Expanding repertoire of SARS-CoV-2 deletion mutations contributes to evolution of highly transmissible variants.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
05 01 2023
05 01 2023
Historique:
received:
13
08
2021
accepted:
19
12
2022
entrez:
5
1
2023
pubmed:
6
1
2023
medline:
10
1
2023
Statut:
epublish
Résumé
The emergence of highly transmissible SARS-CoV-2 variants and vaccine breakthrough infections globally mandated the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 2.13 million SARS-CoV-2 genomes from 188 countries/territories (up to June 2021) and performed whole-genome viral sequencing from 102 COVID-19 patients, including 43 vaccine breakthrough infections. We identified 92 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a 3-month window. Deletions in the Spike protein N-terminal domain were highly enriched for these 'surge-associated mutations' (Odds Ratio = 14.19, 95% CI 6.15-32.75, p value = 3.41 × 10
Identifiants
pubmed: 36604461
doi: 10.1038/s41598-022-26646-5
pii: 10.1038/s41598-022-26646-5
pmc: PMC9815892
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Vaccines
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
257Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM144273
Pays : United States
Informations de copyright
© 2023. The Author(s).
Références
COVID-19 map—johns Hopkins Coronavirus resource Center. https://coronavirus.jhu.edu/map.html .
Mallapaty, S. India’s massive COVID surge puzzles scientists. Nature 592, 667–668 (2021).
doi: 10.1038/d41586-021-01059-y
Pawlowski, C. et al. FDA-authorized COVID-19 vaccines are effective per real-world evidence synthesized across a multi-state health system. Med (N Y). 2, 979–992 (2021).
Corchado-Garcia, J. et al. Analysis of the Effectiveness of the Ad26.COV2.S Adenoviral Vector Vaccine for Preventing COVID-19. JAMA Netw. Open. 4, e2132540 (2021).
doi: 10.1001/jamanetworkopen.2021.32540
Dagan, N. et al. BNT162b2 mRNA Covid-19 vaccine in a nationwide mass vaccination setting. N. Engl. J. Med. 384, 1412–1423 (2021).
doi: 10.1056/NEJMoa2101765
Hacisuleyman, E. et al. Vaccine breakthrough infections with SARS-CoV-2 variants. N. Engl. J. Med. 384, 2212–2218 (2021).
doi: 10.1056/NEJMoa2105000
Kustin, T. et al. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals. Nat. Med. 27, 1379–1384 (2021).
doi: 10.1038/s41591-021-01413-7
CDC. SARS-CoV-2 variant classifications and definitions. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html (2021).
COVID-19 Virtual Press conference transcript—10 May 2021. https://www.who.int/publications/m/item/covid-19-virtual-press-conference-transcript---10-may-2021 .
Barnes, C. O. et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 588, 682–687 (2020).
doi: 10.1038/s41586-020-2852-1
Zost, S. J. et al. Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein. Nat. Med. 26, 1422–1427 (2020).
doi: 10.1038/s41591-020-0998-x
Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450–456 (2020).
doi: 10.1038/s41586-020-2571-7
McCallum, M. et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 184, 2332-2347.e16 (2021).
doi: 10.1016/j.cell.2021.03.028
Cerutti, G. et al. Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe 29, 819-833.e7 (2021).
doi: 10.1016/j.chom.2021.03.005
McCarthy, K. R. et al. Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. Science 371, 1139–1142 (2021).
doi: 10.1126/science.abf6950
Shu, Y. & McCauley, J. GISAID: Global initiative on sharing all influenza data—From vision to reality. Euro Surveill. 22, 30494 (2017).
doi: 10.2807/1560-7917.ES.2017.22.13.30494
Ritchie, H. et al. Coronavirus pandemic (COVID-19). Our World in Data (2020).
Chi, X. et al. A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science 369, 650–655 (2020).
doi: 10.1126/science.abc6952
Acevedo, M. L. et al. Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda. bioRxiv https://doi.org/10.1101/2021.06.28.21259673 (2021).
doi: 10.1101/2021.06.28.21259673
Planas, D. et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 596, 276–280 (2021).
doi: 10.1038/s41586-021-03777-9
Edara, V.-V. et al. Infection and vaccine-induced neutralizing-antibody responses to the SARS-CoV-2 B.1.617 variants. N. Engl. J. Med. 385, 664–666 (2021).
doi: 10.1056/NEJMc2107799
Supasa, P. et al. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell 184, 2201-2211.e7 (2021).
doi: 10.1016/j.cell.2021.02.033
Zhou, D. et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Cell 184, 2348-2361.e6 (2021).
doi: 10.1016/j.cell.2021.02.037
Avanzato, V. A. et al. Case study: Prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with cancer. Cell 183, 1901-1912.e9 (2020).
doi: 10.1016/j.cell.2020.10.049
Musicò, A. et al. SARS-CoV-2 epitope mapping on microarrays highlights strong immune-response to N protein region. Vaccines (Basel) 9, 35 (2021).
doi: 10.3390/vaccines9010035
Liu, Y. et al. Neutralizing activity of BNT162b2-elicited serum. N. Engl. J. Med. 384, 1466–1468 (2021).
doi: 10.1056/NEJMc2102017
Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021).
doi: 10.1038/s41586-021-03398-2
Mercatelli, D. & Giorgi, F. M. Geographic and genomic distribution of SARS-CoV-2 mutations. Front. Microbiol. 11, 1800 (2020).
doi: 10.3389/fmicb.2020.01800
Badua, C. L. D. C., Baldo, K. A. T. & Medina, P. M. B. Genomic and proteomic mutation landscapes of SARS-CoV-2. J. Med. Virol. 93, 1702–1721 (2021).
doi: 10.1002/jmv.26548
Liang, C., Rong, L., Russell, R. S. & Wainberg, M. A. Deletion mutagenesis downstream of the 5’ long terminal repeat of human immunodeficiency virus type 1 is compensated for by point mutations in both the U5 region and gag gene. J. Virol. 74, 6251–6261 (2000).
doi: 10.1128/JVI.74.14.6251-6261.2000
Hasell, J. et al. A cross-country database of COVID-19 testing. Sci. Data 7, 345 (2020).
doi: 10.1038/s41597-020-00688-8
COG-UK. https://pangolin.cog-uk.io/ .
Nextclade. https://clades.nextstrain.org/ .