A human coronavirus evolves antigenically to escape antibody immunity
Open accessPreprint — published as 10.1371/journal.ppat.1009453
Abstract
There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these “future” viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8–17 years later. The decreased neutralization of “future” viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.
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
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?
Other groups have reported comparable findings with vaccinee and convalescent plasma across various pseudotype and authentic virus assays.
“In addition, similar results have been reported by others using vaccinee and convalescent plasmas and a variety of different pseudotype and authentic virus assays15,31,45–49.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [49]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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 · see citing works
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873 · see citing works
Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine
Polack, F. P., Thomas, S. J., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Perez, J. L., Pérez Marc, G., Moreira, E. D., Zerbini, C., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2034577 · Cited by 14,592 · see citing works
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586 · see citing works
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
Huerta‐Cepas, J., Serra, F., & Peer Bork, B. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw046 · Cited by 2,239 · see citing works
SARS-CoV-2 vaccines in development
Krammer, F. (2020) · Nature · doi:10.1038/s41586-020-2798-3 · Cited by 2,098 · see citing works
Starr, T. N., Greaney, A. J., Hilton, S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.012 · Cited by 1,956 · see citing works
Self-citationIdentification of a new human coronavirus
van der Hoek, L., Pyrć, K., Jebbink, M. F., Vermeulen-Oost, W., Berkhout, R. J. M., Wolthers, K. C., Dillen, P. M. E. W., Kaandorp, J. C., Spaargaren, J., & Berkhout, B. (2004) · Nature Medicine · doi:10.1038/nm1024 · Cited by 1,868 · see citing works
Mapping the Antigenic and Genetic Evolution of Influenza Virus
Smith, D. J., Lapedes, A. S., de Jong, J. C., Bestebroer, T. M., Rimmelzwaan, G. F., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2004) · Science · doi:10.1126/science.1097211 · Cited by 1,868 · see citing works
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Galili, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv428 · Cited by 1,826 · see citing works
Evolution of antibody immunity to SARS-CoV-2
Gaebler, C., Wang, Z., Lorenzi, J. C. C., Muecksch, F., Finkin, S., Tokuyama, M., Cho, A., Jankovic, M., Schaefer-Babajew, D., Oliveira, T. Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03207-w · Cited by 1,674 · see citing works
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 · see citing works
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 · see citing works
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., MUMFORD, J. A., & Holmes, E. C. (2004) · Science · doi:10.1126/science.1090727 · Cited by 1,370 · see citing works
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 · see citing works
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343 · see citing works
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 · see citing works
Sanjuán, R., Nebot, M. R., Chirico, N., Mansky, L. M., & Belshaw, R. D. (2010) · Journal of Virology · doi:10.1128/jvi.00694-10 · Cited by 1,247 · see citing works
Rogers, T. F., Zhao, F., Huang, D., Beutler, N., Burns, A., He, W.-T., Limbo, O., Smith, C., Song, G., Woehl, J., et al. (2020) · Science · doi:10.1126/science.abc7520 · Cited by 1,230 · see citing works
TreeTime: Maximum-likelihood phylodynamic analysis
Sagulenko, P., Puller, V., & Neher, R. A. (2017) · Virus Evolution · doi:10.1093/ve/vex042 · Cited by 1,201 · see citing works
Robust neutralizing antibodies to SARS-CoV-2 infection persist for months
Wajnberg, A., Amanat, F., Firpo, A., Altman, D. R., Bailey, M. J., Mansour, M., McMahon, M., Meade, P., Mendu, D. R., Muellers, K., et al. (2020) · Science · doi:10.1126/science.abd7728 · Cited by 1,195 · see citing works
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 · see citing works
Self-citationTan, C. W., Chia, W. N., Qin, X., Liu, P., Chen, M. I.-C., Tiu, C. K., Hu, Z., Chen, V. C.-W., Young, B. E., Sia, W. R., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0631-z · Cited by 1,162 · see citing works
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147 · see citing works
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 · see citing works
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 · see citing works
Potently neutralizing and protective human antibodies against SARS-CoV-2
Zost, S. J., Gilchuk, P., Case, J. B., Binshtein, E., Chen, R. E., Nkolola, J. P., Schäfer, A., Reidy, J. X., Trivette, A., Nargi, R. S., et al. (2020) · Nature · doi:10.1038/s41586-020-2548-6 · Cited by 1,041 · see citing works
Rapid Decay of Anti–SARS-CoV-2 Antibodies in Persons with Mild Covid-19
Ibarrondo, F. J., Fulcher, J. A., Goodman-Meza, D., Elliott, J., Hofmann, C., Hausner, M. A., Ferbas, K. G., Tobin, N. H., Aldrovandi, G. M., & Yang, O. O. (2020) · New England Journal of Medicine · doi:10.1056/nejmc2025179 · Cited by 1,021 · see citing works
Greaney, A. J., Starr, T. N., Gilchuk, P., Zost, S. J., Binshtein, E., Loes, A. N., Hilton, S. K., Huddleston, J., Eguia, R., Crawford, K. H. D., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.11.007 · Cited by 1,016 · see citing works
Self-citationHuman aminopeptidase N is a receptor for human coronavirus 229E
Yeager, C. L., Ashmun, R. A., Williams, R. K., Cardellichio, C. B., Shapiro, L. H., Look, A. T., & Holmes, K. V. (1992) · Nature · doi:10.1038/357420a0 · Cited by 941 · see citing works
Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers
Lumley, S. F., O’Donnell, D., Stoesser, N. E., Matthews, P. C., Howarth, A., Hatch, S. B., Marsden, B. D., Cox, S., James, T., Warren, F., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2034545 · Cited by 940 · see citing works
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040152 · Cited by 920 · see citing works
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 · see citing works
A New Virus Isolated from the Human Respiratory Tract.
Hamre, D. M., & Procknow, J. J. (1966) · Experimental Biology and Medicine · doi:10.3181/00379727-121-30734 · Cited by 888 · see citing works
Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine
(2021) · New England Journal of Medicine · doi:10.1056/nejmc2036242 · Cited by 831 · see citing works
Hofmann, H., Pyrc, K., van der Hoek, L., Geier, M., Berkhout, B., & Pöhlmann, S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409465102 · Cited by 824 · see citing works
GARD: a genetic algorithm for recombination detection
Pond, S. L. K., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl474 · Cited by 811 · see citing works
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 · see citing works
Structural insights into coronavirus entry
(2019) · Advances in Virus Research · doi:10.1016/bs.aivir.2019.08.002 · Cited by 769 · see citing works
Seasonal coronavirus protective immunity is short-lasting
Edridge, A. W. D., Kaczorowska, J., Hoste, A. C. R., Bakker, M., Klein, M., Loens, K., Jebbink, M. F., Matser, A., Kinsella, C. M., Rueda, P., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1083-1 · Cited by 767 · see citing works
Prospective mapping of viral mutations that escape antibodies used to treat COVID-19
Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. W., Choudhary, M. C., Dingens, A. S., Li, J. Z., & Bloom, J. D. (2021) · Science · doi:10.1126/science.abf9302 · Cited by 743 · see citing works
Self-citationCrawford, 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 727 · see citing works
Self-citationDurability of Responses after SARS-CoV-2 mRNA-1273 Vaccination
Widge, A. T., Rouphael, N. G., Jackson, L. A., Anderson, E. J., Roberts, P. C., Makhene, M., Chappell, J. D., Denison, M. R., Stevens, L. J., Pruijssers, A. J., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmc2032195 · Cited by 722 · see citing works
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Network for Genomic Surveillance in South Africa, Cele, S., COMMIT-KZN Team, Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03471-w · Cited by 651 · see citing works
Functional SARS-CoV-2-Specific Immune Memory Persists after Mild COVID-19
Rodda, L. B., Netland, J., Shehata, L., Pruner, K. B., Morawski, P. A., Thouvenel, C. D., Takehara, K. K., Eggenberger, J., Hemann, E. A., Waterman, H. R., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.029 · Cited by 647 · see citing works
The time course of the immune response to experimental coronavirus infection of man
Callow, K. A., Parry, H. F., Sergeant, M., & Tyrrell, D. A. J. (1990) · Epidemiology and Infection · doi:10.1017/s0950268800048019 · Cited by 598 · see citing works
Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P. (2021) · Science · doi:10.1126/science.abf6950 · Cited by 535 · see citing works
Addetia, A., Crawford, K. H. D., Dingens, A., Zhu, H., Roychoudhury, P., Huang, M.-L., Jerome, K. R., Bloom, J. D., & Greninger, A. L. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.02107-20 · Cited by 525 · see citing works
Self-citationDenison, 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 490 · see citing works
Antibody landscapes after influenza virus infection or vaccination
Fonville, J. M., Wilks, S. H., James, S. L., Fox, A., Ventresca, M., Aban, M., Xue, L., Jones, T. C., H., L. N. M., Thái, P. Q., et al. (2014) · Science · doi:10.1126/science.1256427 · Cited by 475 · see citing works
Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors
Yu, X., Tsibane, T., McGraw, P. A., House, F. S., Keefer, C. J., Hicar, M. D., Tumpey, T. M., Pappas, C., Perrone, L. A., Martinez, O., et al. (2008) · Nature · doi:10.1038/nature07231 · Cited by 448 · see citing works
Couch, R. B., & Kasel, J. A. (1983) · Annual Review of Microbiology · doi:10.1146/annurev.mi.37.100183.002525 · Cited by 426 · see citing works
Integrating influenza antigenic dynamics with molecular evolution
Bedford, T., Suchard, M. A., Lemey, P., Dudas, G., Gregory, V., Hay, A. J., McCauley, J. W., Russell, C. A., Smith, D. J., & Rambaut, A. (2014) · eLife · doi:10.7554/elife.01914 · Cited by 410 · see citing works
Lemey, P., Rambaut, A., Bedford, T., Faria, N. R., Bielejec, F., Baele, G., Russell, C. A., Smith, D. J., Pybus, O. G., Brockmann, D., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1003932 · Cited by 398 · see citing works
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 397 · see citing works
Long term trends in the evolution of H(3) HA1 human influenza type A.
Fitch, W. M., Bush, R. M., Bender, C. A., & Cox, N. J. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.15.7712 · Cited by 394 · see citing works
Hulswit, R. J. G., Lang, Y., Bakkers, M. J. G., Li, W., Li, Z., Schouten, A., Ophorst, B., van Kuppeveld, F. J. M., Boons, G., Bosch, B., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809667116 · Cited by 380 · see citing works
Bertram, S., Dijkman, R., Habjan, M., Heurich, A., Gierer, S., Glowacka, I., Welsch, K., Winkler, M., Schneider, H., Hofmann-Winkler, H., et al. (2013) · Journal of Virology · doi:10.1128/jvi.03372-12 · Cited by 341 · see citing works
Crawford, K. H. D., Dingens, A. S., Eguia, R., Wolf, C. R., Wilcox, N., Logue, J. K., Shuey, K., Casto, A. M., Fiala, B., Wrenn, S., et al. (2021) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiaa618 · Cited by 265 · see citing works
Self-citationDiscordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses
Sandbulte, M. R., Westgeest, K. B., Gao, J., Xu, X., Klimov, A. I., Russell, C. A., Burke, D. F., Smith, D. J., Fouchier, R. A. M., & Eichelberger, M. C. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113801108 · Cited by 264 · see citing works
Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses
Neher, R. A., Bedford, T., Daniels, R. S., Russell, C. A., & Shraiman, B. I. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1525578113 · Cited by 233 · see citing works
The human coronavirus HCoV-229E S-protein structure and receptor binding
Li, Z., Tomlinson, A. C. A., Wong, A. H. M., Zhou, D., Desforges, M., Talbot, P. J., Benlekbir, S., Rubinstein, J. L., & Rini, J. M. (2019) · eLife · doi:10.7554/elife.51230 · Cited by 217 · see citing works
Lee, J. M., Huddleston, J., Doud, M. B., Hooper, K. A., Wu, N. C., Bedford, T., & Bloom, J. D. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806133115 · Cited by 202 · see citing works
Self-citationThe inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
Thyagarajan, B., & Bloom, J. D. (2014) · eLife · doi:10.7554/elife.03300 · Cited by 196 · see citing works
Self-citationA simple protein-based surrogate neutralization assay for SARS-CoV-2
Abe, K. T., Li, Z., Samson, R., Samavarchi‐Tehrani, P., Valcourt, E. J., Wood, H., Budylowski, P., Dupuis, A. P., Girardin, R. C., Rathod, B., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.142362 · Cited by 192 · see citing works
Immune history shapes specificity of pandemic H1N1 influenza antibody responses
Li, Y., Myers, J. L., Bostick, D., Sullivan, C. B., Madara, J. J., Linderman, S. L., Liu, Q., Carter, D. M., Wrammert, J., Esposito, S., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20130212 · Cited by 184 · see citing works
Age-specific differences in the dynamics of protective immunity to influenza
Ranjeva, S. L., Subramanian, R., Fang, V. J., Leung, G. M., Ip, D., Perera, R. A. P. M., Peiris, M. J. S., Cowling, B. J., & Cobey, S. E. (2019) · Nature Communications · doi:10.1038/s41467-019-09652-6 · Cited by 184 · see citing works
A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection
Alsoussi, W. B., Turner, J. S., Case, J. B., Zhao, H., Schmitz, A. J., Zhou, J. Q., Chen, R. E., Lei, T., Rizk, A. A., McIntire, K. M., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.2000583 · Cited by 181 · see citing works
Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses
Nelson, M. I., Simonsen, L., Viboud, C. G., Miller, M. A., & Holmes, E. C. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030131 · Cited by 158 · see citing works
Reed, S. E. (1984) · Journal of Medical Virology · doi:10.1002/jmv.1890130208 · Cited by 147 · see citing works
Zhou, H., Chen, Y., Zhang, S., Niu, P., Qin, K., Jia, W., Huang, B., Zhang, S., Lan, J., Zhang, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10897-4 · Cited by 142 · see citing works
Liu, Z., VanBlargan, L. A., Bloyet, L.-M., Rothlauf, P. W., Chen, R. E., Stumpf, S., Zhao, H., Errico, J. M., Theel, E. S., Liebeskind, M. J., et al. (2020) · doi:10.1101/2020.11.06.372037 · Cited by 135 · see citing works
Protease-Mediated Entry via the Endosome of Human Coronavirus 229E
Kawase, M., Shirato, K., Matsuyama, S., & Taguchi, F. (2008) · Journal of Virology · doi:10.1128/jvi.01933-08 · Cited by 132 · see citing works
Echave, J., & Wilke, C. O. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-033819 · Cited by 131 · see citing works
Callow, K. A. (1985) · Journal of Hygiene · doi:10.1017/s0022172400062410 · Cited by 119 · see citing works
Coronavirus infections in working adults. Eight-year study with 229 E and OC 43.
Hendley, J. O., Fishburne, H. B., & Gwaltney, J. M. (1972) · PubMed · doi:10.1164/arrd.1972.105.5.805 · Cited by 118 · see citing works
Lee, J. M., Eguia, R. T., Zost, S. J., Choudhary, S., Wilson, P. C., Bedford, T., Stevens‐Ayers, T., Boeckh, M., Hurt, A. C., Lakdawala, S. S., et al. (2019) · eLife · doi:10.7554/elife.49324 · Cited by 112 · see citing works
Self-citationReceptor-binding loops in alphacoronavirus adaptation and evolution
Wong, A. H. M., Tomlinson, A. C. A., Zhou, D., Satkunarajah, M., Chen, K., Sharon, C., Desforges, M., Talbot, P. J., & Rini, J. M. (2017) · Nature Communications · doi:10.1038/s41467-017-01706-x · Cited by 109 · see citing works
Strength and tempo of selection revealed in viral gene genealogies
Bedford, T., Cobey, S. E., & Pascual, M. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-220 · Cited by 98 · see citing works
Kistler, K. E., & Bedford, T. (2021) · eLife · doi:10.7554/elife.64509 · Cited by 94 · see citing works
Genetic drift of human coronavirus OC43 spike gene during adaptive evolution
Ren, L., Zhang, Y., Li, J., Xiao, Y., Zhang, J., Wang, Y., Chen, L., Paranhos‐Baccalà, G., & Wang, J. (2015) · Scientific Reports · doi:10.1038/srep11451 · Cited by 76 · see citing works
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Spielman, S. J., Weaver, S., Shank, S. D., Magalis, B. R., Li, M., & Pond, S. L. K. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9074-0_14 · Cited by 73 · see citing works
Aldridge, R. W., Lewer, D., Beale, S., Johnson, A. M., Zambon, M. C. F. A., Hayward, A. C., Fragaszy, E., & Flu Watch Group (2020) · Wellcome Open Research · doi:10.12688/wellcomeopenres.15812.2 · Cited by 71 · see citing works
Chibo, D., & Birch, C. J. (2006) · Journal of General Virology · doi:10.1099/vir.0.81662-0 · Cited by 70 · see citing works
Fulton, B. O., Sachs, D. M., Beaty, S. M., Won, S. T., Lee, B., Palese, P., & Heaton, N. S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.054 · Cited by 68 · see citing works
Dingens, A. S., Crawford, K. H. D., Adler, A., Steele, S. L., Lacombe, K., Eguia, R. T., Amanat, F., Walls, A. C., Wolf, C. R., Murphy, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18178-1 · Cited by 68 · see citing works
Self-citationEvolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Pond, S. L. K., Murrell, B., & Poon, A. F. Y. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-585-5_10 · Cited by 64 · see citing works
Muñoz-Alía, M. Á., Nace, R. A., Zhang, L., & Russell, S. J. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100225 · Cited by 60 · see citing works
Schmidt, O. W., ALLAN, I. D., Cooney, M. K., Foy, H. M., & Fox, J. P. (1986) · American Journal of Epidemiology · doi:10.1093/oxfordjournals.aje.a114315 · Cited by 49 · see citing works
Antigenic Maps of Influenza A(H3N2) Produced With Human Antisera Obtained After Primary Infection
Fonville, J. M., Fraaij, P. L. A., de Mutsert, G., Wilks, S., van Beek, R., Fouchier, R. A. M., & Rimmelzwaan, G. F. (2015) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiv367 · Cited by 41 · see citing works
Shirato, K., Kawase, M., Watanabe, O., Hirokawa, C., Matsuyama, S., Nishimura, H., & Taguchi, F. (2012) · Journal of General Virology · doi:10.1099/vir.0.043117-0 · Cited by 40 · see citing works
Phylogenomics and bioinformatics of SARS-CoV
Lió, P. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.01.005 · Cited by 36 · see citing works
A simple protein-based surrogate neutralization assay for SARS-CoV-2Preprint
Abe, K. T., Li, Z., Samson, R., Samavarchi-Tehrani, P., Valcourt, E. J., Wood, H., Budylowski, P., Dupuis, A. P., Girardin, R. C., Rathod, B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.10.197913 · Cited by 20 · see citing works
Functional SARS-CoV-2-specific immune memory persists after mild COVID-19
Rodda, L. B., Netland, J., Shehata, L., Pruner, K. B., Morwaski, P. A., Thouvenel, C. D., Takehara, K. K., Eggenberger, J., Hemann, E. A., Waterman, H. R., et al. (2021) · The Journal of Immunology · doi:10.4049/jimmunol.206.supp.62.06 · Cited by 18 · see citing works
Serology and Energetics of Cross-Reactions Among the H3 Antigens of Influenza Viruses
Underwood, P. A. (1980) · Infection and Immunity · doi:10.1128/iai.27.2.397-404.1980 · Cited by 16 · see citing works
Coronavirus Infections in Working Adults
Hendley, J. O., Fishburne, H. B., & Gwaltney, J. M. (2015) · American Review of Respiratory Disease · Cited by 15 · see citing works
Kistler, K. E., & Bedford, T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.30.352914 · Cited by 14 · see citing works
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) · The Journal of Immunology · doi:10.4049/jimmunol.206.supp.30.13 · Cited by 7 · see citing works
Flagged first, then by citations
3 of the 101 references couldn’t be matched to a known paper.
Research works printed but not linked: 5
- Kemp, S. (2020). Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion | medRxiv. BioRxiv.
- Kemp, S.A., Collier, D.A., Datir, R., Gayed, S., Jahun, A., Hosmillo, M., Ferreira, I., Rees-Spear, C., Mlcochova, P., Lumb, I.U., et al. (2020). Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion. MedRxiv 2020.12.05.20241927.
- Lumley, S.F., O'Donnell, D., Stoesser, N.E., Matthews, P.C., Howarth, A., Hatch, S.B., Marsden, B.D., Cox, S., James, T., Warren, F., et al. (2020). Antibodies to SARS-CoV-2 are associated with protection against reinfection. MedRxiv 2020.11.18.20234369.
- Muñoz-Alía, M.Á., Nace, R.A., Zhang, L., and Russell, S.J. (2020). Pathogenic measles viruses cannot evolve to bypass vaccine-induced neutralizing antibodies. BioRxiv 2020.10.22.351189.
- Thomson, E. (2020). The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity | bioRxiv. BioRxiv.
Cited by
Sorted by citations
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343 · see citing works
SARS-CoV-2 variant biology: immune escape, transmission and fitness
Carabelli, A. M., Peacock, T. P., Thorne, L., Harvey, W. T., Hughes, J., de Silva, T. I., Peacock, S. J., Barclay, W., de Silva, T. I., Towers, G. J., et al. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00841-7 · Cited by 1,293 · see citing works
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 · see citing works
Self-citationThe 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 · see citing works
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
Starr, T. N., Czudnochowski, N., Liu, Z., Zatta, F., Park, Y., Addetia, A., Pinto, D., Beltramello, M., Hernandez, P., Greaney, A. J., et al. (2021) · Nature · doi:10.1038/s41586-021-03807-6 · Cited by 495 · see citing works
Self-citationStarr, T. N., Greaney, A. J., Dingens, A. S., & Bloom, J. D. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100255 · Cited by 470 · see citing works
Self-citationThe coronavirus is here to stay — here’s what that means
Phillips, N. (2021) · Nature · doi:10.1038/d41586-021-00396-2 · Cited by 445 · see citing works
After the pandemic: perspectives on the future trajectory of COVID-19
Telenti, A., Arvin, A. M., Corey, L., Corti, D., Diamond, M., García‐Sastre, A., Garry, R. F., Holmes, E. C., Pang, P. S., & Virgin, H. W. (2021) · Nature · doi:10.1038/s41586-021-03792-w · Cited by 440 · see citing works
Immunological characteristics govern the transition of COVID-19 to endemicity
Lavine, J. S., Bjornstad, O. N., & Antia, R. (2021) · Science · doi:10.1126/science.abe6522 · Cited by 416 · see citing works
Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
Yuan, M., Huang, D., Lee, C.-C. D., Wu, N. C., Jackson, A. M., Zhu, X., Liu, H., Peng, L., van Gils, M. J., Sanders, R. W., et al. (2021) · doi:10.1101/2021.02.16.430500 · Cited by 364 · see citing works
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 316 · see citing works
Kundu, R., Narean, J. S., Wang, L., Fenn, J., Pillay, T. D., Derqui, N., Conibear, E., Koycheva, A., Davies, M., Tolosa-Wright, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27674-x · Cited by 308 · see citing works
Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution
Starr, T. N., Greaney, A. J., Hannon, W. W., Loes, A. N., Hauser, K., Dillen, J., Ferri, E., Farrell, A. G., Dadonaite, B., McCallum, M., et al. (2022) · bioRxiv · doi:10.1126/science.abo7896 · Cited by 282 · see citing works
Self-citationThe changing epidemiology of SARS-CoV-2
Koelle, K., Martin, M. A., Antia, R., Lopman, B. A., & Dean, N. E. (2022) · Science · doi:10.1126/science.abm4915 · Cited by 295 · see citing works
Greaney, A. J., Loes, A. N., Gentles, L. E., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abi9915 · Cited by 244 · see citing works
Self-citationEpidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
Saad-Roy, C. M., Morris, S. E., Metcalf, C. J. E., Mina, M. J., Baker, R. E., Farrar, J., Holmes, E. C., Pybus, O. G., Graham, A. L., Levin, S. A., et al. (2021) · Science · doi:10.1126/science.abg8663 · Cited by 214 · see citing works
The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges
Malik, J. A., Ahmed, S., Aroosa, M., Shinde, M., Bender, O., Alshammari, F., Ansari, M., & Anwar, S. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.12.014 · Cited by 201 · see citing works
Beyond Omicron: what’s next for COVID’s viral evolution
Callaway, E. (2021) · Nature · doi:10.1038/d41586-021-03619-8 · Cited by 189 · see citing works
Implications of diversity in sperm size and function for sperm competition and fertility
Gomendio, M., & Roldán, E. R. S. (2008) · The International Journal of Developmental Biology · doi:10.1387/ijdb.082595mg · Cited by 185 · see citing works
Prolonged evolution of the human B cell response to SARS-CoV-2 infection
Sakharkar, M., Rappazzo, C. G., Wieland-Alter, W. F., Hsieh, C.-L., Wrapp, D., Esterman, E. S., Kaku, C. I., Wec, A. Z., Geoghegan, J. C., McLellan, J. S., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abg6916 · Cited by 174 · see citing works
SARS-CoV-2 evolution and vaccines: cause for concern?
Williams, T., & Burgers, W. A. (2021) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(21)00075-8 · Cited by 163 · see citing works
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 149 · see citing works
Focosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 148 · see citing works
An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain
Greaney, A. J., Starr, T. N., & Bloom, J. D. (2022) · Virus Evolution · doi:10.1093/ve/veac021 · Cited by 147 · see citing works
Self-citationMoodley, A., Stegger, M., BAĞCIGİL, A. F., Baptiste, K. E., Loeffler, A., Lloyd, D. H., Williams, N. J., Leonard, N., Abbott, Y., Skov, R. L., et al. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl394 · Cited by 146 · see citing works
Antigenic drift: Understanding COVID-19
Yewdell, J. W. (2021) · Immunity · doi:10.1016/j.immuni.2021.11.016 · Cited by 145 · see citing works
Convergent Evolution in SARS-CoV-2 Spike Creates a Variant Soup from Which New COVID-19 Waves Emerge
Focosi, D., Quiroga, R., McConnell, S. A., Johnson, M. C., & Casadevall, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032264 · Cited by 132 · see citing works
SARS-CoV-2 evolution in the Omicron era
Roemer, C., Sheward, D. J., Hisner, R., Gueli, F., Sakaguchi, H., Frohberg, N., Schoenmakers, J., Sato, K., O’Toole, A. N., Rambaut, A., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01504-w · Cited by 129 · see citing works
Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity
Mengist, H. M., Kombe, A. J. K., Mekonnen, D., Abebaw, A., Getachew, M., & Jin, T.-C. (2021) · Seminars in Immunology · doi:10.1016/j.smim.2021.101533 · Cited by 114 · see citing works
de Souza, W. M., Amorim, M. R., Sesti‐Costa, R., Coimbra, L. D., Brunetti, N. S., de Toledo-Teixeira, D. A., de Souza, G. F., Muraro, S. P., Parise, P. L., Barbosa, P. P., et al. (2021) · The Lancet Microbe · doi:10.1016/s2666-5247(21)00129-4 · Cited by 111 · see citing works
Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity
Aguilar-Bretones, M., Fouchier, R. A. M., Koopmans, M., & van Nierop, G. P. (2023) · Journal of Clinical Investigation · doi:10.1172/jci162192 · Cited by 104 · see citing works
Taft, J. M., Weber, C. R., Gao, B., Ehling, R. A., Han, J., Frei, L., Metcalfe, S. W., Overath, M. D., Yermanos, A., Kelton, W., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.024 · Cited by 113 · see citing works
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 100 · see citing works
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 99 · see citing works
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 92 · see citing works
Tortorici, M. A., Walls, A. C., Joshi, A., Park, Y., Eguia, R. T., Miranda, M. C., Kepl, E., Dosey, A. M., Stevens‐Ayers, T., Boeckh, M. J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.019 · Cited by 87 · see citing works
Self-citationThe success of SARS-CoV-2 vaccines and challenges ahead
Subbarao, K. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.016 · Cited by 90 · see citing works
Anand, U., Jakhmola, S., Indari, O., Jha, H. C., Chen, Z., Tripathi, V. S., & de la Lastra, J. M. P. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.658519 · Cited by 83 · see citing works
In search of a pan-coronavirus vaccine: next-generation vaccine design and immune mechanisms
Cankat, S., Demael, M. U., & Swadling, L. (2023) · Cellular & Molecular Immunology · doi:10.1038/s41423-023-01116-8 · Cited by 84 · see citing works
Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit
Hurlburt, N. K., Homad, L. J., Sinha, I. R., Jennewein, M. F., MacCamy, A. J., Wan, Y.-H., Boonyaratanakornkit, J. B., Sholukh, A. M., Jackson, A. M., Zhou, P.-P., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03262-7 · Cited by 77 · see citing works
The landscape of antibody binding in SARS-CoV-2 infection
Heffron, A. S., McIlwain, S. J., Amjadi, M. F., Baker, D. A., Khullar, S., Armbrust, T., Halfmann, P., Kawaoka, Y., Sethi, A. K., Palmenberg, A. C., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001265 · Cited by 76 · see citing works
Instructing durable humoral immunity for COVID-19 and other vaccinable diseases
Bhattacharya, D. (2022) · Immunity · doi:10.1016/j.immuni.2022.05.004 · Cited by 63 · see citing works
A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance
Bourassa, L. A., Perchetti, G. A., Phung, Q., Lin, M. J., Mills, M. G., Roychoudhury, P., Harmon, K. G., Reed, J. C., & Greninger, A. L. (2021) · Journal of Clinical Virology · doi:10.1016/j.jcv.2021.104900 · Cited by 66 · see citing works
Self-citationAhn, J. Y., Lee, J., Suh, Y. S., Song, Y. G., Choi, Y.-J., Lee, K. H., Seo, S. H., Song, M., Oh, J., Kim, M., et al. (2022) · The Lancet Microbe · doi:10.1016/s2666-5247(21)00358-x · Cited by 67 · see citing works
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy
Greaney, A. J., Starr, T. N., Eguia, R. T., Loes, A. N., Khan, K., Karim, F., Cele, S., Bowen, J. E., Logue, J. K., Corti, D., et al. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010248 · Cited by 56 · see citing works
Self-citationAn atlas of continuous adaptive evolution in endemic human viruses
Kistler, K. E., & Bedford, T. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.09.012 · Cited by 65 · see citing works
Muñoz-Alía, M. Á., Nace, R. A., Zhang, L., & Russell, S. J. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100225 · Cited by 60 · see citing works
The ins and outs of SARS-CoV-2 variants of concern (VOCs)
Salehi-Vaziri, ., Fazlalipour, M., Khorrami, S. M. S., Azadmanesh, K., Pouriayevali, M. H., Jalali, T., Shoja, Z., & Maleki, A. (2022) · Archives of Virology · doi:10.1007/s00705-022-05365-2 · Cited by 58 · see citing works
Pollett, S. D., Conte, M. A., Sanborn, M. A., Jarman, R. G., Lidl, G. M., Modjarrad, K., & Berry, I. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-96626-8 · Cited by 59 · see citing works
The evolutionary dynamics of endemic human coronaviruses
Jo, W. K., Drosten, C., & Drexler, J. F. (2021) · Virus Evolution · doi:10.1093/ve/veab020 · Cited by 57 · see citing works
Wang, C., Hesketh, E. L., Shamorkina, T. M., Li, W., Franken, P. J., Drabek, D., van Haperen, R., Townend, S., van Kuppeveld, F. J. M., Grosveld, F. G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30658-0 · Cited by 51 · see citing works
Deep mutational scanning for therapeutic antibody engineering
Hanning, K. R., Minot, M., Warrender, A. K., Kelton, W., & Reddy, S. T. (2021) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2021.11.010 · Cited by 51 · see citing works
Human coronavirus HKU1 recognition of the TMPRSS2 host receptor
McCallum, M., Park, Y., Stewart, C., Sprouse, K. R., Addetia, A., Brown, J. T., Tortorici, M. A., Gibson, C. A., Wong, E., Ieven, M. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.06.006 · Cited by 49 · see citing works
COVID-19, the first pandemic in the post-genomic era
van Dorp, L., Houldcroft, C. J., Richard, D., & Balloux, F. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.07.002 · Cited by 46 · see citing works
SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs
Alizon, S., & Sofonea, M. T. (2021) · Journal of Evolutionary Biology · doi:10.1111/jeb.13896 · Cited by 46 · see citing works
Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies
Rouzine, I. M., & Rozhnova, G. (2023) · Communications Medicine · doi:10.1038/s43856-023-00320-x · Cited by 47 · see citing works
A biophysical model of viral escape from polyclonal antibodies
Yu, T. C., Thornton, Z., Hannon, W. W., DeWitt, W. S., Radford, C. E., Matsen, F. A., IV, & Bloom, J. D. (2022) · Virus Evolution · doi:10.1093/ve/veac110 · Cited by 45 · see citing works
Self-citationAntigenic escape selects for the evolution of higher pathogen transmission and virulence
Sasaki, A., Lion, S., & Boots, M. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01603-z · Cited by 42 · see citing works
Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses
Dijokaite-Guraliuc, A., Das, R., Zhou, D., Ginn, H. M., Liu, C., Duyvesteyn, H. M. E., Huo, J., Nutalai, R., Supasa, P., Selvaraj, M., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112271 · Cited by 45 · see citing works
The past, current and future epidemiological dynamic of SARS-CoV-2
Balloux, F., Tan, C. C. S., Swadling, L., Richard, D., Jenner, C., Maini, M. K., & van Dorp, L. (2022) · Oxford Open Immunology · doi:10.1093/oxfimm/iqac003 · Cited by 37 · see citing works
Anderson, E. M., Li, S. H., Awofolaju, M., Eilola, T., Goodwin, E. C., Bolton, M. J., Gouma, S., Manzoni, T. B., Hicks, P. D., Goel, R. R., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111496 · Cited by 35 · see citing works
Herd immunity, vaccination and moral obligation
Bullen, M., Heriot, G., & Jamrozik, E. (2023) · Journal of Medical Ethics · doi:10.1136/jme-2022-108485 · Cited by 42 · see citing works
Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Ghafari, M., Liu, Q., Dhillon, A., Katzourakis, A., & Weissman, D. B. (2022) · Frontiers in Virology · doi:10.3389/fviro.2022.942555 · Cited by 35 · see citing works
Al‐Tawfiq, J. A., Hoang, V. T., Bui, N. L., Chu, D., & Memish, Z. A. (2022) · Journal of Epidemiology and Global Health · doi:10.1007/s44197-022-00032-w · Cited by 34 · see citing works
Immuno-epidemiology and the predictability of viral evolution
Saad-Roy, C. M., Metcalf, C. J. E., & Grenfell, B. T. (2022) · Science · doi:10.1126/science.abn9410 · Cited by 33 · see citing works
PARIS and SPARTA: Finding the Achilles’ Heel of SARS-CoV-2
Simon, V. R., Kota, V. K., Bloomquist, R. F., Hanley, H. B., Forgacs, D., Pahwa, S. G., Pallikkuth, S., Miller, L. G., Schaenman, J. M. D., Yeaman, M. R., et al. (2022) · mSphere · doi:10.1128/msphere.00179-22 · Cited by 28 · see citing works
Shao, N., Zhang, C., Dong, J., Sun, L., Chen, X., Xie, Z., Xu, B., An, S., Zhang, T., & Yang, F. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1023847 · Cited by 32 · see citing works
An overview of current drugs and prophylactic vaccines for coronavirus disease 2019 (COVID-19)
Bahrami, A. A., Azargoonjahromi, A., Sadraei, S., Aarabi, A., Payandeh, Z., & Rajabibazl, M. (2022) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-022-00339-3 · Cited by 32 · see citing works
Cheng, Z., Elmes, M. J., Kirkup, S. E., Abayasekara, D. R. E., & Wathes, D. C. (2004) · Journal of Endocrinology · doi:10.1677/joe.0.1820249 · Cited by 31 · see citing works
Garrett, M. E., Galloway, J. G., Wolf, C., Logue, J. K., Franko, N., Chu, H. Y., Matsen, F. A., IV, & Overbaugh, J. (2022) · eLife · doi:10.7554/elife.73490 · Cited by 30 · see citing works
Tsai, K., Lee, Y.-C., & Tseng, T.-S. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.698365 · Cited by 32 · see citing works
Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host
Forni, D., Cagliani, R., Arrigoni, F., Benvenuti, M., Mozzi, A., Pozzoli, U., Clerici, M., GIOIA, L. D., & Sironi, M. (2021) · Virus Evolution · doi:10.1093/ve/veab061 · Cited by 28 · see citing works
Shooting at a Moving Target—Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development
Günl, F., Mecate-Zambrano, A., Rehländer, S., Hinse, S., Ludwig, S., & Brunotte, L. (2021) · Vaccines · doi:10.3390/vaccines9101052 · Cited by 27 · see citing works
Rattanapisit, K., Bulaon, C. J. I., Khorattanakulchai, N., Shanmugaraj, B., Wangkanont, K., & Phoolcharoen, W. (2021) · PLoS ONE · doi:10.1371/journal.pone.0253574 · Cited by 26 · see citing works
How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology
Waterlow, N. R., van Leeuwen, E., Davies, N. G., CMMID COVID-19 Working Group, Flasche, S., & Eggo, R. M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2108395118 · Cited by 26 · see citing works
Lawrenz, J., Xie, Q., Zech, F., Weil, T., Seidel, A., Krnavek, D., van der Hoek, L., Münch, J., Müller, J. A., & Kirchhoff, F. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciac057 · Cited by 25 · see citing works
The challenge of emerging SARS-CoV-2 mutants to vaccine development
Li, R., Liu, J., & Zhang, H. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.03.001 · Cited by 24 · see citing works
Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics
Tortorici, M. A., Choi, A., Gibson, C. A., Lee, J., Brown, J. T., Stewart, C., Joshi, A., Harari, S., Willoughby, I., Treichel, C., et al. (2025) · Nature · doi:10.1038/s41586-025-09155-z · Cited by 24 · see citing works
Self-citationCicaloni, V., Costanti, F., Pasqui, A., Bianchini, M., Niccolai, N., & Bongini, P. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.891418 · Cited by 23 · see citing works
Kumar, S., Delipan, R., Chakraborty, D., Kanjo, K., Singh, R., Singh, N., Siddiqui, S., Tyagi, A., Jha, V., Thakur, K. G., et al. (2023) · Journal of Virology · doi:10.1128/jvi.00922-23 · Cited by 22 · see citing works
Which ‘imperfect vaccines’ encourage the evolution of higher virulence?
Bull, J. J., & Antia, R. (2022) · Evolution Medicine and Public Health · doi:10.1093/emph/eoac015 · Cited by 22 · see citing works
Fischer, R. J., Port, J. R., Holbrook, M. G., Yinda, C. K., Creusen, M., ter Stege, J., de Samber, M., & Munster, V. J. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.2c02822 · Cited by 22 · see citing works
Weil, T., Lawrenz, J., Seidel, A., Münch, J., & Müller, J. A. (2022) · Antiviral Research · doi:10.1016/j.antiviral.2022.105343 · Cited by 21 · see citing works
Bolton, M. J., Santos, J. J. D. S., Arevalo, C. P., Griesman, T., Watson, M., Li, S. H., Bates, P. F., Ramage, H. R., Wilson, P. C., & Hensley, S. E. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2216521120 · Cited by 21 · see citing works
Starr, T. N., Czudnochowski, N., Zatta, F., Park, Y., Liu, Z., Addetia, A., Pinto, D., Beltramello, M., Hernandez, P., Greaney, A. J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.06.438709 · Cited by 24 · see citing works
Self-citationHeterologous humoral immunity to human and zoonotic coronaviruses: Aiming for the achilles heel
Ng, K. W., Faulkner, N., Wrobel, A. G., Gamblin, S. J., & Kassiotis, G. (2021) · Seminars in Immunology · doi:10.1016/j.smim.2021.101507 · Cited by 19 · see citing works
Richard, D., Shaw, L. P., Lanfear, R., Corbett-Detig, R. B., Hinrichs, A. S., McBroome, J., Turakhia, Y., Acman, M., Owen, C. J., Tan, C. C. S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.06.442903 · Cited by 20 · see citing works
Persistence of immunity to SARS-CoV-2 over time in the ski resort Ischgl
Borena, W., Bánki, Z., Bates, K., Winner, H., Riepler, L., Rössler, A., Pipperger, L., Theurl, I., Falkensammer, B., Ulmer, H., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103534 · Cited by 18 · see citing works
Uncertainty around the Long-Term Implications of COVID-19
Desforges, M., Gurdasani, D., Hamdy, A., & Leonardi, A. J. (2021) · Pathogens · doi:10.3390/pathogens10101267 · Cited by 18 · see citing works
Vermeulen, C. J., Dijkman, R., de Wit, S. J., Bosch, B., Heesterbeek, H., & Schaik, G. V. (2023) · Avian Pathology · doi:10.1080/03079457.2023.2177140 · Cited by 19 · see citing works
Rational design of a booster vaccine against COVID-19 based on antigenic distance
Hu, Y., Yuen, T. T., Gong, H.-R., Hu, B., Hu, J., Lin, X., Li, R., Zhou, C. L., Chen, L., Wang, X., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.07.004 · Cited by 20 · see citing works
Shared N417-Dependent Epitope on the SARS-CoV-2 Omicron, Beta, and Delta Plus Variants
Moyo-Gwete, T., Madzivhandila, M., Mkhize, N. N., Kgagudi, P., Ayres, F., Lambson, B. E., Manamela, N. P., Richardson, S. I., Makhado, Z., van der Mescht, M. A., et al. (2022) · Journal of Virology · doi:10.1128/jvi.00558-22 · Cited by 18 · see citing works
SARS-CoV-2: The Interplay Between Evolution and Host Immunity
Case, J. B., Jain, S., Suthar, M. S., & Diamond, M. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-083122-043054 · Cited by 22 · see citing works
Structural Dynamics and Molecular Evolution of the SARS-CoV-2 Spike Protein
Wolf, K., Kwan, J. C., & Kamil, J. P. (2022) · mBio · doi:10.1128/mbio.02030-21 · Cited by 18 · see citing works
Omicron’s message on vaccines: Boosting begets breadth
Wesemann, D. R. (2022) · Cell · doi:10.1016/j.cell.2022.01.006 · Cited by 16 · see citing works
Laroche, A., Delgado, M. L. O., Chalopin, B., Cuniasse, P., DuBois, S. G., Sierocki, R., Gallais, F., Debroas, S., Bellanger, L., Simon, S., et al. (2022) · mAbs · doi:10.1080/19420862.2022.2076775 · Cited by 17 · see citing works
Reduced B cell antigenicity of Omicron lowers host serologic response
Tubiana, J., Xiang, Y., Fan, L., Wolfson, H. J., Chen, K., Schneidman‐Duhovny, D., & Shi, Y. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111512 · Cited by 18 · see citing works
Logue, J., Johnson, R. M., Patel, N., Zhou, B., Maciejewski, S. M., Foreman, B. M., Zhou, H., Portnoff, A. D., Tian, J.-H., Rehman, A., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-35606-6 · Cited by 21 · see citing works
Immunisation, asymptomatic infection, herd immunity and the new variants of COVID 19Preprint
Grant, A., & Hunter, P. R. (2021) · medRxiv · doi:10.1101/2021.01.16.21249946 · Cited by 17 · see citing works
Waning immunity drives respiratory virus evolution and reinfection
Bull, J. J., Koelle, K., & Antia, R. (2025) · Evolution Medicine and Public Health · doi:10.1093/emph/eoaf002 · Cited by 16 · see citing works
- Authors
- Eguia, R., Crawford, K. H. D., Stevens-Ayers, T., Kelnhofer-Millevolte, L., Greninger, A. L., Englund, J. A., Boeckh, M. J., & Bloom, J. D.
- Affiliations
- Fred Hutch Cancer Center (US)
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Bloom, Jesse D.
- ORCID
- Venue
- PLoS Pathogens
- Publisher
- openRxiv
- Published
- 2020-12-18
- Volume
- 17
- Issue
- 4
- Pages
- e1009453-e1009453
- ISSN
- 1553-7366 (ISSN-L)
- PMC
- PMC8031418
- OpenAlex
- W3144378969
- Cited by
- 258
- References
- 101
- Citations by year
- 2026: 7 · 2025: 21 · 2024: 11 · 2023: 33 · 2022: 69 · 2021: 103 · 2020: 2 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 3 · 2013: 1
- FWCI
- 17.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- PLoS Pathogens (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- Pfizer
- AstraZeneca
- GlaxoSmithKline
- Sanofi
- Fred Hutchinson Cancer Research Center
- Regeneron Pharmaceuticals
- Moderna
- National Institutes of Health
- Sanofi Pasteur
- National Institute of General Medical Sciences (T32GM007266)
- National Institute of Allergy and Infectious Diseases (R01AI127893, F30AI149928, R01AI141707)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- HCoV-229E, antigenic evolution, antibody escape, neutralizing antibodies, spike protein, receptor binding domain, coronavirus evolution
- MeSH terms
- SARS-CoV-2, Antibodies, Viral, Humans, Coronavirus 229E, Human, Immune Evasion, Antibodies, Neutralizing
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
