PreprintCited by 1,178SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesSARS-CoV-2 detection and testing

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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

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Greaney, Allison J., Loes, Andrea N., Crawford, Katharine H.D., Starr, Tyler N., Malone, Keara D., Chu, Helen Y., Bloom, Jesse D.·2021·Cell Host & Microbe

DOI 10.1101/2020.12.31.425021PMC PMC7869748

Preprint — published as 10.1016/j.chom.2021.02.003 · Paper page

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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 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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Fluorescent nanodiamond-based spin-enhanced lateral flow immunoassay for detection of SARS-CoV-2 nucleocapsid protein and spike protein from different variants
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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function
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Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies
Muecksch, F., Weisblum, Y., Barnes, C. O., Schmidt, F., Schaefer-Babajew, D., Lorenzi, J. C. C., Flyak, A. I., DeLaitsch, A. T., Huey-Tubman, K. E., Hou, S., et al. (2021) · doi:10.1101/2021.03.07.434227 · Cited by 39
“…resistance to class 1, 2 and 3 antibodies in cell culture has repeatedly identified K417, E484 and N501 substitutions, with E484K giving the most pervasive effects against polyclonal plasma (Baum et al., 2020; Greaney et al., 2021; Liu et al., 2021; Wang et al., 2021; Weisblum et al., 2020).”
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Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis
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A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS‐CoV‐2 variants and wild‐type of the virus
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A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil
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BackgroundInfluential
Spike Protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasionPreprint
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Background
Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations
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“The E484K mutation, located in the RBD, not only enhanced binding with ACE2, it also exhibited strong or moderate resistance to several human neutralizing antibodies and human convalescent sera [52,76,78,80,82,83], which indicates this mutation is important in the viral evolution to escape neutralizing antibodies.”
Background

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: Greaney, Allison J.
Loes, Andrea N.
Crawford, Katharine H.D.
Starr, Tyler N.
Chu, Helen Y.
Bloom, Jesse D.
Venue: Cell Host & Microbe
Publisher: openRxiv
Published: 2021-01-04
Volume: 29
Issue: 3
Pages: 463-476.e6
ISSN: 1931-3128 (ISSN-L)
DOI: 10.1101/2020.12.31.425021
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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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

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