells (Hep G2); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); mouse mammary tumor (MMT 060562); TRI cells; MRC 5 cells; and FS4 cells. Mammalian host cell lines suitable for antibody production also include those described in, for example, Yazaki and Wu, Methods in Molecular Biology, Vol.248 (B. K. C. Lo, ed., Humana Press, Totowa, N.J.), pp.255- 268 (2003). In certain embodiments, a host cell is a prokaryotic cell, such as an E. coli. The expression of peptides in prokaryotic cells such as E. coli is well established (see, e.g., Pluckthun, A. Bio/Technology 9:545-551 (1991). For example, antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat. Nos.5,648,237; 5,789,199; and 5,840,523. In particular embodiments, the cell may be transfected with a vector according to the present description with an expression vector. The term "transfection" refers to the introduction of nucleic acid molecules, such as DNA or RNA (e.g. mRNA) molecules, into cells, such as into eukaryotic cells. In the context of the present description, the term "transfection" encompasses any method known to the skilled person for introducing nucleic acid molecules into cells, such as into eukaryotic cells, including into mammalian cells. Such methods encompass, for example, electroporation, lipofection, e.g., based on cationic lipids and/or liposomes, calcium phosphate precipitation, nanoparticle based transfection, virus based transfection, or transfection based on cationic polymers, such as DEAE-dextran or polyethylenimine, etc. In certain embodiments, the introduction is non-viral. Moreover, host cells of the present disclosure may be transfected stably or transiently with a vector according to the present disclosure, e.g. for expressing an
antibody, or an antigen-binding fragment thereof, according to the present disclosure. In such embodiments, the cells may be stably transfected with the vector as described herein. Alternatively, cells may be transiently transfected with a vector according to the present disclosure encoding an antibody or antigen-binding fragment or immunogenic composition as disclosed herein. In any of the presently disclosed embodiments, a polynucleotide may be heterologous to the host cell. Accordingly, the present disclosure also provides recombinant host cells that heterologously express an antibody or antigen-binding fragment or immunogenic polypeptide of the present disclosure. For example, the cell may be of a species that is different to the species from which the antibody was fully or partially obtained (e.g., CHO cells expressing a human antibody or an engineered human antibody). In some embodiments, the cell type of the host cell does not express the antibody or antigen- binding fragment in nature. Moreover, the host cell may impart a post-translational modification (PTM; e.g., glysocylation or fucosylation) on the antibody or antigen- binding fragment or immunogenic composition that is not present in a native state of the antibody or antigen-binding fragment (or in a native state of a parent antibody from which the antibody or antigen binding fragment was engineered or derived). Such a PTM may result in a functional difference (e.g., reduced immunogenicity). Accordingly, an antibody or antigen-binding fragment or immunogenic polypeptide of the present disclosure that is produced by a host cell as disclosed herein may include one or more post-translational modification that is distinct from the antibody (or parent antibody) or amino acid sequence in its native state (e.g., a human antibody produced by a CHO cell can comprise a more post-translational modification that is distinct from the antibody when isolated from the human and/or produced by the native human B cell or plasma cell). Insect cells useful expressing a protein of interest are known in the art and include, for example, Spodoptera frugipera Sf9 cells, Trichoplusia ni BTI-TN5B1-4 cells, and Spodoptera frugipera SfSWT01 “MimicTM” cells. See, e.g., Palmberger et al., J. Biotechnol.153(3-4):160-166 (2011). Numerous baculoviral strains have been
identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells. Eukaryotic microbes such as filamentous fungi or yeast are also suitable hosts for cloning or expressing protein-encoding vectors, and include fungi and yeast strains with "humanized" glycosylation pathways, resulting in the production of an antibody or other protein with a partially or fully human glycosylation pattern. See Gerngross, Nat. Biotech.22:1409-1414 (2004); Li et al., Nat. Biotech.24:210-215 (2006). Plant cells can also be utilized as hosts for expressing a polypeptide, antibody, or antigen-binding fragment of the present disclosure. For example, PLANTIBODIES™ technology (described in, for example, U.S. Pat. Nos.5,959,177; 6,040,498; 6,420,548; 7,125,978; and 6,417,429) employs transgenic plants to produce antibodies. In certain embodiments, the host cell comprises a mammalian cell. In particular embodiments, the host cell is a CHO cell, a HEK293 cell, a PER.C6 cell, a Y0 cell, a Sp2/0 cell, a NS0 cell, a human liver cell, a myeloma cell, or a hybridoma cell. In a related aspect, the present disclosure provides methods for producing an antibody, antigen-binding fragment, or immunogenic composition, wherein the methods comprise culturing a host cell of the present disclosure under conditions and for a time sufficient to produce the antibody, or the antigen-binding fragment. Methods useful for isolating and purifying recombinantly produced proteins, by way of example, may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant antibody into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin. One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide. These purification methods may also be employed when isolating an immunogen from its natural environment. Methods for large scale production of one or more of the isolated/recombinant antibody, antigen-binding fragment, or polypeptide described herein include batch cell culture, which is monitored and controlled to maintain appropriate culture conditions.
Purification of soluble proteins may be performed according to methods described herein and known in the art and that comport with laws and guidelines of domestic and foreign regulatory agencies. Compositions that comprise any one or more of the presently disclosed antibodies, antigen-binding fragments, immunogenic polypeptides, polynucleotides, vectors, or host cells, singly or in any combination, can further comprise a pharmaceutically acceptable carrier, excipient, or diluent. Carriers, excipients, and diluents are discussed in further detail herein. In certain embodiments, a composition comprises a first vector comprising a first plasmid, and a second vector comprising a second plasmid, wherein the first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL of the antibody or antigen-binding fragment thereof, or encoding an immunogenic polypeptide. In certain embodiments, a composition comprises a polynucleotide (e.g., mRNA) coupled to a suitable delivery vehicle or carrier. Exemplary vehicles or carriers for administration to a human subject include a lipid or lipid-derived delivery vehicle, such as a liposome, solid lipid nanoparticle, oily suspension, submicron lipid emulsion, lipid microbubble, inverse lipid micelle, cochlear liposome, lipid microtubule, lipid microcylinder, or lipid nanoparticle (LNP) or a nanoscale platform (see, e.g., Li et al. Wilery Interdiscip Rev. Nanomed Nanobiotechnol.11(2):e1530 (2019)). Principles, reagents, and techniques for designing appropriate mRNA and and formulating mRNA-LNP and delivering the same are described in, for example, Pardi et al. (J Control Release 217345-351 (2015)); Thess et al. (Mol Ther 23: 1456-1464 (2015)); Thran et al. (EMBO Mol Med 9(10):1434-1448 (2017); Kose et al. (Sci. Immunol.4 eaaw6647 (2019); and Sabnis et al. (Mol. Ther.26:1509-1519 (2018)), which techniques, include capping, codon optimization, nucleoside modification, purification of mRNA, incorporation of the mRNA into stable lipid nanoparticles (e.g., ionizable cationic lipid/phosphatidylcholine/cholesterol/PEG-lipid; ionizable lipid:distearoyl PC:cholesterol:polyethylene glycol lipid), and subcutaneous, intramuscular,
intradermal, intravenous, intraperitoneal, and intratracheal administration of the same, are incorporated herein by reference. Methods and Uses Also provided herein are methods for use of an antibody or antigen-binding fragment, nucleic acid, vector, cell, or composition of the present disclosure in the diagnosis of SARS coronavirus (e.g., in a human subject, or in a sample obtained from a human subject). Methods of diagnosis (e.g., in vitro, ex vivo) may include contacting an antibody, antibody fragment (e.g., antigen binding fragment) with a sample. Such samples may be isolated from a subject, for example an isolated tissue sample taken from, for example, nasal passages, sinus cavities, salivary glands, lung, liver, pancreas, kidney, ear, eye, placenta, alimentary tract, heart, ovaries, pituitary, adrenals, thyroid, brain, skin or blood. The methods of diagnosis may also include the detection of an antigen/antibody complex, in particular following the contacting of an antibody or antibody fragment with a sample. Such a detection step can be performed at the bench, i.e. without any contact to the human or animal body. Examples of detection methods are well-known to the person skilled in the art and include, e.g., ELISA (enzyme-linked immunosorbent assay), including direct, indirect, and sandwich ELISA. Also provided herein are methods of treating a subject using an antibody or antigen-binding fragment, nucleic acid, vector, cell, immunogenic polypeptide, or composition, wherein the subject has, is believed to have, or is at risk for having an infection by a SARS coronavirus. "Treat," "treatment," or "ameliorate" refers to medical management of a disease, disorder, or condition of a subject (e.g., a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat). In general, an appropriate dose or treatment regimen comprising an antibody or composition of the present disclosure is administered in an amount sufficient to elicit a therapeutic or prophylactic benefit. Therapeutic or prophylactic/preventive benefit includes improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state;
delay or prevention of disease progression; remission; survival; prolonged survival; or any combination thereof. In certain embodiments, prophylactic/preventative benefit includes induction of a host immune response (e.g., production of antibodies, activation of immunologically competent cells, production of pro-inflammatory cytokines, or the like) against a SARS coronavirus surface glycoprotein or RBD thereof. Immunogenic polypeptides and compositions may be used, for example, as vaccines. In certain embodiments, therapeutic or prophylactic/preventive benefit includes reduction or prevention of hospitalization for treatment of a SARS-CoV-2 infection (i.e., in a statistically significant manner). In certain embodiments, therapeutic or prophylactic/preventive benefit includes a reduced duration of hospitalization for treatment of a SARS-CoV-2 infection (i.e., in a statistically significant manner). In certain embodiments, therapeutic or prophylactic/preventive benefit includes a reduced or abrogated need for respiratory intervention, such as intubation and/or the use of a respirator device. In certain embodiments, therapeutic or prophylactic/preventive benefit includes reversing a late-stage disease pathology and/or reducing mortality. A "therapeutically effective amount" or "effective amount" of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition of this disclosure refers to an amount of the composition or molecule sufficient to result in a therapeutic effect, including protection from infection by a SARS coronavirus; improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay of disease progression; remission; survival; or prolonged survival in a statistically significant manner. When referring to an individual active ingredient, administered alone, a therapeutically effective amount refers to the effects of that ingredient or cell expressing that ingredient alone. When referring to a combination, a therapeutically effective amount refers to the combined amounts of active ingredients or combined adjunctive active ingredient with a cell expressing an active ingredient that
results in a therapeutic effect, whether administered serially, sequentially, or simultaneously. Accordingly, in certain embodiments, methods are provided for treating a SARS coronavirus infection in a subject, wherein the methods comprise administering to the subject an effective amount of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition as disclosed herein. In some embodiments, a presently disclosed antibody or antigen-binding fragment can be administered with an immunogenic polypepide or immunogenic composition (e.g., concurrently, or in a sequence, or simultaneously, optionally from 1 to 5 minutes apart, or up to 4 hours apart, or up to 12 hours apart, or up to 1 day apart, or up to 7 days apart, or up to one month apart). Subjects that can be treated by the present disclosure are, in general, human and other primate subjects, such as monkeys and apes for veterinary medicine purposes. Other model organisms, such as mice and rats, may also be treated according to the present disclosure. In any of the aforementioned embodiments, the subject may be a human subject. The subjects can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects. A number of criteria are believed to contribute to high risk for severe symptoms or death associated with a SARS CoV-2 infection. These include, but are not limited to, age, occupation, general health, pre-existing health conditions, and lifestyle habits. In some embodiments, a subject treated according to the present disclosure comprises one or more risk factors. In certain embodiments, a human subject treated according to the present disclosure is an infant, a child, a young adult, an adult of middle age, or an elderly person. In certain embodiments, a human subject treated according to the present disclosure is less than 1 year old, or is 1 to 5 years old, or is between 5 and 125 years old (e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 125 years old, including any and all ages therein or therebetween). In certain embodiments, a human subject treated according to the present disclosure is 0- 19 years old, 20-44 years old, 45-54 years old, 55-64 years old, 65-74 years old, 75-84
years old, or 85 years old, or older. Persons of middle, and especially of elderly age are believed to be at particular risk. In particular embodiments, the human subject is 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older. In some embodiments, the human subject is male. In some embodiments, the human subject is female. In certain embodiments, a human subject treated according to the present disclosure is a resident of a nursing home or a long-term care facility, is a hospice care worker, is a healthcare provider or healthcare worker, is a first responder, is a family member or other close contact of a subject diagnosed with or suspected of having a SARS-CoV-2 infection, is overweight or clinically obese, is or has been a smoker, has or had chronic obstructive pulmonary disease (COPD), is asthmatic (e.g., having moderate to severe asthma), has an autoimmune disease or condition (e.g., diabetes), and/or has a compromised or depleted immune system (e.g., due to AIDS/HIV infection, a cancer such as a blood cancer, a lymphodepleting therapy such as a chemotherapy, a bone marrow or organ transplantation, or a genetic immune condition), has chronic liver disease, has cardiovascular disease, has a pulmonary or heart defect, works or otherwise spends time in close proximity with others, such as in a factory, shipping center, hospital setting, or the like. In certain embodiments, a subject treated according to the present disclosure has received a vaccine for SARS-CoV-2 and the vaccine is determined to be ineffective, e.g., by post-vaccine infection or symptoms in the subject, by clinical diagnosis or scientific or regulatory criteria. In certain embodiments, treatment is administered as peri-exposure prophylaxis. In certain embodiments, treatment is administered to a subject with mild-to-moderate disease, which may be in an outpatient setting. In certain embodiments, treatment is administered to a subject with moderate-to-severe disease, such as requiring hospitalization. Typical routes of administering the presently disclosed compositions thus include, without limitation, oral, topical, transdermal, inhalation, parenteral, sublingual, buccal, rectal, vaginal, and intranasal. The term "parenteral", as used herein, includes
subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques. In certain embodiments, administering comprises administering by a route that is selected from oral, intravenous, parenteral, intragastric, intrapleural, intrapulmonary, intrarectal, intradermal, intraperitoneal, intratumoral, subcutaneous, topical, transdermal, intracisternal, intrathecal, intranasal, and intramuscular. In particular embodiments, a method comprises orally administering the antibody, antigen- binding fragment, polynucleotide, vector, host cell, or composition to the subject. Pharmaceutical compositions according to certain embodiments of the present invention are formulated so as to allow the active ingredients contained therein to be bioavailable upon administration of the composition to a patient. Compositions that will be administered to a subject or patient may take the form of one or more dosage units, where for example, a tablet may be a single dosage unit, and a container of a herein described an antibody or antigen-binding in aerosol form may hold a plurality of dosage units. Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art; for example, see Remington: The Science and Practice of Pharmacy, 20th Edition (Philadelphia College of Pharmacy and Science, 2000). The composition to be administered will, in any event, contain an effective amount of an antibody or antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition of the present disclosure, for treatment of a disease or condition of interest in accordance with teachings herein. A composition may be in the form of a solid or liquid. In some embodiments, the carrier(s) are particulate, so that the compositions are, for example, in tablet or powder form. The carrier(s) may be liquid, with the compositions being, for example, an oral oil, injectable liquid or an aerosol, which is useful in, for example, inhalatory administration. When intended for oral administration, the pharmaceutical composition is preferably in either solid or liquid form, where semi solid, semi liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid. As a solid composition for oral administration, the pharmaceutical composition may be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like. Such a solid composition will typically contain one or more
inert diluents or edible carriers. In addition, one or more of the following may be present: binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, gum tragacanth or gelatin; excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, corn starch and the like; lubricants such as magnesium stearate or Sterotex; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; a flavoring agent such as peppermint, methyl salicylate or orange flavoring; and a coloring agent. When the composition is in the form of a capsule, for example, a gelatin capsule, it may contain, in addition to materials of the above type, a liquid carrier such as polyethylene glycol or oil. The composition may be in the form of a liquid, for example, an elixir, syrup, solution, emulsion or suspension. The liquid may be for oral administration or for delivery by injection, as two examples. When intended for oral administration, preferred compositions contain, in addition to the present compounds, one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer. In a composition intended to be administered by injection, one or more of a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent may be included. Liquid pharmaceutical compositions, whether they be solutions, suspensions or other like form, may include one or more of the following adjuvants: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer’s solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. Physiological saline is a preferred adjuvant. An injectable pharmaceutical composition is preferably sterile.
A liquid composition intended for either parenteral or oral administration should contain an amount of an antibody or antigen-binding fragment as herein disclosed such that a suitable dosage will be obtained. Typically, this amount is at least 0.01% of the antibody or antigen-binding fragment in the composition. When intended for oral administration, this amount may be varied to be between 0.1 and about 70% of the weight of the composition. Certain oral pharmaceutical compositions contain between about 4% and about 75% of the antibody or antigen-binding fragment. In certain embodiments, pharmaceutical compositions and preparations according to the present invention are prepared so that a parenteral dosage unit contains between 0.01 to 10% by weight of antibody or antigen-binding fragment prior to dilution. The composition may be intended for topical administration, in which case the carrier may suitably comprise a solution, emulsion, ointment or gel base. The base, for example, may comprise one or more of the following: petrolatum, lanolin, polyethylene glycols, bee wax, mineral oil, diluents such as water and alcohol, and emulsifiers and stabilizers. Thickening agents may be present in a composition for topical administration. If intended for transdermal administration, the composition may include a transdermal patch or iontophoresis device. The pharmaceutical composition may be intended for rectal administration, in the form, for example, of a suppository, which will melt in the rectum and release the drug. The composition for rectal administration may contain an oleaginous base as a suitable nonirritating excipient. Such bases include, without limitation, lanolin, cocoa butter and polyethylene glycol. A composition may include various materials which modify the physical form of a solid or liquid dosage unit. For example, the composition may include materials that form a coating shell around the active ingredients. The materials that form the coating shell are typically inert, and may be selected from, for example, sugar, shellac, and other enteric coating agents. Alternatively, the active ingredients may be encased in a gelatin capsule. The composition in solid or liquid form may include an agent that binds to the antibody or antigen-binding fragment of the disclosure and thereby assists in the delivery of the compound. Suitable agents that may act in this capacity include monoclonal or polyclonal antibodies, one or more proteins or a liposome. The
composition may consist essentially of dosage units that can be administered as an aerosol. The term aerosol is used to denote a variety of systems ranging from those of colloidal nature to systems consisting of pressurized packages. Delivery may be by a liquefied or compressed gas or by a suitable pump system that dispenses the active ingredients. Aerosols may be delivered in single phase, bi phasic, or tri phasic systems in order to deliver the active ingredient(s). Delivery of the aerosol includes the necessary container, activators, valves, subcontainers, and the like, which together may form a kit. One of ordinary skill in the art, without undue experimentation, may determine preferred aerosols. It will be understood that compositions of the present disclosure also encompass carrier molecules for polynucleotides, as described herein (e.g., lipid nanoparticles, nanoscale delivery platforms, and the like). The pharmaceutical compositions may be prepared by methodology well known in the pharmaceutical art. For example, a composition intended to be administered by injection can be prepared by combining a composition that comprises an antibody, antigen-binding fragment thereof, or immunogenic polypeptide as described herein and optionally, one or more of salts, buffers and/or stabilizers, with sterile, distilled water so as to form a solution. A surfactant may be added to facilitate the formation of a homogeneous solution or suspension. Surfactants are compounds that non-covalently interact with the peptide composition so as to facilitate dissolution or homogeneous suspension of the antibody or antigen-binding fragment thereof or immunogenic polypeptide in the aqueous delivery system. In general, an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome (e.g., a decrease in frequency, duration, or severity of diarrhea or associated dehydration, or inflammation, or longer disease-free and/or overall survival, or a lessening of symptom severity). For prophylactic use, a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder. Prophylactic benefit of the compositions administered according to the methods
described herein can be determined by performing pre-clinical (including in vitro and in vivo animal studies) and clinical studies and analyzing data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques, all of which can readily be practiced by a person skilled in the art. Compositions are administered in an effective amount (e.g., to treat a SARS coronavirus infection), which will vary depending upon a variety of factors including the activity of the specific compound employed; the metabolic stability and length of action of the compound; the age, body weight, general health, sex, and diet of the subject; the mode and time of administration; the rate of excretion; the drug combination; the severity of the particular disorder or condition; and the subject undergoing therapy. In certain embodiments, tollowing administration of therapies according to the formulations and methods of this disclosure, test subjects will exhibit about a 10% up to about a 99% reduction in one or more symptoms associated with the disease or disorder being treated as compared to placebo-treated or other suitable control subjects. Generally, a therapeutically effective daily dose of an antibody or antigen binding fragment is (for a 70 kg mammal) from about 0.001 mg/kg (i.e., 0.07 mg) to about 100 mg/kg (i.e., 7.0 g); preferably a therapeutically effective dose is (for a 70 kg mammal) from about 0.01 mg/kg (i.e., 0.7 mg) to about 50 mg/kg (i.e., 3.5 g); more preferably a therapeutically effective dose is (for a 70 kg mammal) from about 1 mg/kg (i.e., 70 mg) to about 25 mg/kg (i.e., 1.75 g). For polynucleotides, vectors, host cells, and related compositions of the present disclosure, a therapeutically effective dose may be different than for an antibody or antigen-binding fragment. In certain embodiments, a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition to the subject at 2, 3, 4, 5, 6, 7, 8, 9, 10 times, or more. In certain embodiments, a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition to the subject a plurality of times, wherein a second or successive administration is performed at about 6, about 7, about 8, about 9, about 10, about 11,
about 12, about 24, about 48, about 74, about 96 hours, or more, following a first or prior administration, respectively. In certain embodiments, a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition at least one time prior to the subject being infected by the Wuhan coronavirus. Compositions comprising an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or immunogenic polypeptide of the present disclosure may also be administered simultaneously with, prior to, or after administration of one or more other therapeutic agents. Such combination therapy may include administration of a single pharmaceutical dosage formulation which contains a compound of the invention and one or more additional active agents, as well as administration of compositions comprising an antibody or antigen-binding fragment or immunogenic polypeptide of the disclosure and each active agent in its own separate dosage formulation. For example, an antibody or antigen-binding fragment thereof or immunogenic polypeptide as described herein and the other active agent can be administered to the patient together in a single oral dosage composition such as a tablet or capsule, or each agent administered in separate oral dosage formulations. Similarly, an antibody or antigen-binding fragment or immunogenic polypeptide as described herein and the other active agent can be administered to the subject together in a single parenteral dosage composition such as in a saline solution or other physiologically acceptable solution, or each agent administered in separate parenteral dosage formulations. Where separate dosage formulations are used, the compositions comprising an antibody or antigen-binding fragment or immunogenic polypeptide and one or more additional active agents can be administered at essentially the same time, i.e., concurrently, or at separately staggered times, i.e., sequentially and in any order; combination therapy is understood to include all these regimens. In certain embodiments, a combination therapy is provided that comprises any two or more compositions (antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition) of the present disclosure.
In a related aspect, uses of the presently disclosed antibodies, antigen-binding fragments, vectors, host cells, immunogenic polypeptides, and compositions are provided. In certain embodiments, an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition is provided for use in a method of treating a SARS coronavirus infection in a subject. In certain embodiments, an antibody, antigen-binding fragment, polynucleotide, vector, host cell, immunogenic polypeptide, or composition is provided for use in a method of manufacturing or preparing a medicament for treating a SARS coronavirus infection in a subject. The present disclosure also provides the following Embodiments. Embodiment 1. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD) when the RBD is in an open conformation and/or when the RBD is in a closed conformation. Embodiment 2. The antibody or antigen-binding fragment of Embodiment 1, wherein the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein RBD is in an open conformation, and when the RBD is in a closed conformation. Embodiment 3. The antibody or antigen-binding fragment of Embodiment 1 or 2, wherein the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein is comprised in a trimer thereof, wherein, optionally, each surface glycoprotein of the trimer can be simultaneously bound to a separate antibody or antigen-binding fragment of Embodiment 1 or Embodiment 2.
Embodiment 4. The antibody or antigen-binding fragment of any one of Embodiments 1-3, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein RBD of a SARS coronavirus and/or of another sarbecovirus that is not SARS-CoV-2. Embodiment 5. The antibody or antigen-binding fragment of any one of Embodiments 1-4, wherein the SARS-CoV-2 surface glycoprotein is in prefusion conformation. Embodiment 6. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD), wherein the binding comprises contacting one or more amino acid residues of the RBD that are different from the amino acid residues of the RBD that contact a human ACE2 when the SARS CoV-2 surface glycoprotein is bound to the human ACE2, wherein, optionally, the antibody or antigen-binding fragment does not compete with human ACE2 for binding to the RBD. Embodiment 7. The antibody or antigen-binding fragment of Embodiment 6, wherein binding of the antibody or antigen-binding fragment to the RBD does not comprise contacting an RBD amino acid residue that contacts a human ACE2 when the surface glycoprotein is bound to the human ACE2. Embodiment 8. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD), wherein the binding to the RBD comprises contacting any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, D442, K444, R509, C336, and K444 according to SEQ ID NO.:165.
Embodiment 9. The antibody or antigen-binding fragment of any one of Embodiments 1-8, wherein binding of the antibody or antigen-binding fragment to the RBD comprises contacting amino acid N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated. Embodiment 10. The antibody or antigen-binding fragment of any one of Embodiments 1-9, wherein binding of the antibody or antigen-binding fragment to the RBD comprises contacting amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, D442, and R509, and, optionally, one or both of C336 and K444, according to SEQ ID NO.:165. Embodiment 11. An antibody, or an antigen-binding fragment thereof, that is capable of binding to an epitope in a sarbecovirus surface glycoprotein receptor binding domain (RBD), wherein the epitope comprises an asparagine amino acid residue that is or that corresponds to amino acid residue N343 of SEQ ID NO.:165, wherein, optionally, the correspondence is determined according to sequence alignment of (i) a sarbecovirus surface glycoprotein or RBD amino acid sequence containing the asparagine amino acid residue with (ii) SEQ ID NO.:165. Embodiment 12. The antibody or antigen-binding fragment of Embodiment 11, wherein the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 is glycosylated. Embodiment 13. The antibody or antigen-binding fragment of Embodiment 12, wherein the glycosylation of the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 comprises a fucose. Embodiment 14. The antibody or antigen-binding fragment of any one of Embodiments 11-13, wherein the asparagine amino acid residue (N) that is or that
corresponds to N343 of SEQ ID NO.:165 is comprised in an amino acid sequence N-X- T, X being any amino acid except for P, and preferably being A. Embodiment 15. The antibody or antigen-binding fragment of Embodiment 14, wherein the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence
(SEQ ID NO.:234), or a variant thereof having one, two, three, four or five amino acid substitutions, provided that the sequence N-X-T is present, X being any amino acid except for P, and preferably being A. Embodiment 16. The antibody or antigen-binding fragment of Embodiment 14 or 15, wherein the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence
(SEQ ID NO.:235), or is comprised in a variant sequence of SEQ ID NO.:235 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions relative to SEQ ID NO.:235, provided that the amino acid sequence N-X-T is present, X being any amino acid except for P, and preferably being A, wherein optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:235 independently comprises a conservative substitution or a non-conservative substitution. Embodiment 17. An antibody, or an antigen-binding fragment thereof, that is capable of binding in a target region in a SARS coronavirus (e.g., SARS-CoV-2) surface glycoprotein, wherein the target region comprises any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165.
Embodiment 18. The antibody or antigen-binding fragment of Embodiment 17, wherein the target region comprises amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. Embodiment 19. The antibody or antigen-binding fragment of Embodiment 17, wherein the target region comprises amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. Embodiment 20. The antibody or antigen-binding fragment of Embodiment 17, wherein the target region comprises amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165. Embodiment 21. The antibody or antigen-binding fragment of any one of Embodiments 17-20, wherein the target region comprises amino acids T333-C361, according to SEQ ID NO.:165. Embodiment 22. The antibody or antigen-binding fragment of Embodiment 21, wherin the target region further comprises amino acids N440-K444, according to SEQ ID NO.:165. Embodiment 23. The antibody or antigen-binding fragment of Embodiment 21 or 22, wherin the target region further comprises amino acid R509, according to SEQ ID NO.:165. Embodiment 24. The antibody or antigen-binding fragment of any one of Embodiments 1-23, wherein the antibody or antigen-binding fragment is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2
that comprises any one or more of the following mutations relative to SEQ ID NO.:165: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. Embodiment 25. The antibody or antigen-binding fragment of any one of Embodiments 1-24, which is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2 that comprises any one or more of the following mutations in RBD relative to SEQ ID NO.:165: N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q; E340D; L335S; L441F; L441I; L441R; L441V; T345S; T345I; T345N; T333I; T333K; N334D; N334Y; N260S; N360A; N360Y; I332V; R509K; R509T; C336S. Embodiment 26. The antibody or antigen-binding fragment of Embodiment 24 or Embodiment 25, wherein the antibody or antigen-binding fragment is capable of neutralizing the SARS-CoV-2 infection with a potency that is less than 3-fold reduced as compared to the potency with which the antibody or antigen-binding fragment neutralizes infection by a SARS-CoV-2 that comprises the amino acid sequence of SEQ ID NO.:165. Embodiment 27. The antibody or antigen-binding fragment of any one of Embodiments 1-26, which is a IgG, IgA, IgM, IgE, or IgD isotype. Embodiment 28. The antibody or antigen-binding fragment of any one of Embodiments 1-27, which is an IgG isotype selected from IgG1, IgG2, IgG3, and IgG4. Embodiment 29. The antibody or antigen-binding fragment of any one of Embodiments 1-28, which is human, humanized, or chimeric.
Embodiment 30. The antibody or antigen-binding fragment of any one of Embodiments 1-29, wherein the antibody, or the antigen-binding fragment, comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab. Embodiment 31. The antibody or antigen-binding fragment of any one of Embodiments 1-30, wherein the antibody or antigen-binding fragment is a multi-specific antibody or antigen binding fragment. Embodiment 32. The antibody or antigen-binding fragment of Embodiment 31, wherein the antibody or antigen binding fragment is a bispecific antibody or antigen-binding fragment. Embodiment 33. The antibody or antigen-binding fragment of any one of Embodiments 1-32, wherein the antibody or antigen-binding fragment further comprises a Fc polypeptide or a fragment thereof. Embodiment 34. The antibody or antigen-binding fragment of Embodiment 33, wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to a FcRn as compared to a reference Fc polypeptide that does not comprise the mutation; and/or (ii) a mutation that enhances binding to a FcγR as compared to a reference Fc polypeptide that does not comprise the mutation. Embodiment 35. The antibody or antigen-binding fragment of Embodiment 27, wherein the mutation that enhances binding to a FcRn comprises: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I; Q311I; D376V; T307A; E380A; or any combination thereof.
Embodiment 36. The antibody or antigen-binding fragment of Embodiment 34 or 35, wherein the mutation that enhances binding to FcRn comprises: (i) M428L/N434S; (ii) M252Y/S254T/T256E; (iii) T250Q/M428L; (iv) P257I/Q311I; (v) P257I/N434H; (vi) D376V/N434H; (vii) T307A/E380A/N434A; or (viii) any combination of (i)-(vii). Embodiment 37. The antibody or antigen-binding fragment of any one of Embodiments 34-36, wherein the mutation that enhances binding to FcRn comprises M428L/N434S. Embodiment 38. The antibody or antigen-binding fragment of any one of Embodiments 34-37, wherein the mutation that enhances binding to a FcγR comprises S239D; I332E; A330L; G236A; or any combination thereof. Embodiment 39. The antibody or antigen-binding fragment of any one of Embodiments 34-38, wherein the mutation that enhances binding to a FcγR comprises: (i) S239D/I332E; (ii) S239D/A330L/I332E; (iii) G236A/S239D/I332E; or (iv) G236A/A330L/I332E. Embodiment 40. The antibody or antigen-binding fragment of any one of Embodiments 1-39, which comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or which is aglycosylated and/or afucosylated.
Embodiment 41. The antibody or antigen-binding fragment of any one of Embodiments 1-40, comprising a L234A mutation, a L235A mutation, or both. Embodiment 42. An isolated polynucleotide encoding the antibody or antigen-binding fragment of any one of Embodiments 1-41, or encoding a VH, a heavy chain, a VL, and/or a light chain of the antibody or the antigen-binding fragment. Embodiment 43. The isolated polynucleotide of Embodiment 42, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA). Embodiment 44. The isolated polynucleotide of Embodiment 42 or 43, which is codon-optimized for expression in a host cell. Embodiment 45. A recombinant vector comprising the polynucleotide of any one of Embodiments 42-44. Embodiment 46. A host cell comprising the polynucleotide of any one of Embodiments 42-44 and/or the vector of Embodiment 45, wherein the polynucleotide is heterologous to the host cell. Embodiment 47. A human B cell comprising the polynucleotide of any one of Embodiments 42-44, wherein polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized. Embodiment 48. A composition comprising: (i) the antibody or antigen-binding fragment of any one of Embodiments 1- 41; (ii) the polynucleotide of any one of Embodiments 42-44; (iii) the recombinant vector of Embodiment 45;
(iv) the host cell of Embodiment 46; and/or (v) the human B cell of Embodiment 47, and a pharmaceutically acceptable excipient, carrier, or diluent. Embodiment 49. A method of treating a sarbecovirus infection in a subject, the method comprising administering to the subject an effective amount of: (i) the antibody or antigen-binding fragment of any one of Embodiments 1- 41; (ii) the polynucleotide of any one of Embodiments 42-44; (iii) the recombinant vector of Embodiment 45; (iv) the host cell of Embodiment 46; (v) the human B cell of Embodiment 47; and/or (vi) the composition of Embodiment 48. Embodiment 50. The method of Embodiment 49, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both. Embodiment 51. A method for in vitro diagnosis of a sarbecovirus infection, the method comprising: (i) contacting a sample from a subject with an antibody or antigen-binding fragment of any one of Embodiments 1-41; and (ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigen binding fragment, wherein, optionally, the sarbecovirus comprises SARS-CoV-2, SARS-CoV, or both. Embodiment 52. The method of Embodiment 51, wherein the sample comprises blood isolated from the subject.
Embodiment 53. The antibody or antigen-binding fragment of any one of Embodiments 1-41, the polynucleotide of any one of Embodiments 42-44, the recombinant vector of Embodiment 45, the host cell of Embodiment 46, the human B cell of Embodiment 47, and/or the composition of Embodiment 48, for use in a method of treating or diagnosing a sarbecovirus infection in a subject. Embodiment 54. The antibody or antigen-binding fragment of any one of Embodiments 1-41, the polynucleotide of any one of Embodiments 42-44, the recombinant vector of Embodiment 45, the host cell of Embodiment 46, the human B cell of Embodiment 47, and/or the composition of Embodiment 48, for use in the manufacture of a medicament for treating a sarbecovirus infection in a subject. Embodiment 55. The antibody or antigen-binding fragment of any one of Embodiments 1-41, the polynucleotide of any one of Embodiments 42-44, the recombinant vector of Embodiment 45, the host cell of Embodiment 46, the human B cell of Embodiment 47, and/or the composition of Embodiment 48 for use of Embodiment 53 or 54, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both. Embodiment 56. An immunogenic composition comprising: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution
present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 333-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-361 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or fifteen amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iv) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 440-444 of SEQ ID NO.:165, or a variant of residues 440-444 of SEQ ID NO.:165 comprising one or two amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (v) a polypeptide comprising or consisting essentially of, in N- to C- terminal direction (a) residues 333-361 of SEQ ID NO.:165, in sequence, (b) residues 440-444 or 440-445 of SEQ ID NO.:165, in sequence, and (c) disposed between and connecting (a) and (b), either (1) an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of residues 362-439 of SEQ ID NO.:165 or (2) a linker amino acid sequence having a length of from four to about fifteen, from four to about twenty, or from four to about thirty amino acids; and/or (vi) a polypeptide comprising or consisting essentially of a variant amino acid sequence of residues 333-509 of SEQ ID NO.:165, the variant amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%
identity to the amino acid sequence of residues 333-509 of SEQ ID NO.:165, provided that: (a) amino acid residues 333-337, 339-341, 343-346, 354, 356-361, 440-442, 444, and 509 are as in SEQ ID NO.:165; or (b) one or more of the following amino acid mutations relative to SEQ ID NO.:165 is present in the polypeptide: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. Embodiment 57. The immunogenic composition of Embodiment 56, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. Embodiment 58. The immunogenic compostion of Embodiment 56 or 57, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full- length SARS-CoV-2 surface glycoprotein. Embodiment 59. The immunogenic compostion of any one of Embodiments 56-58, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168. Embodiment 60. The immunogenic composition of any one of Embodiments 56-59, further comprising an adjuvant. Embodiment 61. An isolated polynucleotide that encodes: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid
sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 333-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-361 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or fifteen amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iv) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 440-444 of SEQ ID NO.:165, or a variant of residues 440-444 of SEQ ID NO.:165 comprising one or two amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (v) a polypeptide comprising or consisting essentially of, in N- to C- terminal direction (a) residues 333-361 of SEQ ID NO.:165, in sequence, (b) residues 440-444 or 440-445 of SEQ ID NO.:165, in sequence, and (c) disposed between and connecting (a) and (b), either (1) an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of residues 362-439 of SEQ ID NO.:165 or (2) a linker amino acid sequence having a length of from four to about fifteen, from four to about twenty, or from four to about thirty amino acids; and/or (vi) a polypeptide comprising or consisting essentially of a variant amino acid sequence of residues 333-509 of SEQ ID NO.:165, the variant amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence of residues 333-509 of SEQ ID NO.:165, provided that: (a) amino acid residues 333-337, 339-341, 343-346, 354, 356-361, 440-442, 444, and 509 are as in SEQ ID NO.:165; or (b) one or more of the following amino acid mutations relative to SEQ ID NO.:165 is present in the polypeptide: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. Embodiment 62. The polynucleotide of Embodiment 61, wherein the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. Embodiment 63. The polynucleotide of Embodiment 61 or 62, wherein the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein. Embodiment 64. The polynucleotide of any one of Embodiments 61-63, wherein the encoded polypeptide of (i), (ii), (iii), (iv), and/or (v) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168.
Embodiment 65. The polynucleotide of any one of Embodiments 61-64, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA). Embodiment 66. A composition comprising the polynucleotide of any one of Embodiments 42-49 or 61-65 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform. Embodiment 67. A recombinant vector comprising the polynucleotide of any one of Embodiments 61-65. Embodiment 68. A host cell comprising the polynucleotide of any one of Embodiments 61-65 and/or the vector of Embodiment 67. Embodiment 69. A composition comprising the polynucleotide of any one of Embodiments 61-65, the vector of Embodiment 67, and/or the host cell of Embodiment 68, and a pharmaceutically acceptable carrier, excipient, or diluent. Embodiment 70. A method of inducing an immune response in a subject against a sarbecovirus surface glycoprotein, the method comprising administering to the subject an effective amount of (i) the immunogenic composition of any one of Embodiments 56-60, (ii) the polynucleotide of any one of Embodiments 61-65, (iii) the vector of Embodiment 67, (iv) the host cell of Embodiment 68, and/or the composition of Embodiment 66 or 69. Embodiment 71. The method of Embodiment 70, wherein the sarbecovirus comprises SARS-CoV-2, SARS, or both.
Embodiment 72. The immunogenic composition of any one of Embodiments 56-60, the polynucleotide of any one of Embodiments 61-65, the vector of Embodiment 67, the host cell of Embodiment 67, and/or the composition of Embodiment 66 or 69, for use in a method of inducing an immune response in a subject, wherein, optionally, the immune response comprises an immune response against a sarbecovirus surface glycoprotein. Embodiment 73. The immunogenic composition of any one of Embodiments 56-60, the polynucleotide of any one of Embodiments 61-65, the vector of Embodiment 67, the host cell of Embodiment 68, and/or the composition of Embodiment 66 or 69, for use the manufacture of a medicament for inducing an immune response in a subject, wherein, optionally, the immune response comprises an immune response against a sarbecovirus surface glycoprotein. Embodiment 74. The immunogenic composition of any one of Embodiments 56-60, the polynucleotide of any one of Embodiments 61-65, the vector of Embodiment 67, the host cell of Embodiment 68, and/or the composition of Embodiment 66 or 69, for use of Embodiment 72 or 73, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both. Table 2. Sequences
EXAMPLES EXAMPLE 1 HUMAN MONOCLONAL ANTIBODIES THAT BIND SPIKE PROTEIN OF SARS-COV-2 B cells from a donor with previous SARS-CoV infection were sorted and immortalized with EBV and screened in 384-well plates (method described in European patent EP1597280B1, which method is incorporated herein by reference). Two weeks after immortalization, supernatants of immortalized B cells were tested for antibody binding to SARS-CoV-2 Spike ("S") protein using a flow cytometry-based method. Briefly, ExpiCHO cells were transfected with S protein of SARS-CoV-2 (strain BetaCoV/Wuhan-Hu-1/2019), or with an empty plasmid as a negative control. Fourteen monoclonal antibodies were identified that bind SARS- CoV-2 S, and were termed SARS-CoV-2 S300 through SARS-CoV-2 S312 and SARS- CoV-2 S315, respectively. Binding data for SARS-CoV-2 S300 through SARS-CoV-2 S310 are shown in Figures 4A and 4B (in these figures, the antibodies are identified as "S300"-"S310", respectively). Graphs showing positive binding are indicated with boxes. The heavy chain complementarity determining region (CDR)3 and light chain (L)CDR3 amino acid sequences of certain of these antibodies, along with the percent identity of the variable region gene sequences to germline (IMGT; imgt.org), are provided in Table 3.
EXAMPLE 2 BINDING OF ANTIBODIES TO RBD OF SARS-COV-2 USING OCTET Strepavidin biosensors (Pall ForteBio) were used to immobilize anti-Strep Tag II antibody at 3ug/ml (clone 5A9F9, Biotin, LabForce AG, Muttenz CH), after a hydration step for 10 minutes with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002Λ Tween-20, 0.005% NaN3 in PBS). SARS-CoV-2 RBD with a Strep Tag II (produced in-house) was then loaded for 6 min at a concentration of 4 µg/ml in KB. Antibodies from B cell supernatant were allowed to associate for 1620 seconds (27 minutes). To observe dissociation, sensors were moved from the antibody solution into KB and antibody dissociation was monitored. The "S303" mAb comprises the S303-v1 VH and VL amino acid sequences provided in Table 2 (SEQ ID NOs.:63 and 67, respectively). The "S309" mAb comprises the S309-v1 VH and S309-v13 VL amino acid sequences provided in Table 2 (SEQ ID NOs.: 105 and 168, respectively). The alleles encoding SEQ ID NOs.:109 and 147-150 from S309 B cell were determined to be non-productive; SEQ ID NO.:168 was the productive allele. Comparison of the binding curves for S303 and S309 mAbs to SARS-CoV-2 RBD (Figures 1A and 1B) indicates that S303 has both a faster on-rate and a faster off- rate than S309, suggesting that S309 may bind to SARS-CoV-2 RBD with higher affinity. EXAMPLE 3 ASSESSING BINDING OF ANTIBODIES TO RBD OF SARS-COV-2 AND SARS-COV-1 USING OCTET Unless the context clearly indicates otherwise (e.g., that antibodies were present in B cell supernatant, or an antibody Fab fragment was used), antibodies of the present disclosure are described in this and the subsequent Examples as recombinantly expressed human IgG1, in some cases with amino acid mutations in the Fc, as described herein.
Binding affinity of three SARS-CoV/SARS-CoV-2 cross-reactive recombinant antibodies (S303 rIgG1, S304 rIgG1, S309 rIgG1) and two SARS-CoV-1 specific antibodies (S109 rIgG1, S230 rIgG1) was tested by biolayer interferometry (BLI) using Octet. Affinity was measured by immobilizing the antibody on sensors and dipping the sensors into wells containing different concentrations of RBD. Kinetics of antibody binding to RBD were recorded during the association phase, after which the sensors were dipped into buffer without antibody to observe kinetics of antibody detaching from the RBD during the dissociation phase. Briefly, protein A biosensors (Pall ForteBio) were used to immobilize recombinant antibodies at 2.7ug/ml for 1 minute, after a hydration step for 10 minutes with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002Λ Tween-20, 0.005% NaN3 in PBS). Association curves were recorded for 5 minutes by incubating the antibody-coated sensors with different concentrations of SARS-CoV-1 RBD (Sino Biological) or SARS-CoV-2 RBD (produced in house in Expi-CHO cells; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947). The highest RBD concentration tested was 10ug/ml, then 1:2.5 serially diluted. Dissociation was recorded for 9 minutes by moving the sensors to wells containing KB. Affinities, represented by KD values, were calculated using a global fit model (Octet). Octet Red96 (ForteBio) equipment was used. Figures 6A-6E show association and dissociation curves for antibodies using the highest RBD concentration tested (10μg/ml). The switch from RBD solution to buffer is indicated with a vertical dashed line. Three cross-reactive antibodies (S303 rIgG1, S304 rIgG1 (VH of SEQ ID NO.:79, VL of SEQ ID NO.:73), S309 rIgG1 (VH of SEQ ID NO.:105, VL of SEQ ID NO.:168) and two SARS-CoV-1 specific antibodies (S230 and S109) were tested. All antibodies showed strong binding to SARS-CoV-1 RBD. S230 and S109 did not bind to SARS-CoV-2 RBD. Binding of S303 rIgG1, S304 rIgG1, and S309 rIGg1 to SARS-CoV-2 RBD was in the nanomolar to sub-picomolar range, with S309 rIgG1 showing the highest affinity. KD values are indicated below the graphs in Figures 6A-6E. KD values are estimates (KD=<1.0x10-12M) if the
antibody binding is very strong and dissociation is slow. An exact KD for S309 rIgG1 could not be measured by this assay since the dissociation was too slow. EXAMPLE 4 NEUTRALIZATION OF SARS-COV-2 INFECTION Replication-incompetent viruses pseudotyped with the SARS-CoV-2 S gene (isolate BetaCoV/Wuhan-Hu-1/2019; accession number MN908947) were produced using methods as previously described (Temperton NJ, et al. (2005) Longitudinally profiling neutralizing antibody response to SARS coronavirus with pseudotypes. Emerg Infect Dis 11(3):411–416). Briefly, HEK293T/17 cells were cotransfected with a SARS-CoV-2 S-expressing plasmid (phCMV1, Genlantis) and with a complementing viral–genome reporter gene vector, pNL4-3. Luc+.E-R+. A single-cycle infectivity assay was used to measure the neutralization of luciferase-encoding virions pseudotyped with the SARS-CoV-2 S protein, as previously described (Temperton NJ, et al. (2007) A sensitive retroviral pseudotype assay for influenza H5N1-neutralizing antibodies. Influenza Other Respi Viruses 1(3):105–112.). Briefly, appropriate dilutions of the virion-containing culture supernatants were preincubated at 37°C for 1 h with antibodies at various concentrations, and the virus–mAb mixtures were then added to Vero E6 cells that had been seeded the day before infection. The cells were then lysed with Steady-Glo reagent (Promega, E2520), and the relative luminescence units (RLU) in the cell lysates were determined on a luminometer microplate reader (Synergy H1 Hybrid Multi-Mode Reader; Biotek). The reduction of infectivity was determined by comparing the RLU in the presence and absence of antibody and expressed as percentage of neutralization. Antibodies S300-v1 (VH: SEQ ID NO.:1; VL: SEQ ID NO.:5), S301, S302, S303-v1 (VH SEQ ID NO.:63; VL SEQ ID NO.:67), S304 (VH SEQ ID NO.:79; VL SEQ ID NO.:83), S306 (VH SEQ ID NO.:87; VL SEQ ID NO.:91), S307 (VH SEQ ID NO.:239; VL SEQ ID NO.:243), S308-v1, S309 (comprising the S309-v1 VH sequence set forth in SEQ ID NO: 105 and the S309-v13 VL sequence set forth in SEQ ID NO: 168), and S310 were tested for neutralization function (Table 4, Figure 2A). Antibodies
SARS-CoV-2 S300-v1 and SARS-CoV-2 S309 neutralized SARS-CoV-2 infection (Figures 2A and 2B). Table 4. Percent neutralization of infection by antibodies (titration series)
Additional neutralization assays were carried out using plasma from SARS CoV-1 survivors and antibodies SARS-CoV-2 S309, S311, S312, S303-v1 (rIgG1), S304 (rIgG1), S306 (rIgG1), S310 (rIgG1), and S315 (Figure 3A-3I). Figure 3A shows neutralizing activity of SARS-CoV donor plasma. Figures 3B-3D and 3I show neutralizing activity of supernatant from B cells producing S309, S311, S312, and S315, respectively. Figures 3E-3H show neutralizing activity of recombinant antibody at various concentrations. Using this assay, supernatant containing antibody S309, S311, S312, or S315 neutralizes SARS-CoV-2 infection. Additional neutralization assays were carried out using antibodies S303, S304, S306, S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S310, and S315. Figure 13 shows neutralizing activity of these antibodies at various concentrations against SARS- CoV-2 pseudotyped MLV. DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells. Figure 34 shows neutralizing activity against SARS-CoV-1 pseudotyped MLV by these antibodies at various concentrations. Additional neutralization data for S304, S309, S304 + S309, S315, and S315 + S309 are shown in Figures 36 and 37.
EXAMPLE 5 NEUTRALIZATION OF SARS-COV-2 INFECTION Neutralizing activity of two SARS-CoV-1 and SARS-CoV-2 cross-neutralizing antibodies, S304 rIgG1 and S309 (VH: SEQ ID NO.:105; VL: SEQ ID NO.:168) rIgG1, against SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pp) was assessed. Murine leukemia virus (MLV) pseudotyped with SARS-CoV-2 Spike protein (SARS-CoV-2pp) was used. DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells. SARS-CoV-2pp was activated with trypsin TPCK at 10μg/ml. Activated SARS-CoV-2pp was added to a dilution series of antibodies (starting with 50μg/ml final concentration per antibody, 3-fold dilution). Antibodies were tested at concentrations from 50μg/ml to 0.02μg/ml. For the combination of S304 rIgG1 and S309 rIgG1, starting concentrations were 50μg/ml for each antibody, i.e. the total starting antibody concentration was 100μg/ml. DBT-ACE2 cells were added to the antibody-virus mixtures and incubated for 48 hours. Luminescence was measured after aspirating cell culture supernatant and adding steady-GLO substrate (Promega). In this assay, S309 rIgG1 exhibited a neutralization of infection IC50 of 0.37 μg/ml, and S304 rIgG1 exhibited an IC50 of approximately 17μg/ml. A combination of these two antibodies exhibited an IC50 of 0.077μg/ml. See Figure 7 and Table 5. Table 5. IC50 (μg/ml) of antibodies
Further neutralization assays were carried out using the same procedure for recombinant monoclonal antibodies S309 and S315, singly and in combination. In this assay, S309 exhibited an IC50 of 1.091 μg/ml, and S315 exhibited an IC50 of 25.1 μg/ml. The combination of both of these antibodies exhibited an IC50 of 0.3047 μg/ml. See Figure 23 and Table 6.
Table 6. IC50 (μg/ml) of antibodies and antibody combination
EXAMPLE 6 REACTIVITY OF HUMAN MONOCLONAL ANTIBODIES AGAINST SARS-COV AND SARS-COV-2 Reactivity of additional human mAbs "S311" and "S312" against the spike S1 subunit protein and the RBD of SARS-CoV and SARS-CoV-2 protein was assessed by enzyme-linked immunosorbent assay (ELISA). 96-well plates were coated with recombinant SARS-CoV-2 Spike S1 Subunit Protein (Sino Biological), SARS-CoV-2 RBD (Sino Biological or produced in house; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947), recombinant SARS-CoV Spike S1 Subunit Protein (Sino Biological), or SARS-CoV RBD (Sino Biological). Wells were washed and blocked with PBS+1%BSA for 1 hour at room temperature, and were then incubated with serially diluted mAbs for 1 hour at room temperature. Bound mAbs were detected by incubating alkaline phosphatase- conjugated goat anti-human IgG (Southern Biotechnology: 2040-04) for 1 hour at room temperature, and were developed by 1 mg/ml p-nitrophenylphosphate substrate in 0.1 M glycine buffer (pH 10.4) for 30 min at room temperature. Optical density (OD) values were measured at a wavelength of 405 nm in an ELISA reader (Powerwave 340/96 spectrophotometer, BioTek). Results are shown in Figure 5A (SARS-CoV-2 S311) and Figure 5B (SARS- CoV-2 S312). Further assays were performed to investigate reactivity of antibody variants engineered from S300, S305, or S307 to RBD of SARS-CoV-2 and SARS-CoV-1, using the same procedure described above in this Example. Results are shown in
Figures 38A-38D. Antibody "S300 V4-rIgG1," as shown in Figure 38C, comprises a VH comprising the amino acid sequence of SEQ ID NO.:1 and a VL (Vκ) comprising the amino acid sequence of SEQ ID NO.:234. Antibody "S307 V3-rIgG1," as shown in Figure 38D, comprises a VH comprising the amino acid sequence of SEQ ID NO.: 239 and a VL(Vκ) comprising the amino acid sequence of SEQ ID NO.:243. EXAMPLE 7 NEUTRALIZATION OF SARS-COV-2 INFECTION BY S309 AND S315 Neutralizing activity of recombinant antibodies S309 (VH: SEQ ID NO.:105; VL SEQ ID NO.:168) rIgG1-MLNS and S315 rIgG1-MLNS against SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pp) was determined. These recombinant antibodies included M428L and N434S mutations in the Fc domain (see, e.g., Zalevsky et al., Nat. Biotechnol.28(2):157-159 (2010); this combination of Fc mutations is also referred-to as "MLNS" or "LS" in the present disclosure, including in the drawings). Murine leukemia virus (MLV) pseudotyped with SARS-CoV-2 Spike protein (SARS-CoV-2pp) was used. DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells. SARS-CoV-2pp was activated with trypsin TPCK at 10μg/ml. Activated SARS-CoV-2pp was added to a dilution series of the tested antibody. DBT-ACE2 cells were added to the antibody-virus mixtures and incubated for 48 hours. Luminescence was measured after aspirating cell culture supernatant and adding steady-GLO substrate (Promega). Luciferase signal of infected cells was used to calculate the percentage of neutralization relative to a no-antibody control. S309 rIgG1 MLNS ("S309-rIgG1-LS" in Figure 9) exhibited a neutralization of infection IC50 of approximately 3.9 nM, and S315 rIgG1 MLNS ("S315-rIgG1-LSv1" in Figure 9) exhibited an IC50 of approximately 111.7 mM. See Figure 9. Neutralizing activity of S309-rFab was compared to that of full-length S309 rIgG1 MLNS ("S309-rIgG1-LS" in Figure 10). Full-length S309 rIgG-LS exhibited an IC50 of 3.821 nM, while S309-rFab exhibited an IC50 of 3.532 nM. See Figure 10.
EXAMPLE 8 REACTIVITY OF ANTIBODIES AGAINST RBD OF SARS-COV-1, RBD OF SARS- COV-2, AND ECTODOMAINS OF VARIOUS CORONAVIRUSES Reactivity of monoclonal antibodies against the RBDs of SARS-CoV-1 and SARS-CoV-2 and the Spike proteins of SARS-CoV-1, SARS-CoV-2, OC43 coronavirus, and MERS coronavirus was studied by enzyme-linked immunosorbent assay (ELISA). 384-well shallow ELISA plates were coated with stabilized prefusion Spike protein trimer of SARS-CoV-1, SARS-CoV-2, OC43, or MERS at 1 μg/ml, or with SARS-CoV-2 RBD (produced in house; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947) at 10 μg/ml, or SARS- CoV-1 RBD (Sino Biological) at 1 μg/ml. Wells were washed and blocked with PBS+1% BSA for 1 hour at room temperature, and were then incubated with serially diluted antibody for 1-2 hours at room temperature. Antibodies were tested at a concentration range of 5 to 0.00028 μg/ml. Plates were washed and bound antibodies were detected by incubating alkaline phosphatase-conjugated goat anti-human IgG (Southern Biotechnology: 2040-04) for 1 hour at room temperature followed by color development using 1 mg/ml p- nitrophenylphosphate substrate (Sigma-Aldrich 71768) in 0.1 M glycine buffer (pH 10.4) for 30 min at room temperature. The optical density (OD) values were measured at a wavelength of 405 nm in an ELISA reader (Powerwave 340/96 spectrophotometer, BioTek). The ELISA assay results are shown in Figures 8A-8K and 18A-18J. Recombinant antibodies, some bearing MLNS Fc mutations, are indicated with rIgG1. EXAMPLE 9 BINDING OF ANTIBODIES TO SPIKE PROTEIN OF SARS-COV-1 AND SARS- COV-2 ExpiCHO cells were transfected with phCMV1- SARS-CoV-2-S, SARS- spike_pcDNA.3 (strain SARS), or empty phCMV1 using Expifectamine CHO Enhancer. Two days after transfection, cells were collected for immunostaining with
antibody. An Alexa647-labelled secondary antibody anti-human IgG Fc was used for detection. Binding of monoclonal antibody to transfected cells was analyzed by flow cytometry using a ZE5 Cell Analyzer (Biorard) and FlowJo software (TreeStar). Positive binding was defined by differential staining of CoV-S transfectants versus mock transfectants. Antibody S309 (VH of SEQ ID NO.:105; VL of SEQ ID NO.:168) was tested by flow cytometry at 10 µg/ml for the ability to stain ExpiCHO cells expressing the S protein of SARS-CoV-1 or SARS-CoV-2. Stacked histograms of flow cytometry graphs show antibody dose-dependent binding by S309 to SARS-CoV-1 or SARS-CoV-2 S protein. Results are shown in Figure 11. Binding of monoclonal antibodies S303, S304, S306, S309, S310, S315, S110, S124, S230, and S109 (all expressed as rIgG1) to SARS-CoV-1 S protein and SARS- CoV-2 S protein was measured by flow cytometry. Results are shown in Figures 12A, 12B, 40A, and 40B. Eight of the tested antibodies exhibited EC50 values ranging between 1.4 ng/ml and 6,100 ng/ml for SARS-CoV-2 S protein binding and between 0.8 ng/ml and 254 ng/ml for SARS-CoV-1 S protein binding. Further binding assays using the same procedure were carried out for S309 and four engineered variants of S309 bearing different mutations in VH (N55Q, W50F, W105F, or W50F + G56A + W105F). Results are shown in Figure 27. EC50 values for each antibody tested in these assays are shown in Table 7; the numbers enclosed in parentheses in the "Antibody" column in Table 7 correspond to the figure key in Figure 27. Table 7.
Additional binding assays using the same procedure were carried out using antibodies S303, S304, S306, S309, S310, S315, and comparator antibodies S109, S110, S124, and S230. Results are shown in Figures 33A and 44A (binding to SARS- CoV-2 S protein), and 33B and 44B (binding to SARS-CoV-1 S protein). MFI: mean fluorescence intensity as measured by flow cytometry. The same assay was performed using recombinant antibodies S300 and S307. EXAMPLE 10 BINDING OF ANTIBODIES S309, S303, S304, AND S315 TO RBD OF SARS-COV- 2 AND SARS-COV-1 Affinity of recombinant antibodies S309, S303, S304, and S315 for RBD of CoV-1 and CoV-2 was tested using biolayer interferometry (BLI; Octet). Briefly, His- tagged RBD of SARS-CoV-1 or SARS-CoV-2 was loaded at 3μg/ml in kinetics buffer (KB) for 15 minutes onto anti-HIS (HIS2) biosensors (Molecular Devices, ForteBio). Association of full-length antibodies was performed in KB at 15 μg/ml for 5 minutes. Association of Fab fragments was performed in KB at 5 μg/mL for 5 minutes. Dissociation in KB was measured for 10 minutes. Affinities, represented by KD values, were calculated using a global fit model (Octet). Octet Red96 (ForteBio) equipment was used. Figures 14A-14D show association and dissociation curves for S309, S303, S304, and S315, respectively. Each of these antibodies bound to SARS-CoV-2 and SARS-CoV-1 RBD with nanomolar to sub-picomolar affinity. Figures 20A and 20B show association and dissociation curves for S309 IgG and S309 Fab, respectively. In these figures, the switch from antibody (or Fab) solution to buffer is indicated with a vertical dashed line.
EXAMPLE 11 BINDING OF S309 IGG AND S309 FAB TO SARS-COV-2 S PROTEIN ECTODOMAIN TRIMER AND RBD Affinity and avidity determination of IgG1 and Fab fragment: biotinylated RBD of SARS-CoV-2 (produced in-house; amino acid residues 331-550 of spike protein from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947, biotinylated with EZ-Link NHS-PEG4-Biotin from ThermoFisher) and biotinylated SARS-CoV-22P S avi-tagged were loaded at 7.5 µg/ml in Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002% Tween-20, 0.005% NaN3 in PBS) for 8 minutes onto Streptavidin biosensors (Molecular Devices, ForteBio). Association of IgG1 and Fab with target was performed in KB at 100, 33, 11, 3.6, 1.2 nM for 5 minutes. Dissociation in KB was measured for 10 minutes. KD values were calculated using a 1:1 global fit model (Octet). Results are shown in Figures 41A and 41B. In this assay, S309 IgG bound to the SARS-CoV-2 RBD and to the S ectodomain trimer with sub-picomolar and picomolar avidities, respectively. S309 Fab bound to both the SARS-CoV-2 RBD and the S ectodomain trimer with nanomolar to sub-nanomolar affinities. EXAMPLE 12 COMPETITIVE BINDING OF ANTIBODIES TO RBD OF SARS-COV-1 OR SARS-COV-2 Competitive binding of pairs of monoclonal antibodies to SARS-CoV-1 RBD or SARS-CoV-2 RBD was measured to identify respective binding sites of the antibodies. Strepavidin biosensors (Pall ForteBio) were used to immobilize anti-Strep Tag II antibody at 3ug/ml (clone 5A9F9, Biotin, LabForce AG, Muttenz CH), after a hydration step for 10 min with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002Λ Tween-20, 0.005% NaN3 in PBS). Either SARS-CoV-1 or SARS-CoV-2 RBD with a Strep Tag II (produced in-house) was then loaded for 6 min at a concentration of 4 µg/ml in KB. The first antibody was allowed to associate for a period of time, and then the second antibody was allowed to associate for 7 minutes (420 seconds). Figure 15A
shows competition of antibody pairs for binding to the RBD of SARS-CoV-1. Figure 15B shows competition of antibody pairs for binding to the RBD of SARS-CoV-2. The dashed vertical lines in Figures 15A and 15B indicate the switch from the first antibody, indicated on the left of the matrix, to the second antibody, indicated on top of the matrix. Using these and other data, four antigenic regions or sites (I-IV in Figures 15A and 15B) were identified. EXAMPLE 13 INTERFERENCE WITH RBD:HUMAN ACE2 BINDING The ability of antibodies to interfere with RBD binding to human ACE2 was measured. ACE2-His (Bio-Techne AG) was loaded for 30 minutes at 5 μg/ml in kinetics buffer (KB) onto anti-HIS (HIS2) biosensors (molecular Devices-ForteBio) SARS-CoV-1 RBD-rabbit Fc or SARS-CoV-2 RBD-mouse Fc (Sino Biological Europe GmbH) at 1 μg/ml was associated for 15 mintues, after a preincubation with or without antibody at 30 μg/ml for 30 minutes. Dissociation was monitored for 5 minutes. Figure 16 shows data obtained using antibody S309 or S230. Figures 19A and 19B show data obtained using antibodies S304, S303, or S230 (Figure 19A), or RBD and antibody S315 (Figure 19B). The vertical dashed line in each of Figures 16, 19A, and 19B indicates the start of the loading of RBD with or without antibody. EXAMPLE 14 EFFECTOR FUNCTION OF ANTIBODIES Natural killer (NK)-mediated antibody-dependent cell cytotoxicity (ADCC) can contribute to viral control by killing infected cells displaying viral protein on their surface. To investigate the ability of antibodies to leverage this function, ADCC was interrogated in vitro using human NK cells (isolated from fresh blood of healthy donors using the MACSxpress NK Isolation Kit (Miltenyi Biotec, Cat. Nr.: 130-098-185)) as effector cells and SARS-CoV-2 S-transfected ExpiCHO cells as target cells. Target cells were incubated with different amounts of antibody and after 10 minutes were incubated with primary human NK cells as effector cells at a target:effector ratio of 9:1.
Antibody-dependent cell killing was measured using a LDH release assay (Cytotoxicity Detection Kit (LDH) (Roche; Cat. Nr.: 11644793001)) after 4 hours of incubation at 37°C. Macrophage- or dendritic cell-mediated antibody-dependent cellular phagocytosis (ADCP) can also contribute to viral control by clearing infected cells and by potentially stimulating T cell response with viral antigen presentation. ADCP was tested using peripheral blood mononuclear cells as phagocytes and ExpiCHO transfected with SARS-CoV-2 S fluorescently labeled with PKH67 Fluorescent Cell Linker Kits (Sigma Aldrich, Cat. Nr.: MINI67) as target cells. Target cells were incubated with different amounts of antibody for 10 minutes, followed by incubation with human PBMCs isolated from healthy donors that were fluorescently labeled with Cell Trace Violet (Invitrogen, Cat. Nr.: C34557) at an effector:target ratio of 20:1. After an overnight incubation at 37°C, cells were stained with anti-human CD14-APC antibody (BD Pharmingen, Cat. Nr.: 561708, Clone M5E2) to stain phagocytic cells. Antibody-mediated phagocytosis was determined by flow cytometry, measuring the % of monocytes that were positive for PKH67 fluorescence. Antibodies S309 (VH SEQ ID NO.:105; VL SEQ ID NO.:168), S304, S306, S315, S230, and the combination of S309 and S304, were tested. Figure 17A shows ADCC function of antibodies using primary NK effector cells and SARS-CoV-2 S-expressing ExpiCHO as target cells. Symbols show means±SD of duplicate measurements. Figure 17B shows ADCP function of antibodies using PBMCs as phagocytic cells and PKF67-labelled SARS-CoV-2 S-expressing ExpiCHO as target cells. Symbols show means±SD of duplicate measurements. Fc variants of S309 were tested for ADCC. S309-LS includes the M428L and N434S Fc mutations. S309-GRLR includes the G236R/L328R Fc mutation, which exhibits minimal binding to FcγRs. S309-LS-GAALIE includes the MLNS and GAALIE (G236A/A330L/I332E) Fc mutations. Results are shown in Figure 45. Antibodies S303, S304, S306, S309, S315, and the combination of S309 and S315 were assayed for ADCC and ADCP function. Figure 24A shows ADCC of antibodies using primary NK effector cells and SARS-CoV- or SARS-CoV-2 S-
expressing ExpiCHO as target cells. The graph in Figure 24A shows the % killing determined for one representative donor homozygous for the high affinity FcγRIIIa (symbols show mean±SD). Figure 24B shows area under the curve (AUC) for the responses of cells from donors homozygous for the high affinity FcγRIIIa variant 158V (VV), compared to cells from donors heterozygous for 158V (FV) or homozygous for the low affinity variant 158F (FF) (mean±SD). Figure 25A shows ADCP using PBMCs as phagocytic cells and PKH67-labelled SARS-CoV-2 S-expressing ExpiCHO as target cells, for one representative donor. % ADCP indicates the percentage of monocytes positive for PKH67. Figure 25B shows the area under the curve (AUC) for the responses from multiple donors. EXAMPLE 15 REACTIVITY OF ANTIBODIES TO CELL LYSATE OF SARS-COV-2-INFECTED CELLS Reactivity of antibodies S304, S306, S309, and S310 against cell lysate of SARS-CoV-2-infected VeroE6 cells was measured. Figure 21A shows reactivity of the antibodies, as measured by indirect ELISA S against TX100-extracted lysate of SARS- CoV-2-infected VeroE6 cells. Figure 21B shows reactivity of the antibodies, as measured by indirect ELISA S against SDS extracted (denatured) lysate of SARS-CoV- 2-infected VeroE6 cells. Figure 21C shows reactivity of human SARS-CoV-1 convalescent serum, as measured by indirect ELISA S against TX100-extracted or SDS-extracted lysate of SARS-CoV-2-infected VeroE6 cells. EXAMPLE 16 NEUTRALIZATION OF SARS-COV-2 INFECTION BY ANTIBODIES S304 AND S309, ALONE OR IN COMBINATION Neutralization of SARS-CoV-2 infection by monoclonal antibodies S304 and S309 was assessed using a SARS-CoV-2 live virus assay. The live virus neutralization assay quantifies the number of infected cells by staining for viral nucleoprotein (NP) with an NP-specific polyclonal rabbit serum. Inhibition was assessed by measuring NP
expression at 24 and 45 hours post infection. Enzyme immunoassay (EIA) was used to quantify the level of infection for each antibody dilution tested. Data are shown in Figures 22A-22D. Neutralization was carried out for one hour at room temperature at the indicated antibody concentrations using Vero E6 cells in monolayer in 96-well plates. Wells were infected with 100 TCID50 of virus. After 24 or 45 hours, monolayers were fixed and stained for inhibition of NP expression. When combined, S304 and S309 show a synergistic enhancement of neutralization. EXAMPLE 17 PRODUCTION OF S309 RIGG VARIANT ANTIBODIES Recombinant IgG1 antibodies were produced using the VH and VL sequences of antibody S309. In this example, antibodies are referred-to as "S309-11", "S309-12", "S309-13", "S309-14", and "S309-15", respectively. "S309-11" comprises the wild-type VH sequence (SEQ ID NO: 105) and the wild-type VL sequence (SEQ ID NO: 168) of S309. "S309-12" comprises an N55Q mutation in CDRH2, providing a VH variant sequence (SEQ ID NO: 113) and the wild- type VL sequence (SEQ ID NO: 168) of S309. "S309-13" comprises a W50F mutation in VH (SEQ ID NO: 129) and the wild-type VL sequence (SEQ ID NO: 168) of S309. "S309-14" comprises a W105F VH variant sequence (SEQ ID NO: 119) and the wild- type VL sequence (SEQ ID NO: 168) of S309. "S309-15" comprises a W50F/G56A/W105F VH variant (SEQ ID NO: 172) and the wild-type VL sequence of S309 (SEQ ID NO: 168). S309 recombinant antibody (S309-11) and each of the four variants S309-12 – S309-15 were produced by transient transfection and expression of a plasmid vector encoding the recombinant antibody in HD 293F cells (GenScript). This signal peptide provided superior antibody production as compared to other signal peptides tested. Data not shown. Cells were harvested on day 4 and IgG expression was validated by Western blot and protein A titer analysis.
EXAMPLE 18 BINDING OF S309 RIGG AND VARIANTS TO SARS-COV-2 RBD Binding of recombinant monoclonal antibody S309 and the four S309 variants described in Example 17 (S309-12 – S309-15) to RBD was measured using surface plasmon resonance (SPR). SPR experiments were carried out with a Biacore T200 instrument using a single-cycle kinetics approach. Antibody expressed as IgG was captured on the surface and increasing concentrations of purified SARS-CoV-2 RBD, either glycosylated or deglycosylated form, were injected. SPR was conducted using a sensor chip with anti-human Fc covalently immobilized (GE). Buffer used was 10 mM HEPES pH 7.4, 150 mM NaCl, 3mM EDTA, and 0.05% P20 detergent. Assays were conducted at 25°C. Recombinant antibodies were diluted from supernatant to approximately 2 μg/ml. RBD concentrations were 0.8 nM, 3.1 nM, 12.5 nM, 50 nM, and 200 nM. Glycosylated RBD was obtained by expression in HEK293 cells and purified using one-step Ni affinity purification. Deglycosylated RBD was obtained by expression in-house in Expi293 cells grown in the presence of kifunensine, purification using one-step Ni affinity purification, and treatment with endoglycosidase H. Single- cycle kinetics assays were carried out with 3 minute injections and 20 minute dissociation periods. Association and dissociation kinetics were monitored and fit to a binding model to determine affinity. Results are shown in Figures 30A-30F and Table 8. Table 8.
Binding to deglycosylated RBD was measured in two different SPR assays using different parameters. Experiment 1 used 10-minute injections and an RBD concentration series of 4-fold dilutions from 100 nM. Experiment 2 used 3-minute injections and a concentration series of 4-fold dilutions from 200 nM, as described above. Results are shown in Table 9. Results of Experiment 1 for S309-15 are also shown in Figure 30F, top two panels. Table 9.
Binding of recombinant antibody S309 and the four engineered variants to RBD was measured by surface plasmon resonance (SPR) using the same procedure described
above, except using purified recombinant antibodies rather than cell culture supernatant. Resuts are shown in Table 10. Table 10.
EXAMPLE 19 NEUTRALIZATION OF SARS-COV-2 INFECTION BY S309 ANTIBODIES Neutralizing activity of S309 and the four engineered S309 variants described in Examples 17 and 18 ("S309-12" – "S309-15") was determined using a VSV-based luciferase reporter pseudotyping system (Kerafast). VSV pseudoparticles and antibody were mixed in DMEM and allowed to incubate for 30 minutes at 37 ^C. The infection mixture was then allowed to incubate with Vero E6 cells for 1h at 37 ^C, followed by the addition of DMEM with Pen-Strep and 10% FBS (infection mixture is not removed). The cells were incubated at 37 ^C for 18-24 hours. Luciferase was measured using an Ensight Plate Reader (Perkin Elmer) after the addition of Bio-Glo reagent (Promega). Results are shown in Figure 28. In Figure 28, Variants-11 – 15 correspond to S309-11 – S309-15, respectively. Calculated EC50 values based on this experiment are shown in Table 11.
Table 11.
EXAMPLE 20 ANTIBODY-DEPENDENT ACTIVATION OF HUMAN FCΓRIIIA OR FCΓRIIA Antibody-dependent activation of human FcγRIIIa or FcγRIIa was examined. ExpiCHO cells were transiently transfected with SARS-CoV-2 S (BetaCoV/Wuhan- Hu-1/2019), and incubated with titrated concentrations of antibody for 10 minutes. ExpiCHO cells were then incubated with Jurkat cells expressing FcγRIIIa or FcγRIIa on their surface and stably transfected with NFAT-driven luciferase gene (Promega, Cat. Nr.: G9798 and G7018) at an effector to target ratio of 6:1 for FcγRIIIa and 5:1 for FcγRIIa. Activation of human FcγRs in this bioassay results in the NFAT-mediated expression of the luciferase reporter gene. Luminescence was measured after 21 hours of incubation at 37°C with 5% CO2, using the Bio-Glo-TM Luciferase Assay Reagent according to the manufacturer’s instructions. Antibodies S303, S304, S306, S309, S315, and a combination of S309 and S315 were assayed, along with comparator antibody S230. Results are shown in Figures 31 and 32. EXAMPLE 21 ANALYSIS OF SARS-COV-2 S GLYCOPROTEIN SEQUENCES Analysis of the S glycoprotein sequences of 2,229 SARS-CoV-2 isolates indicated that several mutations have occurred with variable frequency on the SARS- CoV-2 S ectodomain. Figure 35A shows Spike protein variants occurring with a frequency of n>1 as spheres mapped onto the closed and open form of the full trimeric
Spike ectodomain. The RBD and other Spike protein domains are shown as indicated. 40 mutations (out of 2229 total) are shown. Due to lack of detail in the PDB structures, only residue 367 (n=8) is highlighted in the RBD, and residues 476 (n=7) and 483 (n=17) are not. Figure 35B shows the prevalence of variants in Spike glycoprotein by amino acid. Each dot is a distinct variant. The locations of Domain A and RBD are shown. Variants passing a frequency threshold of 0.1% are as indicated. Further analysis of the S glycoprotein sequences was carried out using 11,839 SARS-CoV-2 isolates. Figure 43 shows variants supported by at least two sequences (prevalence greater than 0.01%) rendered as indicated spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. Each dot is a distinct variant. Figure 43 shows Spike protein variants supported by at least two sequences as indicated spheres mapped onto the closed (left) and open (right) form of the full trimeric Spike ectodomain. The RBD and other Spike protein domains are shown in the colors indicated. 171 variants (out of 11,839 total Spike protein sequences analyzed) are shown. Variants are labeled if their prevalence is greater than 1% (D614G only) or if they are located within the RBD. The location of conserved N343 is also indicated. EXAMPLE 22 Neutralization of MLV-S Protein Pseudovirus by Monoclonal Antibody S309 Neutralization of SARS-CoV-2-MLV, SARS-CoV-1-MLV bearing S Protein from various isolates, and other sarbecovirus isolates by monoclonal antibody S309 was assayed. HEK293T cells were co-transfected with a SARS-CoV, SARS-CoV-2, CUHK, GZ02, or WiV1 S encoding-plasmid, an MLV Gag-Pol packaging construct and the MLV transfer vector encoding a luciferase reporter using the Lipofectamine 2000 transfection reagent (Life Technologies) according to the manufacturer’s instructions. Cells were incubated for 5 hours at 37°C with 8% CO2 with OPTIMEM transfection medium. DMEM containing 10% FBS was added for 72 hours. VeroE6 cells or DBT cells transfected with human ACE2 were cultured in DMEM containing 10% FBS, 1% PenStrep and plated into 96 well plates for 16-24 hours. Concentrated pseudovirus with or without serial dilution of antibodies was incubated for 1 hour and
then added to the wells after washing 3X with DMEM. After 2-3 hours DMEM containing 20% FBS and 2% PenStrep was added to the cells for 48 hours. Following 48 hours of infection, One-Glo-EX (Promega) was added to the cells and incubated in the dark for 5-10 minutes prior to reading on a Varioskan LUX plate reader (ThermoFisher). Measurements were done in duplicate and relative luciferase units (RLU) were converted to percent neutralization and plotted with a non-linear regression curve fit in PRISM. Results are shown in Figure 38. S309 was shown to neutralize SARS-CoV-MLVs from isolates of the three phases of the 2002-2003 epidemic with IC50 values of between 120 ng/ml and 180 ng/ml, and to partially neutralize SARSr- CoV39 WIV-1. EXAMPLE 23 Characterization of the Structure of SARS-CoV-2 S Glycoprotein in Complex with the S309 Neutralizing Antibody Fab Fragment The structure of the complex between the S309 Fab fragment and a prefusion stabilized SARS-CoV-2 S Protein ectodomain trimer was characterized using single- particle cryoEM. 3D structure of the trimer with one SB (RBD) domain open and an all closed trimer, each with three S309 Fab fragments bound, was first determined at 4.2 Å and 3.6 Å resolution, respectively (parameters shown below). The resulting structures are shown in Figures 39A, 39B, and 43A-43D. Table 12 shows the cryoEM data collection and refinement statistics used in the analysis. A crystal structure of the S309 Fab fragment was determined at 3.3 Å resolution to assist model building. The X-ray data collection and refinement statistics are shown in Table 13. These data indicate that S309 recognizes a protein/glycan epitope on the SARS- CoV-2 SB, distinct from the receptor-binding motif. The epitope is accessible in both the open and closed S states, explaining the stoichiometric binding of S309 Fab fragment to the S trimer. The S309 paratope is composed of all six CDR loops and buries a surface area of ~1,050Å2 at the interface with SB (RBD) through electrostatic interactions and hydrophobic contacts. The 20-residue long CDRH3 sits atop the SB (RBD) helix comprising residues 337-344 and also contacts the edge of the SB (RBD) five-stranded β-sheet (residues 356-361), overall accounting for ~50% of the buried
surface area. CDRL1 and CDRL2 extend the epitope by interacting with the helix spanning residues 440-444 that is located near the S 3-fold molecular axis. CDRH3 and CDRL2 sandwich the SARS-CoV-2 S glycan at position N343 through contacts with the core fucose moiety (in agreement with the detection of SARS-CoV-2 N343 core- fucosylated peptides by mass-spectrometry) and to a lesser extent with the core N- acetyl-glucosamine. These latter interactions bury an average surface of ~170 Å2 and stabilize the N343 oligosaccharide which is resolved to a much larger extent than in the apo SARS-CoV-2 S structures. Table 12.
Table 13.
Further analysis was carried out using the cryoEM data collection and refinement statistics shown in Table 14 and the X-ray data collection and refinement statistics shown in Table 15. 3D structure of the trimer with one SB (RBD) domain open and an all closed trimer, each with three S309 Fab fragments bound, was determined at 3.7 Å and 3.1 Å resolution, respectively. The resulting structures are shown in Figures 47A-47D. The S309 paratope was shown to be composed of all six CDR loops that bury a surface area of approximately 1,150 Å2 at the interface with SB (RBD) through electrostatic interactions and hydrophobic contacts. The 20-residue long CDRH3 sits atop the SB (RBD) helix comprising residues 337-344 and also contacts the edge of the SB (RBD) five-stranded β-sheet (residues 356-361), overall
accounting for ~50% of the buried surface area. CDRL1 and CDRL2 extend the epitope by interacting with the helix spanning residues 440-444 that is located near the S 3-fold molecular axis. CDRH3 and CDRL2 sandwich the SARS-CoV-2 S glycan at position N343 through contacts with the core fucose moiety (in agreement with the detection of SARS-CoV-2 N343 core-fucosylated peptides by mass-spectrometry) and to a lesser extent with the core N-acetyl-glucosamine. These latter interactions were shown to bury an average surface of ~300 Å2 and stabilize the N343 oligosaccharide which is resolved to a much larger extent than in the apo SARS-CoV-2 S structures. Table 14.
Table 15.
The structural data indicate that 17 out of 22 residues of the S309 epitope are strictly conserved between SARS-CoV-2 and SARS-CoV-1. R346SARS-CoV-2, R357SARS- CoV-2, N354SARS-CoV-2 and L441SARS-CoV-2 are conservatively substituted to K333SARS-CoV, K344SARS-CoV (except for SARS-CoV isolate GZ02 where it is R444SARS-CoV), E341SARS- CoV and I428SARS-CoV, whereas K444SARS-CoV-2 is semi-conservatively substituted to T431SARS-CoV, in agreement with the comparable binding affinities to SARS-CoV and
SARS-CoV-2 S. The oligosaccharide at position N343 is also conserved in both viruses and corresponds to SARS-CoV N330, for which core-fucosylated glycopeptides were detected by mass spectrometry, and would allow for similar interactions with the S309 Fab fragment. Analysis of the S glycoprotein sequences of 2,229 SARS-CoV-2 isolates indicated that several mutations have occurred with variable frequency on the SARS- CoV-2 S ectodomain (see Figures 35A and 35B and Figures 49A and 49B) but no mutations arose within the epitope recognized by S309 mAb. Finally, S309 contact residues showed a high degree of conservation across clade 1, 2 and 3 sarbecovirus human and animal isolates (see Figures 41C and 48C). These data indicate that S309 could neutralize all SARS-CoV-2 isolates circulating to date and other zoonotic sarbecovirus strains. The cryoEM structure of monoclonal antibody S309 bound to SARS-CoV-2 S proteim was combined with the structures of SARS-CoV-2 SB (RBD) and SARS-CoV- 1 SB (RBD) complexed with ACE2. These structures indicate that the S309 Fab fragment engages an epitope distinct from the receptor-binding motif and would not interfere with ACE2 upon binding to S protein. See Figure 40. EXAMPLE 24 BINDING OF MONOCLONAL ANTIBODIES TO DISULFIDE STABILIZED SPIKE PROTEIN Structural changes in the SARS-CoV-1 and SARS-CoV-2 Spike proteins, from a closed to an open conformation, have been reported to enable exposure of the receptor-binding motif, which mediates interaction with ACE2. SARS-CoV-1 and SARS-CoV-2 Spike were engineered to be stabilized in the prefusion closed conformation. In an engineered version of the SARS-CoV-2 Spike protein that comprised the amino acid substitutions R682S, R683G and R685G, K986P and V987P, an inter-molecular disulfide bond was created by substituting cysteines in place of S383 and D985. This engineered Spike protein was recombinantly expressed, and is referred to as SARS-CoV-2 DS Spike or SARS-CoV-2 DS S. Recombinant S proteins (wild-type or disulfide-stabilized) were produced in 500 mL cultures using FreeStyle 293 expression medium (Life Technologies) at 37°C in a
humidified 8% CO2 incubator rotating at 130 r.p.m; The culture was transfected using 293fectin (ThermoFisher Scientific) with cells grown to a density of 106 cells per mL and cultivated for three days. The supernatant was harvested and cells were resuspended for another three days, yielding two harvests. Clarified supernatants were purified using a 5 mL Cobalt affinity column (Takara). Purified protein was concentrated and flash frozen in a buffer containing 50 mM Tris pH 8.0 and 150 mM NaCl prior to cryoEM analysis. Electron microscopy confirmed proper folding of the engineered protein (data not shown). Similarly, a disulfide-stabilized SARS-CoV-1 Spike protein was engineered by substituting cysteines in place of S370 and D969, forming SARS-CoV-1 DS S. Electron microscopy confirmed proper folding of this engineered protein as well (data not shown). For antibody binding experiments, twenty µl of stabilized prefusion trimer of SARS-CoV-2 S protein or SARS-CoV-1 S protein or the disulfide stabilized SARS- CoV-2 DS S or SARS-CoV-1 DS S was coated on 384 well ELISA plates at 1 ng/ µl for 16 hours at 4 °C. After blocking with 80 µl of 1% BSA in TBST, 30 µl of antibody was added to the plates at concentrations between 10 and 0.00000004 ng/ µl and inclubated for one hour at 37 °C. Plates were washed and then incubated with 30 µl of 1/5000 diluted goat anti-human Fc IgG-HRP (Invitrogen A18817). Plates were washed and then 30 µl Substrate TMB microwell peroxidase (Seracare 5120-0083) was added for 5 minutes at room temperature. The colorimetric reaction was stopped by addition of 30 µl of 1N HCl. A450 was read on a Varioskan Lux plate reader (Thermo Scientific). Binding of human monoclonal antibodies S309 and S304 to SARS-CoV-2 DS S and to SARS-CoV-2 S was evaluated. Binding of S309 was indistinguishable between the two constructs, as shown in Figure 50A. S304 interacted with SARS-CoV-2 S in a concentration-dependent manner, but did not bind to SARS-CoV-2 DS S, as shown in Figure 50B. As antibody S304 recognizes an epitope distinct from both the RBM and the S309 epitope, this result suggests that S304 binds to a cryptic epitope that is accessible only when S protein is in the open conformation.
Binding of antibody S309 to SARS-CoV-1 DS S and SARS-CoV-1 S was also evaluated. S309 showed dose-dependent binding to both proteins, as shown in Figure 51. EXAMPLE 25 MATERIALS AND METHODS Flow-cytometry based screening for binding to CoV S protein expressed on mammalian cells ExpiCHO cells were transfected with S protein of SARS-CoV-2, SARS-CoV and MERS-CoV, or with an empty plasmid as a negative control. The monoclonal antibodies were then tested by flow-cytometry at 10 µg/ml for their ability to stain ExpiCHO cells expressing the S protein of 2019-nCoV, SARS-CoV, MERS-CoV or Mock cell transfectants. Transient expression of recombinant SARS-CoV-2 protein The full-length S gene of SARS-CoV-2 strain (2019-nCoV-S) isolate BetaCoV/Wuhan-Hu-1/2019 (accession number MN908947) was codon optimized for human cell expression and cloned into the phCMV1 expression vector (Genlantis). Expi-CHO cells were transiently transfected with phCMV1-SARS-CoV-2-S, phCMV1- MERS-CoV-S (London1/2012), SARS-spike_pcDNA.3 (strain SARS) or the empty phCMV1 (Mock) using Expifectamine CHO Enhancer. Two days after transfection, cells were collected, fixed, or fixed and permeabilized with saponin for immunostaining with a panel of monoclonal antibodies reactive to SARS-CoV Receptor Binding Domain (RBD). An Alexa647-labelled secondary antibody anti-human IgG Fc was used for detection. Binding of antibodies to transfected cells was analyzed by flow- cytometry using a ZE5 Cell Analyzer (Biorard) and FlowJo software (TreeStar). Positive binding was defined by differential staining of CoV-S-transfectants versus mock-transfectants.
Competition experiments using Octet (BLI, biolayer interferometry) Unless otherwise indicated herein, anti-His sensors (BIOSENSOR ANTI- PENTA-HIS (HIS1K)) were used to immobilize the S1 subunit protein of SARS-CoV (Sino Biological Europe GmbH). Sensors were hydrated for 10 min with Kinetics Buffer (KB; 0.01% endotoxin-free BSA, 0.002Λ Tween-20, 0.005% NaN3 in PBS). SARS-CoV S1 subunit protein was then loaded for 8 min at a concentration of 10 µg/ml in KB. Antibodies were associated for 6 min at 15 µg/ml for full length mAbs nCoV-10 and nCov-6 mAbs or 5 µg/ml for Fab nCoV-4, and in a subsequent experiment comprising nCoV-1 all at 10 µg/ml. Competing antibodies were then associated at the same concentration for additional 6 mins. Competition experiments using Octet (BLI, biolayer interferometry) For ACE2 competition experiments, ACE2-His (Bio-Techne AG) was loaded for 30 minutes at 5 µg/ml in KB onto anti-HIS (HIS2) biosensors (Molecular Devices- ForteBio). SARS-CoV-1 RBD-rabbitFc or SARS-CoV-2 RBD-mouseFc (Sino Biological Europe GmbH) at 1 µg/ml was associated for 15 minutes, after a preincubation with or without antibody (30 µg/ml, 30 minutes). Dissociation was monitored for 5 minutes. Affinity determination using Octet (BLI, biolayer interferometry) For KD determination of full-length antibodies, protein A biosensors (Pall ForteBio) were used to immobilize recombinant antibodies at 2.7 μg/ml for 1 minute, after a hydration step for 10 minutes with Kinetics Buffer. Association curves were recorded for 5min by incubating the antibody-coated sensors with different concentration of SARS-CoV-1 RBD (Sino Biological) or SARS-CoV-2 RBD (produced in house; residues 331-550 of spike from BetaCoV/Wuhan-Hu-1/2019, accession number MN908947). Highest RBD concentration tested was 10ug/ml, then 1:2.5 serially diluted. Dissociation was recorded for 9min by moving the sensors to wells containing KB. KD values were calculated using a global fit model (Octet). Octet Red96 (ForteBio) equipment was used.
For KD determination of full-length antibodies compared to Fab fragments, His- tagged RBD of SARS-CoV-1 or SARS-CoV-2 were loaded at 3 µg/ml in KB for 15 minutes onto anti-HIS (HIS2) biosensors (Molecular Devices, ForteBio). Association of full-length antibody and Fab was performed in KB at 15 ug/ml and 5 ug/ml respectively for 5 minutes. Dissociation in KB was measured for 10min. ELISA binding The reactivities of mAbs with SARS-CoV Spike S1 Subunit Protein (strain WH20) protein were determined by enzyme-linked immunosorbent assays (ELISA). Briefly, 96-well plates were coated with 3 µg/ml of recombinant SARS-CoV Spike S1 Subunit Protein (Sino. Biological). Wells were washed and blocked with PBS+1%BSA for 1 h at room temperature and were then incubated with serially diluted mAbs for 1 h at room temperature. Bound mAbs were detected by incubating alkaline phosphatase- conjugated goat anti-human IgG (Southern Biotechnology: 2040-04) for 1 h at room temperature and were developed by 1 mg/ml p-nitrophenylphosphate substrate in 0.1 M glycine buffer (pH 10.4) for 30 min at room temperature. The optical density (OD) values were measured at a wavelength of 405 nm in an ELISA reader (Powerwave 340/96 spectrophotometer, BioTek). Neutralization assay Unless otherwise indicated, Murine leukemia virus (MLV) pseudotyped with SARS-CoV-2 Spike protein (SARS-CoV-2pp) or SARS-CoV-1 Spike protein (SARS- CoV-1pp) were used. DBT cells stably transfected with ACE2 (DBT-ACE2) were used as target cells. SARS-CoV-2pp or SARS-CoV-1pp was activated with trypsin TPCK at 10ug/ml. Activated SARS-CoV-2pp or SARS-CoV-1pp was added to a dilution series of antibodies (starting 50ug/ml final concentration per antibody, 3-fold dilution). DBT- ACE2 cells were added to the antibody-virus mixtures and incubated for 48h. Luminescence was measured after aspirating cell culture supernatant and adding steady- GLO substrate (Promega). Unless otherwise indicated, pseudoparticle neutralization assays use a VSV- based luciferase reporter pseudotyping system (Kerafast). VSV pseudoparticles and
antibody are mixed in DMEM and allowed to incubate for 30 minutes at 37C. The infection mixture is then allowed to incubate with Vero E6 cells for 1h at 37C, followed by the addition of DMEM with Pen-Strep and 10% FBS (infection mixture is not removed). The cells are incubated at 37C for 18-24 hours. Luciferase is measured using an Ensight Plate Reader (Perkin Elmer) after the addition of Bio-Glo reagent (Promega). SPR single-cycle kinetics SPR experiments were carried out with a Biacore T200 instrument using a single-cycle kinetics approach. S309 IgG was captured on the surface and increasing concentrations of purified SARS-CoV-2 RBD, either glycosylated or deglycosylated, were injected. Association and dissociation kinetics were monitored and fit to a binding model to determine affinity. Expression of recombinant antibodies Recombinant antibodies were expressed in ExpiCHO cells transiently co- transfected with plasmids expressing the heavy and light chain as previously described. (Stettler et al. (2016). Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection. Science, 353(6301), 823–826) Monoclonal antibodies S303, S304, S306, S309, S310, and S315 were expressed as rIgG-MLNS antibodies. The MLNS mutation confers a longer half-life in vivo. (Zalevsky et al. (2010) Enhanced antibody half-life improves in vivo activity. Nature Biotechnology, 28(2), 157–159) Sequence alignment SARS-CoV-2 genomics sequences were downloaded from GISAID on March 29th 2020, using the “complete (>29,000 bp)” and “low coverage exclusion” filters. Bat and pangolin sequences were removed to yield human-only sequences. The spike ORF was localized by performing reference protein (YP_009724390.1)-genome alignments with GeneWise2. Incomplete matches and indel-containing ORFs were rescued and included in downstream analysis. Nucleotide sequences were translated in silico using seqkit. Sequences with more than 10% undetermined aminoacids (due to N basecalls) were removed. Multiple sequence alignment was performed using MAFFT.
Variants were determined by comparison of aligned sequences (n=2,229) to the reference sequence using the R/Bioconductor package Biostrings. A similar strategy was used to extract and translate spike protein sequences from SARS-CoV genomes sourced from ViPR (search criteria: SARS-related coronavirus, full-length genomes, human host, deposited before December 2019 to exclude SARS-CoV-2, n=53). Sourced SARS-CoV genome sequences comprised all the major published strains, such as Urbani, Tor2, TW1, P2, Frankfurt1, among others. Pangolin sequences as shown by Tsan-Yuk Lam et al were sourced from GISAID. Bat sequences from the three clades of Sarbecoviruses as shown by Lu et al (Lancet 2020) were sourced from Genbank. Civet and racoon dog sequences were similarly sourced from Genbank. CryoEM sample preparation and data collection 3 μL of SARS-CoV-2 S at 1.6 mg/mL was mixed with 0.45 μL of S309 Fab at 7.4 mg/mL for 1 min at room temperature before application onto a freshly glow discharged 1.2/1.3 UltraFoil grid (300 mesh). Plunge freezing used a vitrobot MarkIV (ThermoFisher Scientific) using a blot force of 0 and 6.5 second blot time at 100% humidity and 25°C. Data were acquired using the Leginon software 45 to control an FEI Titan Krios transmission electron microscope operated at 300 kV and equipped with a Gatan K2 Summit direct detector and Gatan Quantum GIF energy filter, operated in zero-loss mode with a slit width of 20 eV. Automated data collection was carried out using Leginon at a nominal magnification of 130,000x with a pixel size of 0.525 Å with tilt angles ranging between 20˚ and 50˚, as previously described. The dose rate was adjusted to 8 counts/pixel/s, and each movie was acquired in super-resolution mode fractionated in 50 frames of 200 ms.3,900 micrographs were collected in a single session with a defocus range comprised between 1.0 and 3.0 μm. CryoEM data processing Movie frame alignment, estimation of the microscope contrast-transfer function parameters, particle picking and extraction were carried out using Warp 47. Particle images were extracted with a box size of 800 binned to 400 yielding a pixel size of 1.05 Å. For each data set, two rounds of reference-free 2D classification were performed using cryoSPARC 48 to select well-defined particle images. Subsequently, two rounds
of 3D classification with 50 iterations each (angular sampling 7.5˚ for 25 iterations and 1.8˚ with local search for 25 iterations), using our previously reported closed SARS- CoV-2 S structure as initial model, were carried out using Relion 49 without imposing symmetry to separate distinct SARS-CoV-2 S conformations. 3D refinements were carried out using non-uniform refinement along with per-particle defocus refinement in cryoSPARC48. Reported resolutions are based on the gold-standard Fourier shell correlation (FSC) of 0.143 criterion and Fourier shell correlation curves were corrected for the effects of soft masking by high-resolution noise substitution. CryoEM model building and analysis UCSF Chimera and Coot were used to fit atomic models (PDB 6VXX and PDB 6VYB) into the cryoEM maps. The Fab was subsequently manually built using Coot. N-linked glycans were hand-built into the density where visible and the models were refined and relaxed using Rosetta. Glycan refinement relied on a dedicated Rosetta protocol, which uses physically realistic geometries based on prior knowledge of saccharide chemical properties, and was aided by using both sharpened and unsharpened maps. Models were analyzed using MolProbity, EMringer, Phenix and privateer to validate the stereochemistry of both the protein and glycan components. Figures were generated using UCSF ChimeraX. Crystallization and X-ray structure determination of Fab S309 Fab S309 crystals were grown in hanging drop set up with a mosquito at 20°C using 150 nL protein solution in Tris HCl pH 8.0, 150 mM NaCl and 150nL mother liquor solution containing 1.1 M Sodium Malonate, 0.1 M HEPES, pH 7.0 and 0.5% (w/v) Jeffamine ED-2001. Crystals were cryo-protected using the mother liquor solution supplemented with 30% glycerol. The dataset was collected at ALS beamline 5.0.2 and processed to 3.3 Å resolution in space group P41212 using mosflm and Aimless. The structure of Fab S309 was solved by molecular replacement using Phaser and homology models as search models. The coordinates were improved and completed using Coot and refined with REFMAC5. The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent
applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet, including U.S. Provisional Patent Application No.63/005,204, filed on April 3, 2020, U.S. Provisional Patent Application No.63/023,861, filed on May 12, 2020, U.S. Provisional Patent Application No.63/025,927, filed on May 15, 2020, and U.S. Provisional Patent Application No.63/034,194, filed on June 3, 2020, are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, applications and publications to provide yet further embodiments. These and other changes can be made to the embodiments in light of the above- detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.
Claims
CLAIMS What is claimed is: 1. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD) when the RBD is in an open conformation and/or when the RBD is in a closed conformation. 2. The antibody or antigen-binding fragment of claim 1, wherein the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein RBD is in an open conformation, and when the RBD is in a closed conformation. 3. The antibody or antigen-binding fragment of claim 1 or 2, wherein the antibody or antigen-binding fragment is capable of binding to the RBD when the SARS-CoV-2 surface glycoprotein is comprised in a trimer thereof, wherein, optionally, each surface glycoprotein of the trimer can be simultaneously bound to a separate antibody or antigen-binding fragment of claim 1 or claim 2. 4. The antibody or antigen-binding fragment of any one of claims 1-3, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein RBD of a SARS coronavirus and/or of another sarbecovirus that is not SARS-CoV-2. 5. The antibody or antigen-binding fragment of any one of claims 1-4, wherein the SARS-CoV-2 surface glycoprotein is in prefusion conformation. 6. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD), wherein the binding comprises contacting one or more amino acid residues of the RBD that are different from the amino acid residues of the RBD that contact a human ACE2
when the SARS CoV-2 surface glycoprotein is bound to the human ACE2, wherein, optionally, the antibody or antigen-binding fragment does not compete with human ACE2 for binding to the RBD. 7. The antibody or antigen-binding fragment of claim 6, wherein binding of the antibody or antigen-binding fragment to the RBD does not comprise contacting an RBD amino acid residue that contacts a human ACE2 when the surface glycoprotein is bound to the human ACE2. 8. An antibody, or an antigen-binding fragment thereof, that is capable of binding to a SARS-CoV-2 surface glycoprotein receptor binding domain (RBD), wherein the binding to the RBD comprises contacting any one or more of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, D442, K444, R509, C336, and K444 according to SEQ ID NO.:165. 9. The antibody or antigen-binding fragment of any one of claims 1-8, wherein binding of the antibody or antigen-binding fragment to the RBD comprises contacting amino acid N343 according to SEQ ID NO.:165, wherein, optionally, the N343 amino acid residue is glycosylated. 10. The antibody or antigen-binding fragment of any one of claims 1-9, wherein binding of the antibody or antigen-binding fragment to the RBD comprises contacting amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, D442, and R509, and, optionally, one or both of C336 and K444, according to SEQ ID NO.:165. 11. An antibody, or an antigen-binding fragment thereof, that is capable of binding to an epitope in a sarbecovirus surface glycoprotein receptor binding domain
(RBD), wherein the epitope comprises an asparagine amino acid residue that is or that corresponds to amino acid residue N343 of SEQ ID NO.:165, wherein, optionally, the correspondence is determined according to sequence alignment of (i) a sarbecovirus surface glycoprotein or RBD amino acid sequence containing the asparagine amino acid residue with (ii) SEQ ID NO.:165. 12. The antibody or antigen-binding fragment of claim 11, wherein the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 is glycosylated. 13. The antibody or antigen-binding fragment of claim 12, wherein the glycosylation of the asparagine amino acid residue that is or that corresponds to N343 of SEQ ID NO.:165 comprises a fucose. 14. The antibody or antigen-binding fragment of any one of claims 11-13, wherein the asparagine amino acid residue (N) that is or that corresponds to N343 of SEQ ID NO.:165 is comprised in an amino acid sequence N-X-T, X being any amino acid except for P, and preferably being A. 15. The antibody or antigen-binding fragment of claim 14, wherein the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence NITNCLPFGEVFNATR (SEQ ID NO.:234), or a variant thereof having one, two, three, four or five amino acid substitutions, provided that the sequence N-X-T is present, X being any amino acid except for P, and preferably being A. 16. The antibody or antigen-binding fragment of claim 14 or 15, wherein the asparagine amino acid that is or that corresponds to N343 of SEQ ID NO.:165 is N comprised in the amino acid sequence NITNCLPFGEVFNATRFASVYAWNRKRISNCV (SEQ ID NO.:235), or is comprised
in a variant sequence of SEQ ID NO.:235 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions relative to SEQ ID NO.:235, provided that the amino acid sequence N-X-T is present, X being any amino acid except for P, and preferably being A, wherein optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:235 independently comprises a conservative substitution or a non-conservative substitution. 17. An antibody, or an antigen-binding fragment thereof, that is capable of binding in a target region in a SARS coronavirus (e.g., SARS-CoV-2) surface glycoprotein, wherein the target region comprises any one or more (i.e., any 1, any 2, any 3, any 4, any 5, any 6, any 7, any 8, any 9, any 10, any 11, any 12, any 13, any 14, any 15, any 16, any 17, any 18, any 19, any 20, any 21, any 22, or all 23) of amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. 18. The antibody or antigen-binding fragment of claim 17, wherein the target region comprises amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. 19. The antibody or antigen-binding fragment of claim 17, wherein the target region comprises amino acid residues T333, N334, L335, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, K444, and R509, according to SEQ ID NO.:165. 20. The antibody or antigen-binding fragment of claim 17, wherein the target region comprises amino acid residues T333, N334, L335, C336, P337, G339, E340, V341, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, N440, L441, and R509, according to SEQ ID NO.:165.
21. The antibody or antigen-binding fragment of any one of claims 17-20, wherein the target region comprises amino acids T333-C361, according to SEQ ID NO.:165. 22. The antibody or antigen-binding fragment of claim 21, wherin the target region further comprises amino acids N440-K444, according to SEQ ID NO.:165. 23. The antibody or antigen-binding fragment of claim 21 or 22, wherin the target region further comprises amino acid R509, according to SEQ ID NO.:165. 24. The antibody or antigen-binding fragment of any one of claims 1-23, wherein the antibody or antigen-binding fragment is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2 that comprises any one or more of the following mutations relative to SEQ ID NO.:165: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. 25. The antibody or antigen-binding fragment of any one of claims 1-24, which is capable of binding to, and optionally is capable of neutralizing an infection by, a SARS-CoV-2 that comprises any one or more of the following mutations in RBD relative to SEQ ID NO.:165: N440T; N440H; N440Y; N440S; N440I; R346S; R346I; R346T; R346G; N354H; N354G; A344T; A344V; A344P; A344D; R357I; R357K; R357G; D339S; D339V; S359R; S359T; S359G; S359I; K356R; K356E; K356M; K356N; K356T; K356G; V341A; V341P; V341S; E340Q; E340D; L335S; L441F; L441I; L441R; L441V; T345S; T345I; T345N; T333I; T333K; N334D; N334Y; N260S; N360A; N360Y; I332V; R509K; R509T; C336S. 26. The antibody or antigen-binding fragment of claim 24 or claim 25, wherein the antibody or antigen-binding fragment is capable of neutralizing the SARS- CoV-2 infection with a potency that is less than 3-fold reduced as compared to the
potency with which the antibody or antigen-binding fragment neutralizes infection by a SARS-CoV-2 that comprises the amino acid sequence of SEQ ID NO.:165. 27. The antibody or antigen-binding fragment of any one of claims 1-26, which is a IgG, IgA, IgM, IgE, or IgD isotype. 28. The antibody or antigen-binding fragment of any one of claims 1-27, which is an IgG isotype selected from IgG1, IgG2, IgG3, and IgG4. 29. The antibody or antigen-binding fragment of any one of claims 1-28, which is human, humanized, or chimeric. 30. The antibody or antigen-binding fragment of any one of claims 1-29, wherein the antibody, or the antigen-binding fragment, comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab. 31. The antibody or antigen-binding fragment of any one of claims 1-30, wherein the antibody or antigen-binding fragment is a multi-specific antibody or antigen binding fragment. 32. The antibody or antigen-binding fragment of claim 31, wherein the antibody or antigen binding fragment is a bispecific antibody or antigen-binding fragment. 33. The antibody or antigen-binding fragment of any one of claims 1-32, wherein the antibody or antigen-binding fragment further comprises a Fc polypeptide or a fragment thereof.
34. The antibody or antigen-binding fragment of claim 33, wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to a FcRn as compared to a reference Fc polypeptide that does not comprise the mutation; and/or (ii) a mutation that enhances binding to a FcγR as compared to a reference Fc polypeptide that does not comprise the mutation. 35. The antibody or antigen-binding fragment of claim 27, wherein the mutation that enhances binding to a FcRn comprises: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I; Q311I; D376V; T307A; E380A; or any combination thereof. 36. The antibody or antigen-binding fragment of claim 34 or 35, wherein the mutation that enhances binding to FcRn comprises: (i) M428L/N434S; (ii) M252Y/S254T/T256E; (iii) T250Q/M428L; (iv) P257I/Q311I; (v) P257I/N434H; (vi) D376V/N434H; (vii) T307A/E380A/N434A; or (viii) any combination of (i)-(vii). 37. The antibody or antigen-binding fragment of any one of claims 34-36, wherein the mutation that enhances binding to FcRn comprises M428L/N434S. 38. The antibody or antigen-binding fragment of any one of claims 34-37, wherein the mutation that enhances binding to a FcγR comprises S239D; I332E; A330L; G236A; or any combination thereof.
39. The antibody or antigen-binding fragment of any one of claims 34-38, wherein the mutation that enhances binding to a FcγR comprises: or
40. The antibody or antigen-binding fragment of any one of claims 1-39, which comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or which is aglycosylated and/or afucosylated. 41. The antibody or antigen-binding fragment of any one of claims 1-40, comprising a L234A mutation, a L235A mutation, or both. 42. An isolated polynucleotide encoding the antibody or antigen-binding fragment of any one of claims 1-41, or encoding a VH, a heavy chain, a VL, and/or a light chain of the antibody or the antigen-binding fragment. 43. The isolated polynucleotide of claim 42, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA). 44. The isolated polynucleotide of claim 42 or 43, which is codon-optimized for expression in a host cell. 45. A recombinant vector comprising the polynucleotide of any one of claims 42-44.
46. A host cell comprising the polynucleotide of any one of claims 42-44 and/or the vector of claim 45, wherein the polynucleotide is heterologous to the host cell. 47. A human B cell comprising the polynucleotide of any one of claims 42- 44, wherein polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized. 48. A composition comprising: (i) the antibody or antigen-binding fragment of any one of claims 1-41; (ii) the polynucleotide of any one of claims 42-44; (iii) the recombinant vector of claim 45; (iv) the host cell of claim 46; and/or (v) the human B cell of claim 47, and a pharmaceutically acceptable excipient, carrier, or diluent. 49. A method of treating a sarbecovirus infection in a subject, the method comprising administering to the subject an effective amount of: (i) the antibody or antigen-binding fragment of any one of claims 1-41; (ii) the polynucleotide of any one of claims 42-44; (iii) the recombinant vector of claim 45; (iv) the host cell of claim 46; (v) the human B cell of claim 47; and/or (vi) the composition of claim 48. 50. The method of claim 49, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both. 51. A method for in vitro diagnosis of a sarbecovirus infection, the method comprising:
(i) contacting a sample from a subject with an antibody or antigen-binding fragment of any one of claims 1-41; and (ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigen binding fragment, wherein, optionally, the sarbecovirus comprises SARS-CoV-2, SARS-CoV, or both. 52. The method of claim 51, wherein the sample comprises blood isolated from the subject. 53. The antibody or antigen-binding fragment of any one of claims 1-41, the polynucleotide of any one of claims 42-44, the recombinant vector of claim 45, the host cell of claim 46, the human B cell of claim 47, and/or the composition of claim 48, for use in a method of treating or diagnosing a sarbecovirus infection in a subject. 54. The antibody or antigen-binding fragment of any one of claims 1-41, the polynucleotide of any one of claims 42-44, the recombinant vector of claim 45, the host cell of claim 46, the human B cell of claim 47, and/or the composition of claim 48, for use in the manufacture of a medicament for treating a sarbecovirus infection in a subject. 55. The antibody or antigen-binding fragment of any one of claims 1-41, the polynucleotide of any one of claims 42-44, the recombinant vector of claim 45, the host cell of claim 46, the human B cell of claim 47, and/or the composition of claim 48 for use of claim 53 or 54, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both. 56. An immunogenic composition comprising: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid
sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 333-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-361 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or fifteen amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iv) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 440-444 of SEQ ID NO.:165, or a variant of residues 440-444 of SEQ ID NO.:165 comprising one or two amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (v) a polypeptide comprising or consisting essentially of, in N- to C- terminal direction (a) residues 333-361 of SEQ ID NO.:165, in sequence, (b) residues 440-444 or 440-445 of SEQ ID NO.:165, in sequence, and (c) disposed between and connecting (a) and (b), either (1) an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of residues 362-439 of SEQ ID NO.:165 or (2) a linker amino acid sequence having a length of from four to about fifteen, from four to about twenty, or from four to about thirty amino acids; and/or (vi) a polypeptide comprising or consisting essentially of a variant amino acid sequence of residues 333-509 of SEQ ID NO.:165, the variant amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence of residues 333-509 of SEQ ID NO.:165, provided that: (a) amino acid residues 333-337, 339-341, 343-346, 354, 356-361, 440-442, 444, and 509 are as in SEQ ID NO.:165; or (b) one or more of the following amino acid mutations relative to SEQ ID NO.:165 is present in the polypeptide: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. 57. The immunogenic composition of claim 56, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. 58. The immunogenic compostion of claim 56 or 57, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth in SEQ ID NO.:165 and/or does not comprise a full-length SARS- CoV-2 surface glycoprotein. 59. The immunogenic compostion of any one of claims 56-58, wherein the polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168.
60. The immunogenic composition of any one of claims 56-59, further comprising an adjuvant. 61. An isolated polynucleotide that encodes: (i) a polypeptide comprising or consisting essentially of an amino acid sequence comprising residues 333-346 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-346 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (ii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 354-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 354-361 of SEQ ID NO.:165 comprising one, two, three, four, or five, or six amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iii) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 333-361 of SEQ ID NO.:165, or a variant amino acid sequence of residues 333-361 of SEQ ID NO.:165 comprising one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or fifteen amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution; (iv) a polypeptide comprising an amino acid sequence comprising or consisting essentially of residues 440-444 of SEQ ID NO.:165, or a variant of residues 440-444 of SEQ ID NO.:165 comprising one or two amino acid substitutions, wherein, optionally, each amino acid substitution present in the variant sequence of SEQ ID NO.:165 independently comprises a conservative substitution or a non-conservative substitution;
(v) a polypeptide comprising or consisting essentially of, in N- to C- terminal direction (a) residues 333-361 of SEQ ID NO.:165, in sequence, (b) residues 440-444 or 440-445 of SEQ ID NO.:165, in sequence, and (c) disposed between and connecting (a) and (b), either (1) an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of residues 362-439 of SEQ ID NO.:165 or (2) a linker amino acid sequence having a length of from four to about fifteen, from four to about twenty, or from four to about thirty amino acids; and/or (vi) a polypeptide comprising or consisting essentially of a variant amino acid sequence of residues 333-509 of SEQ ID NO.:165, the variant amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence of residues 333-509 of SEQ ID NO.:165, provided that: (a) amino acid residues 333-337, 339-341, 343-346, 354, 356-361, 440-442, 444, and 509 are as in SEQ ID NO.:165; or (b) one or more of the following amino acid mutations relative to SEQ ID NO.:165 is present in the polypeptide: A344S; N440K; N440D; R346K; N354S; N354K; N354D; G339D; S359N; V341I; L335F; P337S; C361T; N334K. 62. The polynucleotide of claim 61, wherein the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise a S1 subunit and a S2 subunit of a SARS-CoV-2 surface glycoprotein. 63. The polynucleotide of claim 61 or 62, wherein the encoded polypeptide of (i), (ii), (iii), (iv), (v), and/or (vi) does not comprise the amino acid sequence set forth
in SEQ ID NO.:165 and/or does not comprise a full-length SARS-CoV-2 surface glycoprotein. 64. The polynucleotide of any one of claims 61-63, wherein the encoded polypeptide of (i), (ii), (iii), (iv), and/or (v) is capable of being bound by an antibody that comprises the VH amino acid sequence set forth in SEQ ID NO.:105 or 113 and the VL amino acid sequence set forth in SEQ ID NO.:168. 65. The polynucleotide of any one of claims 61-64, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA). 66. A composition comprising the polynucleotide of any one of claims 42-49 or 61-65 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform. 67. A recombinant vector comprising the polynucleotide of any one of claims 61-65. 68. A host cell comprising the polynucleotide of any one of claims 61-65 and/or the vector of claim 67. 69. A composition comprising the polynucleotide of any one of claims 61- 65, the vector of claim 67, and/or the host cell of claim 68, and a pharmaceutically acceptable carrier, excipient, or diluent.
70. A method of inducing an immune response in a subject against a sarbecovirus surface glycoprotein, the method comprising administering to the subject an effective amount of (i) the immunogenic composition of any one of claims 56-60, (ii) the polynucleotide of any one of claims 61-65, (iii) the vector of claim 67, (iv) the host cell of claim 68, and/or the composition of claim 66 or 69. 71. The method of claim 70, wherein the sarbecovirus comprises SARS- CoV-2, SARS, or both. 72. The immunogenic composition of any one of claims 56-60, the polynucleotide of any one of claims 61-65, the vector of claim 67, the host cell of claim 67, and/or the composition of claim 66 or 69, for use in a method of inducing an immune response in a subject, wherein, optionally, the immune response comprises an immune response against a sarbecovirus surface glycoprotein. 73. The immunogenic composition of any one of claims 56-60, the polynucleotide of any one of claims 61-65, the vector of claim 67, the host cell of claim 68, and/or the composition of claim 66 or 69, for use the manufacture of a medicament for inducing an immune response in a subject, wherein, optionally, the immune response comprises an immune response against a sarbecovirus surface glycoprotein. 74. The immunogenic composition of any one of claims 56-60, the polynucleotide of any one of claims 61-65, the vector of claim 67, the host cell of claim 68, and/or the composition of claim 66 or 69, for use of claim 72 or 73, wherein the sarbecovirus infection comprises SARS-CoV-2, SARS, or both.
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CN116284359A (en) * | 2023-02-11 | 2023-06-23 | 四川大学 | Broad-spectrum neutralizing nanobody of two targeted novel coronavirus S2 subunit stem helix epitopes and potential application thereof |
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