Abstract

Isolation of the CH103 BnAb lineage

The CH505 donor was enrolled in the CHAVI001 acute HIV-1 infection cohort³⁵ approximately 4 weeks after HIV-1 infection (Supplementary Fig. 1) and followed for more than 3 years. Single genome amplification of 53 plasma viral Env gp160 RNAs (5) from 4 weeks after transmission identified a single clade C transmitted/founder (T/F) virus. Serologic analysis demonstrated the development of autologous neutralizing antibodies at 14 weeks, CD4 binding site (CD4bs) antibodies that bound to a recombinant Env protein (resurfaced core, RSC3)⁵ at 53 weeks, and evolution of plasma cross-reactive neutralizing activity from 41–92 weeks after transmission³⁰ (Fig. 1, Supplementary Table 1, Supplementary Fig. 2). The natural variable regions of heavy- (V_HDJ_H) and light-chain (V_LJ_L) gene pairs of antibodies CH103, CH104, CH106 were isolated from peripheral blood mononuclear cells (PBMC) at 136 weeks after transmission by flow sorting of memory B cells that bound RSC3 Env protein^36,5,13 (Fig. 1b). The V_HDJ_H gene of antibody CH105 was similarly isolated, but no V_LJ_L gene was identified from the same cell. Analysis of characteristics of V_HDJ_H (V_H4–59 [posterior probability, PP = 0.99), D3–16 (PP=0.74), J_H4 [PP= 1.00]) and V_LJ_L (Vλ3–1 [PP=1.00], Jλ1 [PP=1.00]) rearrangements in mAbs CH103, CH104, CH105 and CH106 demonstrated that these antibodies were representatives of a single clonal lineage we designated as the CH103 clonal lineage (Fig. 2, Supplementary Table 2).

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Figure 1

Development of neutralization breadth in donor CH505 and isolation of antibodies

a, Shown are HIV-1 viral RNA copies and reactivity of longitudinal plasmas samples with HIV1-1 YU2 core gp120, RSC3 and negative control RSC3Δ371I(ΔRSC3) proteins. b, PBMCs from week 136 was used for sorting CD19⁺, CD20+, IgG⁺, RSC3⁺ and ΔRSC3⁻ memory B cells (0.198%). Individual cells indicated as orange, blue and green dots yielded mAbs CH103, CH104 and CH106, respectively, as identified by index sorting. c, The neutralization potency and breadth of the CH103 antibody are displayed using a neighbor joining tree created with PHYLIP package. The individual tree branches for 196 HIV-1 Envs representing major circulating clades are colored according to the neutralization IC50 values as indicated. d, Cross competition of CH103 binding to YU2 gp120 by the indicated HIV-1 antibodies, and soluble CD4-Ig was determined by ELISA.

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Figure 2

CH103-clonal family with time of appearance, V_HDJ_H mutations, and HIV-1 Env reactivity

Phylogenies of V_HDJ_H (a) and V_LJ_L (b) sequences from sorted single memory B cells and pyrosequencing. The ancestral reconstructions for each were done using the methods described in the Online Methods. The phylogenetic trees themselves were subsequently computed using neighbor joining on the complete set of DNA sequences (see Online Methods) to illustrate the correspondence of sampling date and read abundance in the context of the clonal history. Within time-point V_H monophyletic clades are collapsed to single branches; variant frequencies are indicated on the right. Isolated mature antibodies are red, pyrosequencing-derived sequences are black. The inferred evolutionary paths to observed matured antibodies are bold. c, Maximum-likelihood phylogram showing the CH103 lineage with the inferred intermediates (circles, I1–4, I7 and I8), and percentage mutated V_H sites and timing (blue), indicated. d, Binding affinity (Kd, nM) of antibodies to autologous CH505 (left box) and heterologous B.63521 were measured by surface plasmon reasonance (SPR) (right box).

Neutralization assays using a previously described^5,37 panel of 196 geographically and genetically diverse Env-pseudoviruses representing the major circulated genetic subtypes and circulating recombinant forms demonstrated that CH103 neutralized 55% of viral isolates with a geometric mean IC₅₀ of 4.54 ug/ml among sensitive isolates (Fig. 1c, Supplementary Table 3). ELISA cross-competition analysis demonstrated that CH103 binding to gp120 was competed by known CD4bs ligands such as mAb VRC01 and the chimeric protein CD4-Ig (Fig. 1d); CH103 binding to RSC3 Env was also substantially diminished by gp120 with P363N and Δ371I mutations known to reduce binding of most CD4bs mAbs (Supplementary Fig. 3)^5,30.

Molecular characterization of the CH103 BnAb lineage

The RSC3 probe isolated CH103, CH104, CH105, and CH106 BnAbs by single cell flow sorting. The CH103 clonal lineage was enriched by V_HDJ_H and V_LJ_L sequences identified by pyrosequencing PBMC DNA^34,38 obtained 66 and 140 weeks after transmission and cDNA antibody transcripts⁶ obtained 6, 14, 53, 92 and 144 weeks after transmission. From pyrosequencing of antibody gene transcripts, we found 457 unique heavy and 171 unique light chain clonal members (Figs. 2a, 2b). For comprehensive study, a representative 14 member BnAb pathway was reconstructed from V_HDJ_H sequences (1AH92U, 1AZCET and 1A102R) recovered by pyrosequencing, and V_HDJ_H genes of the inferred intermediate (I) antibodies (I1–I4, I7, I8)^11,16,34 (Kepler, TB, Submitted, 2012) that were paired and expressed with either the UCA or I2 V_LJ_L depending on the genetic distance of the V_HDJ_H to either the UCA or mature antibodies (Fig. 2c, Supplementary Table 2). The mature CH103, CH104 and CH106 antibodies were paired with their natural V_LJ_L. The CH105 natural V_HD_HJ_H isolated from RSC3 memory B cell sorting was paired with the V_LJ_L of I2.

Whereas the V_HDJ_H mutation frequencies calculated by using the method as described in the Online Methods of the published CD4bs BnAbs VRC01, CH31 and NIH45–46 V_HDJ_H are 30–36%^5–7,22,39, the V_HDJ_H frequencies of CH103 lineage CH103, CH104, CH105 and CH106 are 13–17% (Fig. 2c). Additionally, antibodies in CH103 clonal lineage do not contain the large (>3 nt) insertion or deletion mutations common in VRC01-class of BnAbs (1–3) with the exception of the V_LJ_L of CH103 which contained a 3 aa LCDR1 deletion.

It has been proposed that one reason CD4bs BnAbs are difficult to induce is heterologous HIV-1 Envs do not bind their UCAs^7,18,22. We wondered, however, whether the CH505 T/F Env, the initial driving antigen for the CH103 BnAb lineage, would preferentially bind to early CH103 clonal lineage members and the UCA compared to heterologous Envs. Indeed, a heterologous gp120 T/F Env, B.63521, did not bind to the CH103 UCA (Fig. 2d) but did bind to later members of the clonal lineage. Affinity for this heterologous Env increased four orders of magnitude during somatic evolution of the CH103 lineage, with maximal K_d values of 2.4 to 7.0 nM in the mature CH103–CH106 mAbs (Fig. 2d). The CH103 UCA mAb also did not bind other heterologous T/F Envs AE.427299, B.9021 and C.1086 (Supplementary Table 4), confirming lack of heterologous Env binding to CD4bs UCAs. Moreover, the gp120 Env RSC3 protein was also not bound by the CH103 UCA and earlier members of the clonal lineage (Supplementary Fig. 3a) and no binding was seen with RSC3 mutant proteins known to disrupt CD4bs BnAb binding (Supplementary Fig. 3b).

In contrast to heterologous Envs, the CH505 T/F Env gp140 bound well to all of the candidate UCAs (Supplementary Table 5) with the highest UCA affinity of K_d = 37.5 nM. In addition, the CH505 T/F Env gp140 was recognized by all members of the CH103 clonal lineage (Fig. 2d). Whereas affinity to the heterologous T/F Env B.63521 increased by over four orders of magnitude as the CH103 lineage matured, affinity for the CH505 T/F Env increased by no more than ten fold (Fig. 2d). To directly demonstrate Env escape from CH103 lineage members, autologous recombinant gp140 Envs isolated at weeks 30, 53 and 78 post-infection were expressed and compared with the CH505 T/F Env for binding to the BnAb arm of the CH103 clonal lineage (Supplementary Table 6, Supplementary Fig. 4). Escape mutant Envs could be isolated that were progressively less reactive with the CH103 clonal lineage members. Envs isolated from weeks 30, 53 and 78 lost UCA reactivity and only bound intermediate antibodies 3, 2 and 1 as well as BnAbs CH103, CH104, CH105 and CH106 (Supplementary Table 6). In addition, two Env escape mutants from week-78 viruses also lost either strong reactivity to all intermediate antibodies or to all lineage members (Supplementary Table 6).

To quantify CH103 clonal variants from initial generation to induction of broad and potent neutralization, we used pyrosequencing of antibody cDNA transcripts from five time points, weeks 6, 14, 53, 92 and 144 weeks after transmission (Supplementary Table 7). We found two V_HDJ_H chains closely related to, and possibly members of, the CH103 clonal lineage (Fig. 2a, Supplementary Table 7). Moreover, one of these V_HDJ_H when reconstituted in a full IgG1 backbone and expressed with the UCA V_LJ_L weakly bound the CH505 T/F Env gp140 at endpoint titer of 11 ug/ml (Fig. 2a). These reconstructed antibodies were present concomitant with CH505 plasma autologous neutralizing activity at 14 weeks after transmission (Supplementary Fig. 2). Antibodies that bound the CH505 T/F Env were present in plasma as early as 4 weeks after transmission (data not shown). Both CH103 lineage V_HDJ_H and V_LJ_L sequences peaked at week 53 with 230 and 83 unique transcripts, respectively. V_HDJ_H clonal members fell to 46 at week 144, and V_LJ_L members were 76 at week 144.

Polyreactivity is a common trait of BnAbs, suggesting that the generation of some BnAbs may be controlled by tolerance mechanisms^10,21,40. Conversely, polyreactivity can arise during the somatic evolution of B cells in germinal centers as a normal component of B-cell development⁴¹. The CH103 clonal lineage was evaluated for polyreactivity as measured by HEp-2 cell reactivity and binding to a panel of autoantigens¹⁰. While earlier members of the CH103 clonal lineage were not polyreactive by these measures, polyreactivity was acquired in concert with BnAb activity by the intermediate antibody I2, I1, and clonal members, CH103, CH104 and CH106 (Supplementary Figs. 5a, 5b). The BnAbs CH106 and intermediate antibody I1 also demonstrated polyreactivity in protein arrays with specific reactivity to several human autoantigens, including elongation factor-2 kinase and ubiquitin-protein ligase E3A (Supplementary Figs. 5c and 5d).

Structure of CH103 in complex with HIV-1 gp120

Crystals of the complex between Fab CH103 and the ZM176.66 strain of HIV diffracted to 3.25-Å resolution, and molecular replacement identified solutions for Fab CH103 and for the outer domain of gp120 (Fig. 3a). Inspection of the CH103-gp120 crystal lattice (Supplementary Fig. 6) indicated the absence of the gp120 inner domain was likely related to proteolytic degradation of the extended gp120 core to an outer domain fragment. Refinement to R_work/R_free of 19.6%/25.6% (Supplementary Table 8) confirmed a lack of electron density for gp120 residues N terminal to residue Val 255_gp120 or C terminal to Gly472_gp120 (gp120 residues are numbered according to standard HXB2 nomenclature), and no electron density was observed for residues 301–324_gp120 (V3), 398–411_gp120 (V4) and 421–439_gp120 (β20–21). Superposition of the ordered portions of gp120 (gp120 residues are numbered according to standard HXB2 nomenclature) in complex with CH103 with the fully extended core gp120 bound by antibody VRC01⁷ indicated a highly similar structure (Cα-rmsd 1.16 Å) (Fig. 3b). Despite missing portions of core gp120, the entire CH103 epitope appeared to be present in the electron density for the experimentally observed gp120 outer domain.

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Figure 3

Structure of antibody CH103 in complex with the outer domain of HIV-1 gp120 (OD)

a, Overall structure of complex with gp120 polypeptide depicted in red ribbon and CH103 shown as a molecular surface (heavy chain in green and light chain in blue). Major CH103-binding regions on gp120 are colored orange for Loop D, yellow for the CD4-binding site and purple for Loop V5. b, Superposition of OD bound by CH103 (red) and core gp120 bound by VRC01 (gray) with polypeptide shown in ribbon representation. c, CH103 epitope (green) on OD (red) with the initial CD4-binding site superposed (yellow boundaries) in surface representation. d, Sequence alignment of outer domains of the crystallized gp120 shown on the first line and diverse HIV-1 Envs recognized by CH103. Secondary structure elements are labeled above the alignment with gray dashed lines indicating disordered regions. Symbols in yellow or green denote gp120 OD contacts for CD4 and CH103, respectively, with open circles representing main-chain contacts, open circles with rays representing side-chain contact, and filled circles representing both main-chain and side-chain contacts.

The surface bound by CH103 formed an elongated patch with dimensions of ~40 × 10 Å, which stretched across the site of initial CD4 contact on the outer domain of gp120 (Fig. 3c). The gp120 surface recognized by CH103 correlated well with the initial site of CD4 contact; of the residues contacted by CH103, only eight of these residues were not predicted to interact with CD4. CH103 interacted with these residues through side-chain contact with Ser256_gp120 in loop D, main- and side-chain contacts with His364_gp120 and Leu369_gp120 in the CD4-binding loop, and main- and side-chain contacts with Asn463_gp120 and Asp464_gp120 in the V5 loop (Fig. 3d). Notably, residue 463 is a predicted site of N-linked glycosylation in strain ZM176.66 as well as in the autologous CH505 virus, but electron density for an N-linked glycan was not observed. Overall, of the 22 residues that mAb CH103 was observed to contact on gp120, 14 were expected to interact with CD4 (16 of these residues with antibody VRC01), providing a structural basis for the CD4-epitope specificity of CH103 and its broad recognition (Supplementary Table 9).

Residues 1–215_HC on the antibody heavy chain and 1–209_LC showed well defined backbone densities. Overall, CH103 utilizes a CDR H3 dominated mode of interaction, although all six of the complementarity-determining regions (CDRs) interacted with gp120 as well as the light chain framework region 3 (FWR3) (Supplementary Figs. 7a,b, Supplementary Tables 10 and 11). It is important to note that ~40% of the antibody contact surface was altered by somatic mutation, in two regions, in the CDR H2 and in the CDR L1, L2 and FWR3. In particular, residues 56_HC, 50_LC, 51_LC and 66_LC are altered by somatic mutation to form hydrogen bonds with the CD4-binding loop, loop D and loop V5 of gp120. Nevertheless, 88% of the CH103 V_HD_HJ_H and 44% of the VλJλ contact areas were with amino acids unmutated in the CH103 germline, potentially providing an explanation for the robust binding of the T/F Env to the CH103 UCA (Supplementary Figs. 7c, 7d, and Supplementary Table 12).

Evolution of transmitted/founder Env sequences tracks acquisition of BnAb activity

Using single genome amplification and sequencing²⁴ we tracked the evolution of CH505 env genes longitudinally from the T/F virus through 160 weeks post-transmission (Fig. 4, Supplementary Fig. 8). The earliest recurrent mutation in Env, N279K (HIV-1 HXB2 numbering), was found at 4 weeks post-infection, and was in Env loop D in a CH103 contact residue. By week 14 additional mutations in loop D appeared, followed by mutations and insertions in V1 at week 20. Insertions and mutations in the V5 loop began to accumulate by week 30 (Fig. 4). Thus, the T/F virus began to diversify in key CD4 contact regions starting within 3 months of infection (Supplementary Figs. 8, 9). Loop D and V5 mutations were directly in or adjacent to CH103/Env contact residues. Although the V1 region was not included in the CH103-Env co-crystal, the observed V1 CH505 Env mutations were adjacent to contact residues for CD4 and VRC01 so are likely to be relevant. It is also possible that early V1 insertions (Fig. 4) were selected by inhibiting access to the CD4bs in the trimer or that they arose in response to early T cell pressure. CD4 binding-loop mutations were present by week 78. Once regions that could directly impact CH103-lineage binding began to evolve (loop D, V5, the CD4 binding, loop, and possibly V1), they were under sustained positive selective pressure throughout the study period (Fig. 4, Supplementary Figs. 8, 9, Supplementary Table 13).

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Figure 4

Sequence Logo displaying variation in key regions of CH505 Envs

The frequency of each amino acid variant per site is indicated by its height, deletions are indicated by grey bars. The first recurring mutation, N279K, appears at week 4 (open arrow). The timing of BnAb activity development (from Supplementary Fig. 2 and Supplementary Table 1) is on the left. Viral diversification, which precedes acquisition of breadth, is highlighted by vertical arrows to the right of each region. CD4 and CH103 contact residues, and amino acid position numbers based on HIV-1 HXB2, are shown along the base of each Logo column.

Considerable within-sample virus variability was evident in Env regions that could impact CH103-linage antibody binding, and diversification within these regions preceded neutralization breadth. Expanding diversification early in viral evolution (4–22 weeks after transmission) (Supplementary Figs. 8, 9) coincided with autologous NAbs development, consistent with autologous NAb escape mutations. Mutations that accumulated from weeks 41–78 in CH505 Env contact regions immediately preceded development of NAb breadth (Fig 4, Supplementary Figs. 8, 9). By weeks 30–53, extensive within-sample diversity resulted from both point mutations in and around CH103 contact residues, and to multiple insertions and deletions in V1 and V5 (Supplementary Fig. 9). A strong selective pressure seems to have come into play between weeks 30 and 53, perhaps due to autologous neutralization escape, and neutralization breadth developed after this point (Fig. 4, Supplementary Figs 8, 9). Importantly, due to apparent strong positive selective pressure between week 30 and week 53, there was a dramatic shift in the viral population that is evident in the phylogenetic tree, such that only viruses carrying multiple mutations relative to the T/F, particularly in CH103 contact regions, persisted after week 30. This was followed by extreme and increasing within time-point diversification in key epitope regions, beginning at week 53 (Supplementary Fig. 9). Emergence of antibodies with neutralization breadth occurred during this time (Supplementary Fig. 2, Supplementary Table 1). Thus, plasma breadth evolved in the presence of highly diverse forms of the CH103 epitope contact regions (Fig. 4, Supplementary Fig. 2).

To evaluate and compare the immune pressure on amino acids in the region of CH103 and CD4 contacts, we compared the frequency of mutations in evolving T/F sequences of patient CH505 during the first year of infection and in 16 other acutely infected subjects followed over time (Supplementary Fig. 10). The accumulation of mutations in the CH505 virus population was concentrated in regions likely to be associated with escape from the CH103 lineage (Supplementary Fig. 10a), and diversification of these regions was far more extensive during the first six months of infection in CH505 than in other subjects (Supplementary Fig. 10b). However, by one year into their infections, viruses from the other subjects had also begun to acquire mutations in these regions. Thus, the early and continuing accumulation of mutations in CH103 contact regions may have potentiated the early development of neutralizing antibody breadth in patient CH505.

Neutralization of autologous and heterologous viruses and the CH103 lineage

Heterologous BnAb activity was confined to the later members (I3 and later) of the BnAb arm of the CH103 lineage as manifested by their neutralization capacity of pseudoviruses carrying tier 2 Envs A.Q842 and B.BG1168 (Fig. 5a). Similar results were seen with Envs A.Q168, B.JRFL, B.SF162 and C.ZM106 (Supplementary Tables 14 and 15). In contrast, neutralizing activity of clonal lineage members against the autologous T/F Env pseudovirus appeared earlier with measurable neutralization of the CH505 T/F virus by all members of the lineage after the UCA except mAb 1AH92U (Fig. 5a). Thus, within the CH103 lineage, early intermediate antibodies only neutralized the T/F virus, while later intermediate antibodies gained neutralization breadth, indicating evolution of neutralization breadth with affinity maturation, and CH103–CH106 BnAbs evolved from an early autologous neutralizing antibody response. Moreover, the clonal lineage was heterogeneous, with an arm of the lineage represented in Fig. 5a evolving neutralization breadth and another antibody arm capable of mediating only autologous T/F virus neutralization. While some escape viruses are clearly emerging over time (Supplementary Table 4), it is important to point out that, whereas escape mutant viruses are driving BnAb evolution, the BnAbs remained capable of neutralizing the CH505 T/F virus (Fig. 5a). Of note, the earliest mutations in the heavy chain lineage clustered near the contact points with gp120, and these remained fixed throughout the period of study, while mutations that accumulated later tended to be further from the binding site and may be impacting binding less directly (Supplementary Fig. 11). Thus, stimulation of the CH103 BnAbs occurs in a manner to retain reactivity with the core CD4bs epitope present on the T/F Env. One possibility that might explain this is that the footprint of UCA binding contracts to the central core binding site of the CH103 mature antibody. Obtaining a crystal structure of the UCA with the T/F Env should inform this notion. Another possibility is that because affinity maturation is occurring in the presence of highly diverse forms of the CD4bs epitope, antibodies that favor tolerance of variation in and near the epitope are selected instead of those antibodies that acquire increased affinity for particular escape Envs. In both scenarios, persistence of activity to the T/F form and early viral variants would be expected. Fig. 5b and Supplementary Fig. 11 show views of accumulations of mutations or entropy during the parallel evolution of the antibody paratope and the Env epitope bound by mAb CH103.

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Figure 5

Development of neutralization breadth in the CH103-clonal lineage

a, Phylogenetic CH103 clonal lineage tree showing the IC50 (μg/ml) of neutralization of either the autologous T/F (C.CH505), heterologous tier clades A (A.Q842) and B (B.BG1168) viruses as indicated. b, Interplay between evolving virus and developing clonal lineage mapped on to models of CH103-developmental variants and contemporaneous virus. The outer domain of HIV gp120 is depicted in worm representation, with worm thickness and color (white to red) mapping the degree of per-site sequence diversity at each time point. Models of antibody intermediates are shown in cartoon diagram with somatic mutations at each time point highlighted in spheres and colored red for mutations carried over from I8 to mature antibody, cyan for mutations carried over from I4 to mature antibody, green for mutations carried over from I3 to mature antibody, blue for mutations carried over from I2 to mature antibody, orange for mutations carried over from II to mature antibody, magenta for CH103 mutations from I1. Transient mutations that did not carry all the way to mature antibody are colored in deep olive. The antibody (paratope) residues are shown in surface representation and colored by their chemical types as indicated.

Vaccine Implications

In this study, we demonstrate that the binding of a T/F Env to an UCA B cell receptor of a BnAb lineage was responsible for the induction of broad neutralizing antibodies, thus providing a logical starting place for vaccine-induced CD4bs BnAb clonal activation and expansion. Importantly, the number of mutations required to achieve neutralization breadth was reduced in the CH103 lineage compared to most CD4bs BnAbs, although the CH103 lineage had reduced neutralization breadth compared to more mutated CD4bs BnAbs. Thus, this type of BnAb lineage may be less challenging to attempt to recapitulate by vaccination. By tracking viral evolution through early infection we found that intense selection and epitope diversification in the T/F virus preceded the acquisition of NAb breadth in this individual -- thus demonstrating the viral variants associated with development of BnAbs directly from autologous neutralizing antibodies and illuminating a pathway for induction of similar B cell lineages.

These data have implications for understanding the B cell maturation pathways of the CH103 lineage and for replicating similar pathways in a vaccine setting. First, we demonstrate in CH505 that BnAbs were driven by sequential Env evolution beginning as early as 14 weeks after transmission, a time period compatible with induction of this type of BnAb lineage with a vaccine given the correct set of immunogens. Second, whereas heterologous Envs did not bind with UCAs or early intermediate antibodies of this lineage, the CH505 T/F Env bound remarkably well to the CH103 UCA, and subsequent Envs bound with increased affinity to later clonal lineage members. This suggests that immunizations with similar sequences of Env or Env subunits may drive similar lineages. Third, the CH103 lineage is less complicated than those of the VRC01-class of antibodies because antibodies in this lineage has fewer somatic mutations, and no indels, except CH103 V_L has a deletion of 3 amino acid residues in the LCDR1 region. It should be noted as well that our study is in one patient. Nonetheless, in each BnAb patient, analysis of viral evolution should elucidate a similar pathway of evolved Envs that induce BnAb breadth. The observation that rhesus macaques infected with the CCR5-tropic SHIV-AD8 virus frequently develop neutralization breadth⁴² suggests the notion that certain envelopes may be more likely to induce breadth and potency than others.

Polyreactivity to host molecules in the CH103-lineage arose during affinity maturation in the periphery coincident with BnAb activity. This finding is compatible with the hypothesis that BnAbs may be derived from an inherently polyreactive pool of B cells, with polyreactivity providing a neutralization advantage via heteroligation of Env and host molecules^21,43. Alternatively, as CH103 affinity maturation involves adapting to the simultaneous presence of diverse co-circulating forms of the epitope⁴⁴, the selection of antibodies that can interact with extensive escape-generated epitope diversification may be an evolutionary force that also drives incidental acquisition of polyreactivity.

Thus, a candidate vaccine concept could be to use the CH505 T/F Env or Env subunits (to avoid dominant Env non-neutralizing epitopes) to initially activate an appropriate naïve B cell response, followed by boosting with subsequently evolved CH505 Env variants either given in combination to mimic the high diversity observed in vivo during affinity maturation, or in series, using vaccine immunogens specifically selected to trigger the appropriate maturation pathway by high affinity binding to UCA and antibody intermediates¹¹. These data demonstrate the power of studying subjects followed from the transmission event through the development of plasma BnAb activity for concomitant isolation of both T/F viruses and their evolved quasispecies along with the clonal lineage of induced BnAbs. The finding that the T/F Env can be the stimulator of a potent BnAb and bind optimally to that BnAb UCA is a critical insight for vaccine design, and could allow the induction of BnAbs by targeting UCAs and IAs of BnAb clonal lineage trees¹¹.

Methods

Supplementary Material

Acknowledgements

Footnotes

References