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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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“…the variants, these mutations have been previously reported as increasing the binding affinity between RBD and hACE2 (Barton et al., 2021), also the E484K substitution is known to facilitate evasion from neutralizing antibodies (Andreano et al., 2021; Greaney et al., 2021 ,Weisblum et al., 2020).”
BackgroundGenomic Tracking of SARS-CoV-2 Variants in Myanmar
Oo, K. Z., Htun, Z. W., Aung, N. M., Win, K. K., Linn, K. Z., Htoo, S. P., Aung, P. K., Oo, T. W., Zaw, M. T., Ko, L. Y., et al. (2022) · Vaccines · doi:10.3390/vaccines11010006 · Cited by 1
Pandemic response: Isolationism or solidarity?
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“Previous comprehensive mutational analysis using pseudo-type virus also showed that the impact of amino acid substitutions in three main epitopes in the RBD varied among individuals.(9) Many factors are likely involved in determining which neutralizing epitopes become dominant in an individual.”
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Anraku, Y., Kita, S., Onodera, T., Sato, A., Tadokoro, T., Ito, S., Adachi, Y., Kotaki, R., Suzuki, T., Sasaki, J., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-07827-0 · Cited by 1
Jana, I. D., Kanjo, K., Roy, S., Bhasin, M., Bhattacharya, S., Banerjee, I., Jana, S., Chatterjee, A., Chakraborty, A., Chakraborty, S. K., et al. (2025) · Journal of Virology · doi:10.1128/jvi.00051-25 · Cited by 1
“The majority of human neutralizing antibodies, isolated from convalescent or vaccinated sera, target conformational epitopes in the RBD Receptor Binding Motif (RBM) or in the conserved core of RBD 17–19 .”
InfluentialLópez-Aladid, R., Bueno, L., Farriol-Duran, R., Porta‐Pardo, E., Aguilar, R., Vidal, M., Jiménez, A., Cabrera, R., Vázquez, N., López-Gavín, A., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-00555-9 · Cited by 1
Parry, R. H., Shang, Y., Sng, J. D. J., McMillan, C. L. D., Modhiran, N., Amarilla, A. A., Isaacs, A., Liang, B., Muller, D. A., Rawle, D. J., et al. (2025) · Journal of Medical Virology · doi:10.1002/jmv.70642 · Cited by 1
In Vivo Determinants of Hepatitis C Virus Adaptation and Escape From Neutralizing Antibody AR5A
Velázquez‐Moctezuma, R., Burm, R., Verhoye, L., Collignon, L., Holmbeck, K., Giang, E., Law, M., Bukh, J., Meuleman, P., & Prentoe, J. C. (2025) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2025.101684 · Cited by 1
“Virus variants with broad resistance to NAbs have been identified after vaccination against hepatitis B virus, as well as SARS-CoV-2 responsible for the global COVID-19 pandemic, 63–66 underscoring the importance of studying virus escape mutations in vaccine development.”
RR:C19 Editorial: Immune Escape and Viral Evolution
Borgo, G. M., Huilgol, Y. S., Cronce, M. J., & Bertozzi, S. (2021) · Rapid Reviews COVID-19 · doi:10.1162/2e3983f5.660ac656 · Cited by 1
In Vitro Diagnostics for COVID-19: State-of-the-Art, Future Directions and Role in Pandemic Response
Vashist, S. K., Subramanian, M., & Djoko, G. (2021) · IntechOpen eBooks · doi:10.5772/intechopen.97775 · Cited by 1
The evolutionary ecology of SARS‐CoV‐2: A missing perspective in the One Health approach
Selbach, C., Vanhove, M. P. M., & Mouritsen, K. N. (2021) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14160 · Cited by 1
Harnessing Immunological Targets for COVID-19 Immunotherapy
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A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design
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Overview of the first year of the SARS-CoV-2 pandemic in Serbia and the Pirot County
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Development of PCR test for detection of the SARS-CoV-2 genetic variants alpha, beta, gamma, delta
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Global Biologic Characteristics of Variants of Concern and Variants of Interest of SARS-CoV-2
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Medical technologies assessment in COVID-19
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“Immune escape has been linked to changes in E484K [21].”
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Virus Mutation and Countermeasures
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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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