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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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“Numerous mutations have been identified in SARS-CoV-2 VOCs, the vast majority of which occur on the S protein (28), which plays a critical role in host cell infection and immune response.”
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Marziano, V., Guzzetta, G., Mammone, A., Riccardo, F., Poletti, P., Trentini, F., Manica, M., Siddu, A., Bella, A., Stefanelli, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27532-w · Cited by 55
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Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics
Kudriavtsev, A. V., Vakhrusheva, A., Novoseletsky, V. N., Bozdaganyan, M. E., Шайтан, К. В., Kirpichnikov, M. P., & Sokolova, O. S. (2022) · Viruses · doi:10.3390/v14081603 · Cited by 52
On the road to ending the COVID-19 pandemic: Are we there yet?
Case, J. B., Winkler, E. S., Errico, J. M., & Diamond, M. (2021) · Virology · doi:10.1016/j.virol.2021.02.003 · Cited by 47
How will mass-vaccination change COVID-19 lockdown requirements in Australia?
Zachreson, C., Chang, S. L., Cliff, O. M., & Prokopenko, M. (2021) · The Lancet Regional Health - Western Pacific · doi:10.1016/j.lanwpc.2021.100224 · Cited by 49
The challenges of COVID‐19 Delta variant: Prevention and vaccine development
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Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals
Cohen, A. A., Keeffe, J. R., Schiepers, A., Dross, S., Greaney, A. J., Rorick, A. V., Gao, H., Gnanapragasam, P. N. P., Fan, C., West, A. P., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.052 · Cited by 51
“35,67,68 Here, DMS analyses of recall anti-RBD Abs from molecular fate-mapping studies demonstrated that mosaic-8b immunization boosted class 3 and 4 anti-RBD Abs originally elicited by primary vaccination with mRNA-LNP.”
Self-citationHuang, S., & Wang, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22063060 · Cited by 50
Muecksch, F., Wise, H. M., Templeton, K. E., Batchelor, B., Squires, M., McCance, K., JARVIS, L. M., Malloy, K., Furrie, E., Richardson, C., et al. (2022) · The Lancet Microbe · doi:10.1016/s2666-5247(22)00090-8 · Cited by 48
Durability of mRNA-1273-induced antibodies against SARS-CoV-2 variantsPreprint
Pegu, A., O’Connell, S. E., Schmidt, S. D., O'Dell, S. J., Talana, C. A., Lai, L., Albert, J., Anderson, E. J., Bennett, H., Corbett, K. S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.13.444010 · Cited by 50
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An Overview of Vaccines against SARS-CoV-2 in the COVID-19 Pandemic Era
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Verkhivker, G. M., Agajanian, S., Öztaş, D. Y., & Gupta, G. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00372 · Cited by 40
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 49
“scans of modified binding affinity [38] and/or mapping of escape mutations [53]).”
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From Bench to the Clinic: The Path to Translation of Nanotechnology-Enabled mRNA SARS-CoV-2 Vaccines
Lopez-Cantu, D. O., Wang, X., Carrasco-Magallanes, H., Afewerki, S., Zhang, X., Bonventre, J. V., & Ruiz‐Esparza, G. U. (2022) · Nano-Micro Letters · doi:10.1007/s40820-021-00771-8 · Cited by 49
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“A recent mapping of RBDmutations that escape REGN-COV2 cocktail and Eli Lilly’s LY-CoV016 antibodies (Starr et al., 2021a) using a deep mutational scanning method (Greaney et al., 2021c) revealed several sites whose point mutations mediate escape.”
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A review: Antibody-dependent enhancement in COVID-19: The not so friendly side of antibodies
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Chatterjee, D., Tauzin, A., Marchitto, L., Gong, S. Y., Boutin, M., Bourassa, C., Beaudoin-Bussières, G., Bo, Y., Ding, S., Laumaea, A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110429 · Cited by 46
“…(Gong et al., 2021; Saito et al., 2021) or immune evasion (K417N, N440K, G446S, S477N, E484A/K, Q493R) (Baum et al., 2020; Clark et al., 2021; Greaney et al., 2021a; Greaney et al., 2021b; Greaney et al., 2021c; Liu et al., 2020; Rappazzo et al., 2021; Starr et al., 2021; Weisblum et al., 2020).”
Chakraborty, S. (2021) · International Immunopharmacology · doi:10.1016/j.intimp.2021.108424 · Cited by 47
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 49
Multiplex Biosensing for Simultaneous Detection of Mutations in SARS-CoV-2
Xi, H., Jiang, H., Juhas, M., & Zhang, Y. (2021) · ACS Omega · doi:10.1021/acsomega.1c04024 · Cited by 48
Yang, W.-T., Huang, W.-H., Liao, T.-L., Hsiao, T.-H., Chuang, H.-N., & Liu, P.-Y. (2022) · Infection and Drug Resistance · doi:10.2147/idr.s344099 · Cited by 51
Immunity to SARS-CoV-2: Lessons Learned
FERGIE, J. E., & Srivastava, A. K. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.654165 · Cited by 46
The Genetic Variant of SARS-CoV-2: Would it matter for Controlling the Devastating Pandemic?
Guo, S., Liu, K., & Zheng, J. (2021) · International Journal of Biological Sciences · doi:10.7150/ijbs.59137 · Cited by 46
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“RBD-directed neutralizing antibodies have been shown to compose a large proportion of the neutralizing activity in sera from SARS-CoV-2-infected and vaccinated individuals (Greaney et al., 2021; Piccoli et al., 2020).”
Booster dose of mRNA vaccine augments waning T cell and antibody responses against SARS-CoV-2
Kurt, F. G. Ö., Lepper, A., Gerhards, C., Roemer, M., Lasser, S., Arkhypov, I., Bitsch, R., Bugert, P., Altevogt, P., Gouttefangeas, C., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1012526 · Cited by 48
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 42
“The K417N mutation, which is located in the subdominant, Class 1 epitope (Greaney et al. 2021b) of the SARS-CoV-2 receptor–binding domain (RBD), has little effect on polyclonal antibody escape.”
BackgroundMethodInfluentialSelf-citationMolecular insights into the adaptive evolution of SARS-CoV-2 spike protein
Yao, Z., Zhang, L., Duan, Y., Tang, X., & Lü, J. (2024) · Journal of Infection · doi:10.1016/j.jinf.2024.106121 · Cited by 49
The Development of SARS-CoV-2 Variants: The Gene Makes the Disease
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A point-of-care lateral flow assay for neutralising antibodies against SARS-CoV-2
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Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria
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The impact of Spike mutations on SARS-CoV-2 neutralizationPreprint
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SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants
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High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
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“We also performed an ELISA against the S protein and found that RBD antibody depletion did not affect binding to the S protein (Figure S3B), which is consistent with other studies that have found that the majority of S-protein-binding antibodies target non-RBD epitopes (Greaney et al., 2021; Piccoli et al., 2020).”
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Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution
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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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