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Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies
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Abstract
The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity. To facilitate prospective surveillance for such evolution, we map how convalescent plasma antibodies are impacted by all mutations to the spike's receptor-binding domain (RBD), the main target of plasma neutralizing activity. Binding by polyclonal plasma antibodies is affected by mutations in three main epitopes in the RBD, but longitudinal samples reveal that the impact of these mutations on antibody binding varies substantially both among individuals and within the same individual over time. Despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the RBD's receptor-binding motif. The most important site is E484, where neutralization by some plasma is reduced >10-fold by several mutations, including one in the emerging 20H/501Y.V2 and 20J/501Y.V3 SARS-CoV-2 lineages. Going forward, these plasma escape maps can inform surveillance of SARS-CoV-2 evolution.
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In the citing paper
“This variant has substitutions in the spike protein at T95I, G142D, E154K, D614G, P681R, Q1071H, and L452R, E484Q in its RBD region, which may provide this variant reduced resistance to neutralization by post-vaccination sera [47].”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [47]
Experimental — accuracy not yet measuredIn the citing paper
“The loss of plasma neutralizing activity against B.1.351could be largely attributed to the E484K substitution (Fig. 3b), which has been shown to attenuate the neutralizing activity of convalescent sera 30 .”
From Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 (2021) · cites this paper as [30]
In the citing paper
“Several of the RBD mutations directly affect angiotensin-converting enzyme 2 (ACE2) receptor-binding affinity, which may affect infectivity, viral load, or transmissibility.11, 12, 13, 14”
From Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals (2021) · cites this paper as [11]
In the citing paper
“Continued viral evolution led to the emergence and selection of SARS-CoV-2 variants with enhanced infectivity/transmissibility2,3 4,5 and ability to circumvent drug6 and immune control7,8.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [8]
In the citing paper
“The E484K mutation, which can mediate antibody escape of B.1.351and P.1 variants, has been recently detected in the B.1.1.7 lineage in the United Kingdom, and thus represents a major potential threat for previously immune populations.”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [24]
In the citing paper
“Mutations in the B.1.351and P.1 strains, including E484K and K417N/T, are of high concern, since they partly compromise neutralization generated by previous infection or vaccination [23][24][25] or may increase inherent viral fitness.”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [24]
In the citing paper
“Mutations at F486 are associated with a reduction in neutralizing activity by class 1 (and some class 2) neutralizing antibodies and by polyclonal sera9–11.”
From Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa (2022) · cites this paper as [10]
In the citing paper
“mutations at this position have been associated with a reduction in neutralization by monoclonal antibodies (particularly class 2 antibodies) and polyclonal sera9–11.”
From Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa (2022) · cites this paper as [10]
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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
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020) · Science · doi:10.1126/science.abb2507 · Cited by 8,897
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
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., et al. (2020) · Nature · doi:10.1038/s41586-020-2180-5 · Cited by 5,983
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
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 14×
“…tend to have the largest effect on plasma antibody binding to the RBD, and our neutralization assays (Figures 5A and 5D Brazil) (Faria et al., 2021; Tegally et al., 2020; Voloch et al., 2020); another mutation at the same site (E484Q) has also been found in a smaller number of human isolates…”
InfluentialDetection 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
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
Self-citationData, disease and diplomacy: GISAID's innovative contribution to global health
Elbe, S., & Buckland‐Merrett, G. (2017) · Global Challenges · doi:10.1002/gch2.1018 · Cited by 1,928
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody
Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2349-y · Cited by 1,885
Research works printed but not linked: 1
- Kemp, 2020, Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion, medRxiv
Cited by
Sorted by citations
Items 101–200 of 1,006
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 157
Guedes, I. A., Costa, L. S. C., Santos, K. B., Karl, A. L. M., Rocha, G. K., Teixeira, I. M., Galheigo, M. M., Medeiros, V., Krempser, E., Custódio, F. L., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-84700-0 · Cited by 152
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
Tada, T., Dcosta, B. M., Samanovic, M. I., Herati, R. S., Cornelius, A. R., Zhou, H., Vaill, A., Kazmierski, W., Mulligan, M. J., & Landau, N. R. (2021) · mBio · doi:10.1128/mbio.00696-21 · Cited by 155
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
“Antibodies targeting RBD have been suggested to account for >90% of neutralizing activity in convalescent sera (Greaney et al., 2021; Piccoli et al., 2020), and several neutralizing epitopes on RBD that are targeted by highly potent monoclonal antibodies (mAbs) have been molecularly characterized (Barnes et al.”
Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1
Moulana, A., Dupic, T., Phillips, A. M., Chang, J., Nieves, S., Roffler, A. A., Greaney, A. J., Starr, T. N., Bloom, J. D., & Desai, M. M. (2022) · Nature Communications · doi:10.1038/s41467-022-34506-z · Cited by 156
Self-citationFocosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 150
Chakraborty, C., Sharma, A. R., Bhattacharya, M., & Lee, S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.801522 · Cited by 154
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
“Deep mutational scanning demonstrated that, compared to antibodies inducedby infection, mRNA vaccine-induced serum activity shows a stronger RBDdirected focus with higher epitope breadth (Greaney et al., 2021b).”
Moodley, 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
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
Bispecific IgG neutralizes SARS-CoV-2 variants and prevents escape in mice
Gasparo, R. D., Pedotti, M., Simonelli, L., Nickl, P., Muecksch, F., Cassaniti, I., Percivalle, E., Lorenzi, J. C. C., Mazzola, F., Magrì, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03461-y · Cited by 134
Fast-spreading SARS-CoV-2 variants: challenges to and new design strategies of COVID-19 vaccines
Zhou, W., & Wang, W. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00644-x · Cited by 134
Neutralizing antibodies for the prevention and treatment of COVID-19
Du, L., Yang, Y., & Zhang, X. (2021) · Cellular and Molecular Immunology · doi:10.1038/s41423-021-00752-2 · Cited by 133
Antibody and B cell responses to SARS-CoV-2 infection and vaccination
Röltgen, K., & Boyd, S. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.009 · Cited by 143
Grabowski, F., Kochańczyk, M., & Lipniacki, T. (2022) · Viruses · doi:10.3390/v14020294 · Cited by 121
Jangra, S., Ye, C., Rathnasinghe, R., Stadlbauer, D., PVI study group, Krammer, F., Simon, V. R., Martínez‐Sobrido, L., García‐Sastre, A., & Schotsaert, M. (2021) · medRxiv · doi:10.1101/2021.01.26.21250543 · Cited by 133
Sokal, A., Spaeth, G. B., Fernández, I., Broketa, M., Azzaoui, I., Selle, A. D. L., Vandenberghe, A., Fourati, S., Roeser, A., Meola, A., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.09.011 · Cited by 135
Li, W., Chen, Y., Prévost, J., Ullah, I., Lu, M., Gong, S. Y., Tauzin, A., Gasser, R., Vézina, D., Anand, S. P., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110210 · Cited by 128
“In contrast, ACE2 binding was sensitive to mutations within the RBM consistent with previous results (Greaney et al., 2021b; Starr et al., 2020).”
Fast-spreading COVID variant can elude immune responses
Callaway, E. (2021) · Nature · doi:10.1038/d41586-021-00121-z · Cited by 135
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Laiton‐Donato, K., Franco-Muñoz, C., Álvarez-Díaz, D. A., Ruiz-Moreno, H. A., Usme-Ciro, J. A., Prada-Cardozo, D., Reales-González, J., Corchuelo, S., Herrera-Sepúlveda, M. T., Naizaque, J., et al. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.105038 · Cited by 123
SARS‐CoV‐2 variants and vulnerability at the global level
Chavda, V. P., Patel, A., & Vaghasiya, D. D. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27717 · Cited by 135
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, Á., Rambaut, A., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01504-w · Cited by 130
“Indeed, after in vitro selection with pooled sera from convalescent and vaccinated individuals, ancestral spike proteins evolved several antigenic mutations that were shared with the Omicron variant 4,5 .”
BackgroundTzou, P. L., Tao, K., Pond, S. L. K., & Shafer, R. W. (2022) · PLoS ONE · doi:10.1371/journal.pone.0261045 · Cited by 126
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
Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum
Bates, T. A., Leier, H. C., Lyski, Z. L., McBride, S. K., Coulter, F. J., Weinstein, J. B., Goodman, J. R., Lu, Z., Siegel, S. A. R., Sullivan, P. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25479-6 · Cited by 115
Hunt, A. C., Case, J. B., Park, Y., Cao, L., Wu, K., Walls, A. C., Liu, Z., Bowen, J. E., Yeh, A. H.-W., Saini, S., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abn1252 · Cited by 121
Self-citationA serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry
Valero, J., Civit, L., Dupont, D. M., Selnihhin, D., Reinert, L. S., Idorn, M., Israels, B. A., Bednarz, A., Bus, C., Asbach, B., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2112942118 · Cited by 127
Emerging 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
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
Jette, C. A., Cohen, A. A., Gnanapragasam, P. N. P., Muecksch, F., Lee, Y. E., Huey‐Tubman, K. E., Schmidt, F., Hatziioannou, T., Bieniasz, P. D., Nussenzweig, M. C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109760 · Cited by 99
“Despite both C118 and C022 engaging the a4 helix and residue R408RBD, mutations at this position known to affect class 1 and class 4 anti-RBD antibodies (Greaney et al., 2021) had no effect on these antibodies (Figure S2A).”
Martin, D. P., Lytras, S., Lucaci, A. G., Maier, W., Grüning, B. A., Shank, S. D., Weaver, S., MacLean, O. A., Orton, R. J., Lemey, P., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac061 · Cited by 129
Self-citationGuo, Y., Han, J., Zhang, Y., He, J., Yu, W., Zhang, X., Wu, J., Zhang, S., Kong, Y., Guo, Y., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.877101 · Cited by 118
Chen, X., Chen, Z., Azman, A. S., Sun, R., Lu, W., Zheng, N., Zhou, J., Wu, Q., Deng, X., Zhao, Z., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab646 · Cited by 113
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
Tada, T., Dcosta, B. M., Samanovic-Golden, M., Herati, R. S., Cornelius, A., Mulligan, M. J., & Landau, N. R. (2021) · doi:10.1101/2021.02.05.430003 · Cited by 153
COVID-19 reinfections among naturally infected and vaccinated individuals
Rahman, S., Rahman, M. M., Miah, M., Begum, M. N., Sarmin, M., Mahfuz, M., Hossain, M. E., Rahman, M. Z., Chisti, M. J., Ahmed, T., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-05325-5 · Cited by 111
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75
Wang, Q., Iketani, S., Li, Z., Guo, Y., Yeh, A. Y., Liu, M., Yu, J., Sheng, Z., Huang, Y., Liu, L., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.09.002 · Cited by 108
Resurgence of SARS-CoV-2: Detection by community viral surveillance
REACT study group, Riley, S., Ainslie, K. E. C., Eales, O. D., Walters, C. E., Wang, H., Atchison, C. J., Fronterrè, C., Diggle, P. J., Ashby, D., et al. (2021) · Science · doi:10.1126/science.abf0874 · Cited by 112
Yang, Y., Yang, M., Peng, Y., Liang, Y., Wei, J., Xing, L., Guo, L., Li, X., Li, J., Wang, J., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-021-01051-2 · Cited by 111
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 119
“Initially, DMS data consisting of single point mutations (ED 1 ) were used to train baseline models, with binding/non-binding labels assigned based on minimum affinity required to retain ACE2 binding as previously defined in Starr et al. (2020).”
InfluentialNeutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants
Ikegame, S., Siddiquey, M. N. A., Hung, C.-T., Haas, G. D., Brambilla, L., Oguntuyo, K. Y., Kowdle, S., Chiu, H.-P., Stevens, C. S., Vilardo, A. E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24909-9 · Cited by 141
Genomic reconstruction of the SARS-CoV-2 epidemic in England
Vöhringer, H. S., Sanderson, T., Sinnott, M., Maio, N. D., Nguyen, T., Goater, R., Schwach, F., Harrison, I., Hellewell, J., Ariani, C. V., et al. (2021) · Nature · doi:10.1038/s41586-021-04069-y · Cited by 108
The Emerging Concern and Interest SARS-CoV-2 Variants
Janik, E., Niemcewicz, M., Podogrocki, M., Majsterek, I., & Bijak, M. (2021) · Pathogens · doi:10.3390/pathogens10060633 · Cited by 113
Teruel, N., Mailhot, O., & Najmanovich, R. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009286 · Cited by 99
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
Sonnleitner, 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
Tao, K., Tzou, P. L., Nouhin, J., Bonilla, H. F., Jagannathan, P., & Shafer, R. W. (2021) · Clinical Microbiology Reviews · doi:10.1128/cmr.00109-21 · Cited by 109
Sun, D., Sang, Z., Kim, Y. J., Xiang, Y., Cohen, T., Belford, A. K., Huet, A., Conway, J. F., Sun, J., Taylor, D. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24963-3 · Cited by 96
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
“SARS-CoV-2 exhibits convergent evolution [9–11], and some of the notable mutations that have occurred multiple times independently (like S:501Y and S:484K) appear in multiple VOCs, suggesting positive selection on these mutations.”
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
COVID-19 Pandemic and Vaccines Update on Challenges and Resolutions
Khan, W. H., Hashmi, Z., Goel, A., Ahmad, R., Gupta, K., Khan, N., Alam, I., Ahmed, F., & Ansari, M. A. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.690621 · Cited by 105
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
Could new COVID variants undermine vaccines? Labs scramble to find out
Callaway, E. (2021) · Nature · doi:10.1038/d41586-021-00031-0 · Cited by 102
Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies
Alenquer, M., Ferreira, F., Lousa, D., Valério, M., Medina-Lopes, M., Bergman, M., Gonçalves, J., Demengeot, J., Leite, R. B., Lilue, J., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009772 · Cited by 101
SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants
Srivastava, S., Banu, S., Singh, P., Sowpati, D. T., & Mishra, R. K. (2021) · Journal of Biosciences · doi:10.1007/s12038-021-00145-7 · Cited by 96
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 105
VanBlargan, L. A., Adams, L. J., Liu, Z., Chen, R. E., Gilchuk, P., Raju, S., Smith, B. K., Zhao, H., Case, J. B., Winkler, E. S., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.08.016 · Cited by 87
“Under immune selection pressure, SARSCoV-2 can select for mutations that enable escape from antibody recognition and neutralization (Baum et al., 2020b; Greaney et al., 2021; Liu et al., 2021; Starr et al., 2021b; Suryadevara et al., 2021).”
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
Distant residues modulate conformational opening in SARS-CoV-2 spike protein
Ray, D., Le, L., & Andricioaei, I. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2100943118 · Cited by 89
Martin, D. P., Weaver, S., Tegally, H., San, E. J., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., et al. (2021) · doi:10.1101/2021.02.23.21252268 · Cited by 291
Alagöz, O., Sethi, A. K., Patterson, B. W., Churpek, M. M., Alhanaee, G., Scaria, E., & Safdar, N. (2021) · PLoS ONE · doi:10.1371/journal.pone.0254456 · Cited by 88
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
Bekliz, M., Adea, K., Vetter, P., Eberhardt, C. S., Hosszu-Fellous, K., Vu, D., Puhach, O., Essaidi-Laziosi, M., Waldvogel‐Abramowski, S., Stephan, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31556-1 · Cited by 86
B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity
Lapuente, D., Winkler, T., & Tenbusch, M. (2023) · Cellular and Molecular Immunology · doi:10.1038/s41423-023-01095-w · Cited by 101
An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB
He, Q., Wu, L., Xu, Z., Wang, X., Xie, Y., Chai, Y., Zheng, A., Zhou, J., Qiao, S., Huang, M., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.100991 · Cited by 90
“However, F486L was prevalent in minks,(22) which is also a neutralization escaping site to mAbs.(23) It is interesting that although Q493R was recognized as a contributing factor to immune escape,(6,24,25) the R493Q reversion carried by the BA.”
Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines?
Jia, Z., & Gong, W. (2021) · Journal of Korean Medical Science · doi:10.3346/jkms.2021.36.e124 · Cited by 94
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
West, A. P., Wertheim, J. O., Wang, J. C., Vasylyeva, T. I., Havens, J. L., Chowdhury, M. A., Gonzalez, E., Fang, C. E., Lonardo, S. S. D., Hughes, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25168-4 · Cited by 134
Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants
Chakraborty, C., Sharma, A. R., Bhattacharya, M., Agoramoorthy, G., & Lee, S. (2021) · mBio · doi:10.1128/mbio.01140-21 · Cited by 84
Metal Complexes as Antiviral Agents for SARS‐CoV‐2
Karges, J., & Cohen, S. M. (2021) · ChemBioChem · doi:10.1002/cbic.202100186 · Cited by 86
Dalvie, N. C., Rodriguez‐Aponte, S. A., Hartwell, B. L., Tostanoski, L. H., Biedermann, A. M., Crowell, L. E., Kaur, K., Kumru, O. S., Carter, L. P., Yu, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2106845118 · Cited by 84
COVID-19 vaccines for low- and middle-income countries
Choi, E. M. (2021) · Transactions of the Royal Society of Tropical Medicine and Hygiene · doi:10.1093/trstmh/trab045 · Cited by 77
Xiang, T., Liang, B., Fang, Y., Lu, S., Li, S., Wang, H., Li, H., Yang, X., Shěn, S., Zhu, B., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.708523 · Cited by 84
Wilhelm, A., Toptan, T., Pallas, C., Wolf, T., Goetsch, U., Gottschalk, R., Vehreschild, M. J. G. T., Ciesek, S., & Widera, M. (2021) · Viruses · doi:10.3390/v13091693 · Cited by 82
Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study
Sheward, D. J., Kim, C., Ehling, R. A., Pankow, A. P., Dopico, X. C., Dyrdak, R., Martin, D. P., Reddy, S. T., Dillner, J., Hedestam, G. B. K., et al. (2022) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(22)00129-3 · Cited by 80
Widera, M., Wilhelm, A., Hoehl, S., Pallas, C., Kohmer, N., Wolf, T., Rabenau, H. F., Corman, V. M., Drosten, C., Vehreschild, M. J. G. T., et al. (2021) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiab355 · Cited by 88
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes
Rodriguez-Rivas, J., Croce, G., Muscat, M., & Weigt, M. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2113118119 · Cited by 86
Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain
Tan, T. J. C., Yuan, M., Kuzelka, K., Padron, G. C., Beal, J. R., Chen, X., Wang, Y., Rivera-Cardona, J., Zhu, X., Stadtmueller, B. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24123-7 · Cited by 75
The great escape? SARS-CoV-2 variants evading neutralizing responses
Prévost, J., & Finzi, A. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.010 · Cited by 80
Wang, W. B., Liang, Y., Jin, Y. Q., Zhang, J., Su, J. G., & Li, Q. M. (2021) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2021.108035 · Cited by 83
Three SARS-CoV-2 reinfection cases by the new Variant of Concern (VOC) P.1/501Y.V3Preprint
Naveca, F. G., da Costa, C. F., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Costa, Á., Duarte, D., Silva, G., Mejía, M., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-318392/v1 · Cited by 83
Paredes, M. I., Lunn, S. M., Famulare, M., Frisbie, L. A., Painter, I. S., Burstein, R., Roychoudhury, P., Xie, H. J., Bakhash, S. A. M., Perez, R., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciac279 · Cited by 80
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
Emerging Vaccine-Breakthrough SARS-CoV-2 Variants
Wang, R., Chen, J., Hozumi, Y., Yin, C., & Wei, G. (2022) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.1c00557 · Cited by 82
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
“…some that are in the clinic (imdevimab, casirivimab, sotrovimab, bamlanivimab, etesevimab, AZD8895, and AZD1061 mAbs; see Figure 2A or Table 1 for correspondence between initial and generic names of mAbs) (Dong et al., 2021; Greaney et al., 2021a, 2021b; Starr et al., 2021a, 2021b, 2021c).”
Rotondo, J. C., Martini, F., Maritati, M., Mazziotta, C., Mauro, G. D., Lanzillotti, C., Barp, N., Gallerani, A., Tognon, M. G., & Contini, C. (2021) · Viruses · doi:10.3390/v13091687 · Cited by 81
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
Characterization of a new SARS-CoV-2 variant that emerged in Brazil
Imai, M., Halfmann, P., Yamayoshi, S., Iwatsuki‐Horimoto, K., Chiba, S., Watanabe, T., Nakajima, N., Ito, M., Kuroda, M., Kiso, M., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2106535118 · Cited by 77
Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants
Koehler, M., Ray, A., Moreira, R. A., Juniku, B., Poma, A. B., & Alsteens, D. (2021) · Nature Communications · doi:10.1038/s41467-021-27325-1 · Cited by 72
Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape
Mast, F. D., Fridy, P. C., Ketaren, N. E., Wang, J., Jacobs, E. Y., Olivier, J. P., Sanyal, T., Molloy, K. R., Schmidt, F., Rutkowska, M., et al. (2021) · eLife · doi:10.7554/elife.73027 · Cited by 69
Pan, T. S., Chen, R., He, X., Yuan, Y., Deng, X., Li, R., Yan, H., Yan, S., Liu, J., Zhang, Y., et al. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00848-1 · Cited by 72
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
The global transmission of new coronavirus variants
Zhao, Y., Huang, J., Zhang, L., Chen, S., Gao, J., & Jiao, H. (2021) · Environmental Research · doi:10.1016/j.envres.2021.112240 · Cited by 73
“Compared to the original lineage, the new coronavirus variants show a higher transmissibility and resistance to antibody (Greaney et al., 2021; Volz et al., 2021a, b), for instance, the percentage of people that infected with alpha lineage in the UK had raised from 0.1% in early October to 49.7% in…”
InfluentialGregory, 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
Verkhivker, G. M., Agajanian, S., Öztaş, D. Y., & Gupta, G. (2021) · Biochemistry · doi:10.1021/acs.biochem.1c00139 · Cited by 62
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
Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape
Witte, L., Baharani, V. A., Schmidt, F., Wang, Z., Cho, A., Raspe, R., Guzmán-Cardozo, C., Muecksch, F., Canis, M., Park, D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-35927-0 · Cited by 68
Metadata
- Authors
- Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Fred Hutch Cancer Center (US)
- Corresponding author
- Bloom, Jesse D.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2021-03
- Volume
- 29
- Issue
- 3
- Pages
- 463-476.e6
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC7869748
- OpenAlex
- W3127852352
- Cited by
- 1,178
- References
- 88
- Citations by year
- 2026: 43 · 2025: 64 · 2024: 79 · 2023: 158 · 2022: 361 · 2021: 459
- FWCI
- 83.70
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 374 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell Host & Microbe (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Gates Foundation (INV-004949)
- Howard Hughes Medical Institute
- NIAID (T32AI083203, R01AI141707, F30AI149928, R01AI127893)
- Damon Runyon Cancer Research Foundation (DRG-2381-19)
- Office of Research Infrastructure Programs, National Institutes of Health (S10OD028685)
- National Institutes of Health
- Vanderbilt University
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, spike protein receptor-binding domain, antibody escape mutations, neutralizing antibodies, E484K mutation, antibody epitopes, convalescent plasma, humoral immunity
- MeSH terms
- Protein Domains, COVID-19, SARS-CoV-2, Adult, Aged, Antibodies, Monoclonal, Antibodies, Viral, Binding Sites, Cell Line, Female, Humans, Male, Middle Aged, Mutation, Prospective Studies, Protein Binding, Receptors, Virus, Young Adult, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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