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Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy.

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Author information

Affiliations

  • 1. Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy.
      Authors
    • Equestre M 1
    (1 author)
  • 2. Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy.
      Authors
    • Marcantonio C 2
    • Centofanti F 2
    • Costantino A 2
    • Taffon S 2
    • Tritarelli E 2
    • Nisini R 2
    • Spada E 2
    • Ciccaglione AR 2
    • Bruni R 2
    (9 authors)
  • 3. Clinical Microbiology Unit, Department of Health Sciences, "Magna Grecia" University, 88100 Catanzaro, Italy.
      Authors
    • Marascio N 3
    • Matera G 3
    • Quirino A 3
    (3 authors)
  • 4. Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy.
      Authors
    • Martina A 4
    • Simeoni M 4
    • Pisani G 4
    (3 authors)
  • 5. Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy.
      Authors
    • Suffredini E 5
    (1 author)
    • Show all (8)

ORCIDs linked to this article

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Microorganisms, 05 Nov 2023, 11(11):2711
https://doi.org/10.3390/microorganisms11112711 PMID: 38004723 

Abstract 

We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.

Full text links 

Read article at publisher's site: https://doi.org/10.3390/microorganisms11112711

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Funding 

Funders who supported this work.

Istituto Superiore di Sanità (1)

Italian Ministry of Health (1)