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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies
Open accessPreprint — published as 10.1016/j.chom.2021.02.003 · Paper page
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 serum antibodies are impacted by all mutations to the spike’s receptor-binding domain (RBD), the main target of serum neutralizing activity. Binding by polyclonal serum antibodies is affected by mutations in three main epitopes in the RBD, but there is substantial variation in the impact of mutations 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 sera is reduced >10-fold by several mutations, including one in emerging viral lineages in South Africa and Brazil. Going forward, these serum escape maps can inform surveillance of SARS-CoV-2 evolution.
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“The E484K mutation has been reported to abolish or substantially reduce neutralization by multiple potent monoclonal antibodies and polyclonal convalescent sera in both wild-type and pseudo-virus neutralization assays.12,13,17,18,22”
From Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant (2021) · cites this paper as [13]
Experimental — accuracy not yet measuredIn the citing paper
“The B.1.351 variant is characterized by three deleterious mutations at key antigenic sites in the RBD, including N501Y, K417N, and E484K, with the latter two having particular functional impact.”
From Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant (2021) · cites this paper as [13]
In the citing paper
“From a biological point of view, the breakthrough cases observed in this study might be due to immune evasion, mediated by particular alterations present in these strains 9,[23][24][25][26][27] .”
From Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals (2021) · cites this paper as [23]
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BackgroundInfluentialPreliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant
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“As a consequence, it could alter the effectiveness of current vaccines.(38)”
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SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants
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“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].”
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The effect of spike mutations on SARS-CoV-2 neutralization
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“351 strain do impair neutralization (Greaney et al., 2021; Wibmer et al., 2021).”
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“, 2021), E484K partly impairs neutralization resistance (Greaney et al., 2021), potentially compromising vaccines effectiveness (Baum et al.”
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“One of the mutations in this variant, N501Y, is located in the important receptor-binding domain (RBD) of spike protein, and is predicted to increase binding to human cells and reduce viral neutralization by the monoclonal antibody LY-CoV016 (Greaney et al., 2021; Starr et al., 2020).”
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An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain
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Self-citationPredicting the mutational drivers of future SARS-CoV-2 variants of concern
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“[14] Allison J Greaney, Andrea N Loes, Katharine HD Crawford, Tyler N Starr, Keara D Malone, He406 len Y Chu, and Jesse D Bloom.”
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“We accessed the deep mutation scanning published data by Starr et al., [43] to examine whether these changes would influence RBD and affinity to ACE-2.”
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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
- openRxiv
- Published
- 2021-01-04
- Volume
- 29
- Issue
- 3
- Pages
- 463-476.e6
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC7869748
- OpenAlex
- W3127852352
- Cited by
- 1,178
- References
- 58
- Citations by year
- 2026: 43 · 2025: 64 · 2024: 79 · 2023: 158 · 2022: 361 · 2021: 459
- FWCI
- 83.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cell Host & Microbe (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- Bill and Melinda Gates Foundation (INV-004949)
- Damon Runyon Cancer Research Foundation (DRG-2381-19)
- Washington Research Foundation
- Vanderbilt University
- University of Washington
- National Institutes of Health (1s10od028685-01)
- National Institute of Allergy and Infectious Diseases (R01AI127893, T32AI083203, F30AI149928, R01AI140891, R01AI141707)
- Office of Research Infrastructure Programs, National Institutes of Health (S10OD028685)
- 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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