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Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Open accessPublished version of a preprint
Abstract
Eluding detection: Influenza viruses evade immunity initiated by previous infection, which explains recurrent influenza pandemics. Unlike the error-prone RNA-dependent RNA polymerase of influenza, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related viruses contain polymerases with proofreading activity. However, proofreading cannot correct deletions, which during a long-term persistent infection could result in the generation of viruses showing alteration of entire stretches of amino acids and the structures they form. McCarthy et al. identified an evolutionary signature defined by prevalent and recurrent deletions in the spike protein of SARS-CoV-2 at four antigenic sites. Deletion variants show human-to-human transmission of viruses with altered antigenicity. Science , this issue p. 1139
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“The recent emergence of B.1.1.7,B.1.351and P.1 marks the beginning of SARS-CoV-2 antigenic drift.”
From Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 (2021) · cites this paper as [45]
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Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
GISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535 · cited 1×
“351 (28), first reported in the United Kingdom 159 and South Africa, have deletions in RDRs 1/2 and 4, respectively.”
BackgroundDetection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
Lam, T. T., Jia, N., Zhang, Y.-W., Shum, M. H.-H., Jiang, J.-F., Zhu, H., Tong, Y., Shi, Y., Ni, X.-B., Liao, Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2169-0 · Cited by 1,877
Piccoli, L., Park, Y.-J., Tortorici, M. A., Czudnochowski, N., Walls, A. C., Beltramello, M., Silacci-Fregni, C., Pinto, D., Rosen, L. E., Bowen, J. E., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.037 · Cited by 1,395
A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2
Chi, X., Yan, R., Zhang, J., Zhang, G., Zhang, Y., Hao, M., Zhang, Z., Fan, P., Dong, Y., Yang, Y., et al. (2020) · Science · doi:10.1126/science.abc6952 · Cited by 1,385
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike
Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., Luo, Y., Chan, J. F.-W., Sahi, V., Figueroa, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2571-7 · Cited by 1,349
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., et al. (2020) · eLife · doi:10.7554/elife.61312 · Cited by 1,308
Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host
Choi, B., Choudhary, M. C., Regan, J., Sparks, J. A., Padera, R. F., Qiu, X., Solomon, I. H., Kuo, H.-H., Boucau, J., Bowman, K., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmc2031364 · Cited by 1,246
Correlates of Protection Against SARS-CoV-2 in Rhesus Macaques
McMahan, K., Yu, J., Mercado, N. B., Loos, C., Tostanoski, L. H., Chandrashekar, A., Liu, J., Peter, L., Atyeo, C., Zhu, A., et al. (2021) · Nature · doi:10.1038/s41586-020-03041-6 · Cited by 1,068
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A., & Robertson, D. L. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0771-4 · Cited by 1,014
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.020 · Cited by 1,006
Barnes, C. O., West, A. P., Huey-Tubman, K. E., Hoffmann, M. A. G., Sharaf, N. G., Hoffman, P. R., Koranda, N., Gristick, H. B., Gaebler, C., Muecksch, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.025 · Cited by 795
Crawford, K. H. D., Eguia, R. T., Dingens, A. S., Loes, A. N., Malone, K. D., Wolf, C. R., Chu, H. Y., Tortorici, M. A., Veesler, D., Murphy, M., et al. (2020) · Viruses · doi:10.3390/v12050513 · Cited by 744
Avanzato, V. A., Matson, M. J., Seifert, S. N., Pryce, R., Williamson, B. N., Anzick, S. L., Barbian, K., Judson, S. D., Fischer, E. R., Martens, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.049 · Cited by 720
Minskaia, E., Hertzig, T., Gorbalenya, A., Campanacci, V., Cambillau, C., Canard, B., & Ziebuhr, J. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0508200103 · Cited by 618
Zhou, H., Chen, X., Hu, T., Li, J., Song, H., Liu, Y., Wang, P., Liu, D., Yang, J., Holmes, E. C., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.05.023 · Cited by 589
Denison, M. R., Graham, R. L., Donaldson, E., Eckerle, L. D., & Baric, R. S. (2011) · RNA Biology · doi:10.4161/rna.8.2.15013 · Cited by 501
Shedding of Viable SARS-CoV-2 after Immunosuppressive Therapy for Cancer
Aydillo, T., Gonzalez-Reiche, A. S., Aslam, S., van de Guchte, A., Khan, Z., Obla, A., Dutta, J., van Bakel, H., Aberg, J. A., García‐Sastre, A., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmc2031670 · Cited by 415
Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes
Voss, W. N., Hou, Y. J., Johnson, N. V., Delidakis, G., Kim, J. E., Javanmardi, K., Horton, A. P., Bartzoka, F., Paresi, C., Tanno, Y., et al. (2021) · Science · doi:10.1126/science.abg5268 · Cited by 253
Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp, S. A., Meng, B., Ferriera, I. A., Datir, R., Harvey, W. T., Papa, G., Lytras, S., Collier, D. A., Mohamed, A., Gallo, G., et al. (2020) · doi:10.1101/2020.12.14.422555 · Cited by 252
Watanabe, A., McCarthy, K. R., Kuraoka, M., Schmidt, A. G., Adachi, Y., Onodera, T., Tonouchi, K., Caradonna, T. M., Bajic, G., Song, S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.048 · Cited by 193
Self-citationKlimstra, W. B., Tilston-Lunel, N. L., Nambulli, S., Boslett, J., McMillen, C. M., Gilliland, T., Dunn, M. D., Sun, C., Wheeler, S. E., Wells, A., et al. (2020) · Journal of General Virology · doi:10.1099/jgv.0.001481 · Cited by 137
Self-citationHensley, M. K., Bain, W., Jacobs, J. L., Nambulli, S., Parikh, U. M., Cillo, A. R., Staines, B., Heaps, A., Sobolewski, M. D., Rennick, L. J., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab072 · Cited by 131
Self-citationZhou, H., Chen, X., Hu, T., Li, J., Song, H., Liu, Y., Wang, P., Liu, D., Yang, J. H., Holmes, E. C., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.09.030 · Cited by 118
Parallel evolution of influenza across multiple spatiotemporal scales
Xue, K. S., Stevens‐Ayers, T., Campbell, A. P., Englund, J. A., Pergam, S. A., Boeckh, M., & Bloom, J. D. (2017) · eLife · doi:10.7554/elife.26875 · Cited by 114
Li, D.-P., Edwards, R., Manne, K., Martinez, D. R., Schäfer, A., Alam, S., Wiehe, K., Lu, X.-Z., Parks, R., Sutherland, L. L., et al. (2021) · bioRxiv · doi:10.1101/2020.12.31.424729 · Cited by 62
Voss, W. N., Hou, Y., Johnson, N., Kim, J. E., Delidakis, G., Horton, A. P., Bartzoka, F., Paresi, C. J., Tanno, Y., Abbasi, S. A., et al. (2020) · bioRxiv · doi:10.1101/2020.12.20.423708 · Cited by 57
McNamara, R. P., Caro‐Vegas, C., Landis, J. T., Moorad, R., Pluta, L., Eason, A. B., Thompson, C. M., Bailey, A., Villamor, F. C. S., Lange, P. T., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108352 · Cited by 39
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Research works printed but not linked: 1
- M. K. Hensley et al . Intractable COVID-19 and Prolonged SARS-CoV-2 Replication in a CAR-T-cell Therapy Recipient: A Case Study. Clin. Infect. Dis. ciab072 (2021).10.1093/cid/ciab07233507235 · DOI
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SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Wang, P., Nair, M. S., Liu, L., Iketani, S., Luo, Y., Guo, Y., Wang, M., Yu, J., Zhang, B., Kwong, P. D., et al. (2021) · Nature · doi:10.1038/s41586-021-03398-2 · Cited by 2,312
Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.003 · Cited by 1,178
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., et al. (2021) · Nature · doi:10.1038/s41586-021-03291-y · Cited by 1,097
The biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009
Metadata
- Authors
- McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P.
- Affiliations
- Boston Children's Hospital (US)
- University of Pittsburgh (US)
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Corresponding author
- McCarthy, Kevin R.
- Duprex, W. Paul
- ORCID
- Venue
- Science
- Published
- 2021-03-12
- Volume
- 371
- Issue
- 6534
- Pages
- 1139-1142
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7971772
- OpenAlex
- W3127143267
- Cited by
- 535
- References
- 33
- Citations by year
- 2026: 12 · 2025: 24 · 2024: 42 · 2023: 66 · 2022: 173 · 2021: 216
- FWCI
- 39.43
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Science (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Science
- Funders
- U.S. Department of Veterans Affairs (IK2 BX004886)
- Richard King Mellon Foundation
- Hillman Foundation
- UPMC Immune Transplant and Therapy Center
- The Center for Vaccine Research
- The University of Pittsburgh
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, spike protein, recurrent deletions, antibody escape, neutralizing antibodies, antigenic evolution, adaptive evolution, immune evasion, viral evolution, zoonotic spillover
- MeSH terms
- COVID-19, SARS-CoV-2, Amino Acid Sequence, Antibodies, Viral, Antigens, Viral, Humans, Protein Conformation, Sequence Deletion, Evolution, Molecular, Amino Acid Substitution, Genetic Drift, Immune Evasion, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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