The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
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
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
Flagged first, then by citations
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
Cited by
Sorted by citations
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
N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.028 · Cited by 901
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., Cantoni, D., Scott, S., Logan, N., Ashraf, S., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01143-7 · Cited by 785
Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies
Planas, D., Bruel, T., Grzelak, L., Guivel-Benhassine, F., Staropoli, I., Porrot, F., Planchais, C., Buchrieser, J., Rajah, M. M., Bishop, E., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01318-5 · Cited by 697
Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021
Galloway, S. E., Paul, P., MacCannell, D., Johansson, M. A., Brooks, J. T., MacNeil, A., Slayton, R. B., Tong, S., Silk, B. J., Armstrong, G. L., et al. (2021) · MMWR Morbidity and Mortality Weekly Report · doi:10.15585/mmwr.mm7003e2 · Cited by 609
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity
Motozono, C., Toyoda, M., Zahradnik, J., Saito, A., Nasser, H., Tan, T. S., Ngare, I., Kimura, I., Uriu, K., Kosugi, Y., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.006 · Cited by 586
Structural biology of SARS-CoV-2 and implications for therapeutic development
Yang, H., & Rao, Z. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00630-8 · Cited by 588
New‐onset autoimmune phenomena post‐COVID‐19 vaccination
Chen, Y., Xu, Z., Wang, P., Li, X., Shuai, Z., Ye, D., & Pan, H. (2021) · Immunology · doi:10.1111/imm.13443 · Cited by 520
Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Greaney, A. J., Starr, T. N., Barnes, C. O., Weisblum, Y., Schmidt, F., Caskey, M., Gaebler, C., Cho, A., Agudelo, M., Finkin, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24435-8 · Cited by 433
SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
McCallum, M., Bassi, J., De Marco, A., Chen, A., Walls, A. C., Di Iulio, J., Tortorici, M. A., Navarro, M.-J., Silacci-Fregni, C., Saliba, C., et al. (2021) · Science · doi:10.1126/science.abi7994 · Cited by 412
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Meng, B., Kemp, S. A., Papa, G., Datir, R. P., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109292 · Cited by 407
SARS-CoV-2 within-host diversity and transmission
Lythgoe, K., Hall, M. D., Luca Ferretti, A., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., Andersson, M. I., Otecko, N. O., Wise, E. L., Moore, N. A., et al. (2021) · Science · doi:10.1126/science.abg0821 · Cited by 389
Broad betacoronavirus neutralization by a stem helix–specific human antibody
Pinto, D., Sauer, M. M., Czudnochowski, N., Low, J. S., Tortorici, M. A., Housley, M. P., Noack, J., Walls, A. C., Bowen, J. E., Guarino, B., et al. (2021) · Science · doi:10.1126/science.abj3321 · Cited by 385
Tackling COVID-19 with neutralizing monoclonal antibodies
Corti, D., Purcell, L. A., Snell, G., & Veesler, D. (2021) · Cell · doi:10.1016/j.cell.2021.05.005 · Cited by 386
Suryadevara, N., Shrihari, S., Gilchuk, P., VanBlargan, L. A., Binshtein, E., Zost, S. J., Nargi, R. S., Sutton, R. E., Winkler, E. S., Chen, E. C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.029 · Cited by 345
Novel SARS-CoV-2 variants: the pandemics within the pandemic
Boehm, E., Kronig, I., Neher, R. A., Eckerle, I., Vetter, P., & Kaiser, L. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.05.022 · Cited by 346
The variant gambit: COVID-19’s next move
Plante, J. A., Mitchell, B. M., Plante, K. S., Debbink, K., Weaver, S. C., & Menachery, V. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.020 · Cited by 328
The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic
Otto, S. P., Day, T., Arino, J., Colijn, C., Dushoff, J. G., Li, M., Mechai, S., Domselaar, G. V., Wu, J., Earn, D. J. D., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.06.049 · Cited by 326
Structural biology of SARS-CoV-2: open the door for novel therapies
Yan, W., Zheng, Y., Zeng, X., He, B., & Cheng, W. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00884-5 · Cited by 314
Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants
McCallum, M., Walls, A. C., Sprouse, K. R., Bowen, J. E., Rosen, L. E., Dang, H. V., Marco, A. D., Franko, N., Tilles, S. W., Logue, J. K., et al. (2021) · Science · doi:10.1126/science.abl8506 · Cited by 279
Emerging SARS-CoV-2 Variants and Impact in Global Vaccination Programs against SARS-CoV-2/COVID-19
Gómez, C. E., Perdiguero, B., & Estéban, M. (2021) · Vaccines · doi:10.3390/vaccines9030243 · Cited by 267
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
A human coronavirus evolves antigenically to escape antibody immunity
Eguia, R., Crawford, K. H. D., Stevens-Ayers, T., Kelnhofer-Millevolte, L., Greninger, A. L., Englund, J. A., Boeckh, M. J., & Bloom, J. D. (2020) · doi:10.1101/2020.12.17.423313 · Cited by 258
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
Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection
Hwang, Y., Lu, R., Su, S.-C., Chiang, P.-Y., Ko, S.-H., Ke, F.-Y., Liang, K.-H., Hsieh, T.-Y., & Wu, H. (2022) · Journal of Biomedical Science · doi:10.1186/s12929-021-00784-w · Cited by 247
Structure of SARS-CoV-2 spike protein
Zhang, J., Xiao, T., Cai, Y., & Chen, B. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.08.010 · Cited by 261
Immune responses to two and three doses of the BNT162b2 mRNA vaccine in adults with solid tumors
Shroff, R. T., Chalasani, P., Wei, R., Pennington, D., Quirk, G., Schoenle, M. V., Peyton, K. L., Uhrlaub, J. L., Ripperger, T. J., Jergović, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01542-z · Cited by 235
Sharma, M., Mindermann, S., Smith, D., Leech, G., Snodin, B., Ahuja, J., Sandbrink, J. B., Monrad, J. T., Altman, G., Dhaliwal, G., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26013-4 · Cited by 232
Emerging SARS-CoV-2 variants of concern and potential intervention approaches
Khateeb, J., Li, Y., & Zhang, H. (2021) · Critical Care · doi:10.1186/s13054-021-03662-x · Cited by 231
Bal, A., Destras, G., Gaymard, A., Stefic, K., Marlet, J., Eymieux, S., Regue, H., Semanas, Q., d’Aubarede, C., Billaud, G., et al. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.3.2100008 · Cited by 212
Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe
Thakur, V., Bhola, S., Thakur, P., Patel, S. K. S., Kulshrestha, S., Ratho, R. K., & Kumar, P. (2022) · Infection · doi:10.1007/s15010-021-01734-2 · Cited by 195
The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines
McLean, G. R., Kamil, J. P., Lee, B., Moore, P. L., Schulz, T. F., Muik, A., Şahin, U., Türeci, Ö., & Pather, S. (2022) · mBio · doi:10.1128/mbio.02979-21 · Cited by 193
A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Dadonaite, B., Crawford, K. H. D., Radford, C. E., Farrell, A. G., Yu, T. C., Hannon, W. W., Zhou, P.-P., Andrabi, R., Burton, D. R., Liu, L., et al. (2023) · Cell · doi:10.1016/j.cell.2023.02.001 · Cited by 186
COVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies
Raman, R., Patel, K. J., & Ranjan, K. (2021) · Biomolecules · doi:10.3390/biom11070993 · Cited by 194
Weigang, S., Fuchs, J., Zimmer, G., Schnepf, D., Kern, L., Beer, J., Luxenburger, H., Ankerhold, J., Falcone, V., Kemming, J. S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26602-3 · Cited by 184
Walls, A. C., Miranda, M. C., Schäfer, A., Pham, M. N., Greaney, A., Arunachalam, P. S., Navarro, M.-J., Tortorici, M. A., Rogers, K., O’Connor, M. A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.015 · Cited by 185
“To understand the impact of the full constellation of mutations present in the S proteins of the aforementioned VOCs, we evaluated RBD-NP- andHexaPro S-elicited serum neutralizing activity against corresponding HIV and VSV pseudotyped variants (D614G GMT RBD-NP HIV 5 3 103 and VSV RBD-NP 6 3 102, respectively, and D61…”
BackgroundInfluentialTruong, T., Ryutov, A., Pandey, U., Yee, R., Goldberg, L., Bhojwani, D., Aguayo-Hiraldo, P. I., Pinsky, B. A., Pekosz, A. S., Shen, L., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103355 · Cited by 177
SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses
Agerer, B., Koblischke, M., Gudipati, V., Montaño-Gutierrez, L. F., Smyth, M., Popa, A., Genger, J.-W., Endler, L., Florian, D. M., Mühlgrabner, V., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abg6461 · Cited by 172
Anti-SARS-CoV-2 antibody responses are attenuated in patients with IBD treated with infliximab
Kennedy, N. A., Goodhand, J., Bewshea, C., Nice, R., Chee, D., Lin, S., Chanchlani, N., Butterworth, J. R., Cooney, R., Croft, N. M., et al. (2021) · Gut · doi:10.1136/gutjnl-2021-324388 · Cited by 199
Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy
Ramesh, S., Govindarajulu, M., Parise, R. S., Neel, L. T., Shankar, T., Patel, S., Lowery, P., Smith, F., Dhanasekaran, M., & Moore, T. (2021) · Vaccines · doi:10.3390/vaccines9101195 · Cited by 156
SARS-CoV-2 one year on: evidence for ongoing viral adaptation
Peacock, T. P., Penrice-Randal, R., Hiscox, J. A., & Barclay, W. (2021) · Journal of General Virology · doi:10.1099/jgv.0.001584 · Cited by 155
Anti-SARS-CoV-2 antibody responses are attenuated in patients with IBD treated with infliximab.
Kennedy, N. A., Goodhand, J., Bewshea, C., Nice, R., Chee, D., Lin, S., Chanchlani, N., Butterworth, J. R., Cooney, R. M., Croft, N. M., et al. (2021) · Figshare · doi:10.17863/cam.66211 · Cited by 153
Prevalence of persistent SARS-CoV-2 in a large community surveillance study
Ghafari, M., Hall, M. D., Golubchik, T., Ayoubkhani, D., House, T., MacIntyre-Cockett, G., Fryer, H. R., Thomson, L., Nurtay, A., Kemp, S. A., et al. (2024) · Nature · doi:10.1038/s41586-024-07029-4 · Cited by 161
Graham, C., Seow, J., Huettner, I., Khan, H., Kouphou, N., Acors, S., Winstone, H., Pickering, S., Galão, R. P., Dupont, L., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.03.023 · Cited by 155
Focosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 150
Antibody-mediated neutralization of SARS-CoV-2
Gruell, H., Vanshylla, K., Weber, T., Barnes, C. O., Kreer, C., & Klein, F. (2022) · Immunity · doi:10.1016/j.immuni.2022.05.005 · Cited by 150
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK
Hill, V., du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., Ellaby, N. A. F., Gallagher, E., Groves, N., Jackson, B., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac080 · Cited by 143
From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants
PAPANIKOLAOU, V. S., Chrysovergis, A., Ragos, V., Tsiambas, E., Katsinis, S., Manoli, A., Papouliakos, S. M., Roukas, D., Mastronikolis, S. N., Peschos, D., et al. (2022) · Gene · doi:10.1016/j.gene.2021.146134 · Cited by 149
Evolutionary trajectory of SARS-CoV-2 and emerging variants
Singh, J., Pandit, P., McArthur, A. G., Banerjee, A., & Mossman, K. L. (2021) · Virology Journal · doi:10.1186/s12985-021-01633-w · Cited by 149
Scientific rationale for developing potent RBD-based vaccines targeting COVID-19
Kleanthous, H., Silverman, J. M., Makar, K. W., Yoon, I.-K., Jackson, N. M., & Vaughn, D. W. (2021) · npj Vaccines · doi:10.1038/s41541-021-00393-6 · Cited by 139
Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
Sun, C., Xie, C., Bu, G., Zhong, L., & Zeng, M. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01039-2 · Cited by 149
SARS-CoV-2 in immunocompromised individuals
DeWolf, S., Laracy, J. C., Perales, M., Kamboj, M., van den Brink, M. R. M., & Vardhana, S. A. (2022) · Immunity · doi:10.1016/j.immuni.2022.09.006 · Cited by 143
SARS-CoV-2 immune evasion by variant B.1.427/B.1.429Preprint
McCallum, M., Bassi, J., Marco, A. D., Chen, A., Walls, A. C., di Iulio, J., Tortorici, M. A., Navarro, M.-J., Silacci-Fregni, C., Saliba, C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.31.437925 · Cited by 128
Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants
Mittal, A., Khattri, A., & Verma, V. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010260 · Cited by 124
Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike
Tong, P., Gautam, A. K., Windsor, I. W., Travers, M. E., Chen, Y., Garcia, N., Whiteman, N. B., McKay, L. G. A., Storm, N., Malsick, L. E., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.025 · Cited by 114
Self-citationEmerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis
Thye, A. Y.-K., Law, J. W., Pusparajah, P., Letchumanan, V., Chan, K., & Lee, L. (2021) · Biomedicines · doi:10.3390/biomedicines9101303 · Cited by 121
SARS‐CoV‐2 Omicron variant: Immune escape and vaccine development
Ao, D., Lan, T., He, X., Liu, J., Chen, L., Baptista‐Hon, D. T., Zhang, K., & Wei, X. (2022) · MedComm · doi:10.1002/mco2.126 · Cited by 122
Beaudoin-Bussières, G., Chen, Y., Ullah, I., Prévost, J., Tolbert, W. D., Symmes, K., Ding, S., Benlarbi, M., Gong, S. Y., Tauzin, A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110368 · Cited by 121
Recurrent SARS-CoV-2 mutations in immunodeficient patients
Wilkinson, S., Richter, A., Casey, A., Osman, H. K. E., Mirza, J. D., Stockton, J., Quick, J., Ratcliffe, L., Sparks, N., Cumley, N., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac050 · Cited by 120
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Chaguza, C., Hahn, A. M., Petrone, M. E., Zhou, S., Ferguson, D. J. P., Breban, M. I., Pham, K., Peña-Hernández, M. A., Castaldi, C., Hill, V., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.100943 · Cited by 123
Zhang, S., Huang, W., Ren, L., Ju, X., Gong, M., Rao, J. Y., Sun, L., Li, P., Ding, Q., Wang, J., et al. (2021) · Cell Research · doi:10.1038/s41422-021-00581-y · Cited by 119
Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity
Mengist, H. M., Kombe, A. J. K., Mekonnen, D. S., Abebaw, A., Getachew, M., & Jin, T. (2021) · Seminars in Immunology · doi:10.1016/j.smim.2021.101533 · Cited by 115
SARS-CoV-2 vaccines: a triumph of science and collaboration
Golob, J. L., Lugogo, N. L., Lauring, A. S., & Lok, A. S.-F. (2021) · JCI Insight · doi:10.1172/jci.insight.149187 · Cited by 113
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens
Fischer, W., Giorgi, E. E., Chakraborty, S., Nguyen, K., Tanmoy Bhattacharya, A., Theiler, J. P., Goloboff, P. A., Yoon, H., Abfalterer, W., Foley, B. T., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.05.012 · Cited by 109
Dupont, L., Snell, L. B., Graham, C., Seow, J., Merrick, B., Lechmere, T., Maguire, T. J. A., Hallett, S. R., Pickering, S., Charalampous, T., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00974-0 · Cited by 102
COVID-19: Challenges of Viral Variants
Jacobs, J. L., Haidar, G., & Mellors, J. W. (2022) · Annual Review of Medicine · doi:10.1146/annurev-med-042921-020956 · Cited by 105
Self-citationSonnleitner, S. T., Prelog, M., Sonnleitner, S., Hinterbichler, E., Halbfurter, H., Kopecky, D. B. C., Almanzar, G., Koblmüller, S., Sturmbauer, C., Feist, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30163-4 · Cited by 107
The global epidemic of SARS‐CoV‐2 variants and their mutational immune escape
Tian, D., Sun, Y., Zhou, J., & Ye, Q. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27376 · Cited by 106
Rapid and Parallel Adaptive Mutations in Spike S1 Drive Clade Success in SARS-CoV-2
Kistler, K. E., Huddleston, J., & Bedford, T. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.018 · Cited by 102
The Biological Functions and Clinical Significance of SARS-CoV-2 Variants of Corcern
Akkız, H. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.849217 · Cited by 102
SARS-CoV-2 Evolution and Immune Escape in Immunocompromised Patients
Scherer, E. M., Babiker, A., Adelman, M. W., Allman, B. E., Key, A., Kleinhenz, J., Langsjoen, R. M., Nguyen, P.-V., Onyechi, I., Sherman, J. D., et al. (2022) · New England Journal of Medicine · doi:10.1056/nejmc2202861 · Cited by 94
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infectionPreprint
Karim, F., Moosa, M.-Y. S., Gosnell, B., Cele, S., Giandhari, J., Pillay, S., Tegally, H., Wilkinson, E., San, J., Msomi, N., et al. (2021) · medRxiv · doi:10.1101/2021.06.03.21258228 · Cited by 105
Radvák, P., Kwon, H., Košíková, M., Ortega‐Rodriguez, U., Xiang, R., Phue, J., Shen, R., Rozzelle, J., Kapoor, N., Rabara, T. R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26803-w · Cited by 95
Evolutionary Landscapes of Host-Virus Arms Races
Tenthorey, J. L., Emerman, M., & Malik, H. S. (2022) · Annual Review of Immunology · doi:10.1146/annurev-immunol-072621-084422 · Cited by 102
Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma
Borges, V., Isidro, J., Cunha, M., Cochicho, D., Martins, L., Banha, L., Figueiredo, M., Rebelo, L., Trindade, M. C., Duarte, S., et al. (2021) · mSphere · doi:10.1128/msphere.00244-21 · Cited by 97
Chen, L., Zody, M. C., Germanio, C. D., Martinelli, R., Mediavilla, J. R., Cunningham, M. H., Composto, K., Chow, K. F., Kordalewska, M., Corvelo, A., et al. (2021) · mSphere · doi:10.1128/msphere.00480-21 · Cited by 92
Mlcochova, P., Kemp, S., Dhar, M. S., Papa, G., Meng, B., Mishra, S., Whittaker, C., Mellan, T., Ferreira, I., Datir, R., et al. (2021) · doi:10.1101/2021.05.08.443253 · Cited by 90
Newman, J., Thakur, N., Peacock, T. P., Bialy, D., Elrefaey, A. M. E., Bogaardt, C., Horton, D. L., Ho, S., Kankeyan, T., Carr, C., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01163-3 · Cited by 85
Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., Gasparo, R. D., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.ade0958 · Cited by 88
Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda
Acevedo, M. L., Alonso-Palomares, L., Bustamante, A., Gaggero, A., Paredes, F., Cortés, C. P., Valiente-Echeverría, F., & Soto-Rifo, R. (2021) · doi:10.1101/2021.06.28.21259673 · Cited by 99
Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain
Smith, K. N., Clark, S. A., Shankar, S., Pan, J., Clark, L. E., Yang, P., Coscia, A., McKay, L. G. A., Varnum, H., Brusic, V., et al. (2022) · Science · doi:10.1126/science.abl6251 · Cited by 77
Tackling COVID-19 with neutralizing monoclonal antibodies
Corti, D., Purcell, L. A., Snell, G., & Veesler, D. (2021) · Cell · doi:10.1016/j.cell.2021.07.027 · Cited by 78
“However, this may not necessarily apply to acute viral infections and be a consideration in the treatment of prolonged infections in immunocompromised individuals, such as has been observed with COVID-19 (Avanzato et al., 2020; Choi et al., 2020; Kemp et al., 2021; McCarthy et al., 2021).”
One year of SARS-CoV-2 evolution
Wu, A., Wang, L., Zhou, H., Ji, C., Xia, S., Cao, Y., Meng, J., Ding, X. L., Gold, S., Jiang, T., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.017 · Cited by 73
An early warning system for emerging SARS-CoV-2 variants
Subissi, L., von Gottberg, A., Thukral, L., Worp, N., Munnink, B. B. O., Rathore, S., Abu-Raddad, L. J., Aguilera, X., Alm, E., Archer, B. N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01836-w · Cited by 79
Organ-specific genome diversity of replication-competent SARS-CoV-2
Cleemput, J. V., van Snippenberg, W., Lambrechts, L., Dendooven, A., D’Onofrio, V., Couck, L., Trypsteen, W., Vanrusselt, J., Theuns, S., Vereecke, N., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26884-7 · Cited by 77
Brown, J. C., Goldhill, D. H., Zhou, J., Peacock, T. P., Frise, R., Goonawardane, N., Baillon, L., Kugathasan, R., Pinto, A., McKay, P. F., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.24.432576 · Cited by 70
Machado, B. A. S., Hodel, K. V. S., Fonseca, L. M. D. S., Pires, V. C., Mascarenhas, L. A. B., Andrade, L. P. C. D. S., Moret, M. A., & Badaró, R. J. D. S. (2022) · Vaccines · doi:10.3390/vaccines10040591 · Cited by 79
Evolution of SARS-CoV-2: Review of Mutations, Role of the Host Immune System
Banoun, H. (2021) · The Nephron journals/Nephron journals · doi:10.1159/000515417 · Cited by 77
Ultraprecise Antigen 10-in-1 Pool Testing by Multiantibodies Transistor Assay
Dai, C., Guo, M., Wu, Y., Cao, B., Wang, X., Wu, Y., Kang, H., Kong, D., Zhu, Z., Ying, T., et al. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c08598 · Cited by 75
Gregory, D. A., Trujillo, M., Rushford, C., Flury, A. G., Kannoly, S., San, K. M., Lyfoung, D. T., Wiseman, R. W., Bromert, K. H., Zhou, M.-Y., et al. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010636 · Cited by 72
SARS-CoV-2: is there neuroinvasion?
McQuaid, C., Brady, M., & Deane, R. (2021) · Fluids and Barriers of the CNS · doi:10.1186/s12987-021-00267-y · Cited by 72
Characterization and functional interrogation of the SARS-CoV-2 RNA interactome
Labeau, A., Fery-Simonian, L., Lefèvre‐Utile, A., Pourcelot, M., Bonnet‐Madin, L., Soumelis, V., Lotteau, V., Vidalain, P., Amara, A., & Meertens, L. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110744 · Cited by 75
Dynamics of SARS-CoV-2 Spike Proteins in Cell Entry: Control Elements in the Amino-Terminal Domains
Qing, E., Kicmal, T., Kumar, B., Hawkins, G. M., Timm, E. C., Perlman, S. M., & Gallagher, T. (2021) · mBio · doi:10.1128/mbio.01590-21 · Cited by 69
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
