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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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Online news regarding the spread of the omicron variant in Southeast Asia
Rulinawaty, R., Sjuchro, D. W., Syahrial, S., Badollahi, M. Z., & Hussain, Z. (2022) · Jurnal Studi Komunikasi (Indonesian Journal of Communications Studies) · doi:10.25139/jsk.v6i2.4865 · Cited by 10
Tragni, V., Mercurio, I., Paoletti, D. P., Onofrio, A., Laera, L., Beltrame, L. C., Sgobba, M. N., Guerra, L., Volpicella, M., Grassi, A., et al. (2023) · Journal of Medical Virology · doi:10.1002/jmv.28875 · Cited by 10
Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoringPreprint
Maier, W., Bray, S. A., van den Beek, M., Bouvier, D., Coraor, N., Miladi, M., Singh, B., Rambla, J., Baker, D., Roach, N. P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.25.437046 · Cited by 10
Evaluation of mRNA-1273 against SARS-CoV-2 B.1.351 Infection in Nonhuman PrimatesPreprint
Corbett, K. S., Werner, A. P., Connell, S. O., Gagné, M., Lai, L., Moliva, J. I., Flynn, B. J., Choi, A., Koch, M. J., Foulds, K. E., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.21.445189 · Cited by 11
Predictive Profiling of SARS-CoV-2 Variants by Deep Mutational LearningPreprint
Taft, J. M., Weber, C. R., Gao, B., Ehling, R. A., Han, J., Frei, L., Metcalfe, S. W., Yermanos, A., Kelton, W., & Reddy, S. T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.07.471580 · Cited by 10
“Bloom and colleagues have performed yeast surface display and deep mutational scanning (DMS) ( 28 ) on the entire 201 amino acid RBD of SARS-CoV-2 in order to determine the impact of single-position substitutions on binding to ACE2 and monoclonal or serum antibodies ( 22 , 29 – 32 ).”
BackgroundGiovanetti, M., Fonseca, V., Wilkinson, E., Tegally, H., San, E. J., Althaus, C. L., Xavier, J., Slavov, S. N., Viala, V. L., Lima, A. R. J., et al. (2021) · medRxiv · doi:10.1101/2021.12.27.21268309 · Cited by 10
Verkhivker, G. M., Agajanian, S., Kassab, R., & Krishnan, K. (2022) · Biomolecules · doi:10.3390/biom12070964 · Cited by 11
Bhadane, R. N., & Salo‐Ahen, O. M. H. (2022) · Biomedicines · doi:10.3390/biomedicines10112779 · Cited by 10
Rapid, tunable, and multiplexed detection of RNA using convective array PCR
Sullivan, A. T., Rao, V., Rockwood, T., Gandhi, J., Gruzka, S., O’Connor, L., Wang, B., Ragan, K. B., Zhang, D. Y., & Khodakov, D. A. (2023) · Communications Biology · doi:10.1038/s42003-023-05346-4 · Cited by 9
Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses
Lebedin, M. Y., Ratswohl, C., Garg, A. K., Schips, M., García, C. V., Spatt, L., Thibeault, C., Obermayer, B., Weiner, J. M., Velásquez, I. M., et al. (2024) · iScience · doi:10.1016/j.isci.2024.109330 · Cited by 9
“66 As structural studies imply that around two-thirds of spikes display 1–2 RBDs in an ACE2-available ‘‘up’’-state, 55,59 we suggest that sACE2-mediated masking may further contribute to the dominance of class 2 antibodies.”
BackgroundModeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies
Koopman, J. S., Simon, C. P., Getz, W. M., & Salter, R. M. (2021) · Epidemics · doi:10.1016/j.epidem.2021.100484 · Cited by 9
An Overview of SARS-CoV-2 Molecular Diagnostics in Europe
Davies, E. A., Farooq, H. Z., Brown, B., Tilston, P., McEwan, A. K., Birtles, A., O'Hara, R. W., Ahmad, S. S. Y., Machin, N. W., Hesketh, L. M., et al. (2022) · Clinics in Laboratory Medicine · doi:10.1016/j.cll.2022.02.005 · Cited by 9
Magalis, B. R., Mavian, C. N., Tagliamonte, M. S., Rich, S. N., Cash, M. N., Riva, A., Loeb, J. C., Norris, M. H., Amador, D. M., Zhang, Y., et al. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27726 · Cited by 9
Singh, L., San, J. E., Tegally, H., Brzoska, P. M., Anyaneji, U. J., Wilkinson, E., Clark, L. V., Giandhari, J., Pillay, S., Lessells, R. J., et al. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000774 · Cited by 7
Fung, K.-M., Lai, S.-J., Lin, T.-L., & Tseng, T. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.797132 · Cited by 9
Shim, H. W., Shin, J. H., Shin, S. C., Lee, H. J., So, K. S., Lee, S. Y., Jun, J. W., Seo, J. K., Lee, H. S., Lee, S. Y., et al. (2022) · Diagnostics · doi:10.3390/diagnostics12081924 · Cited by 10
Yogev, O., Weissbrod, O., Battistoni, G., Bressan, D., Naamati, A., Falciatori, I., Berkyurek, A. C., Rasnic, R., Izuagbe, R., Hosmillo, M. D. T., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-04589-5 · Cited by 14
Genetic diversity and evolutionary dynamics of the Omicron variant of SARS-CoV-2 in Morocco
Mazouri, S. E., Essabbar, A., Aanniz, T., Eljaoudi, R., Belyamani, L., Ibrahimi, A., & Ouadghiri, M. (2023) · Pathogens and Global Health · doi:10.1080/20477724.2023.2250942 · Cited by 9
“We estimated the potential mutational escape of SARS-CoV-2 Omicron variant using a mutational antigenic profiling of SARS-CoV-2 RBD against a panel of antibodies targeting diverse RBD epitopes [22].”
MethodBruun, T. U. J., Do, J., Weidenbacher, P. A. B., Utz, A., & Kim, P. S. (2024) · ACS Central Science · doi:10.1021/acscentsci.4c00722 · Cited by 9
Evolving Patterns in COVID-19: The Virus, its Variants and Infectivity-cum-Virulence
Nikhra, V. (2021) · Biomedical Journal of Scientific & Technical Research · doi:10.26717/bjstr.2021.33.005382 · Cited by 9
Young, R., Solis, C. J., Barriga-Fehrman, A., Abogabir, C., Thadani, A. R., Labarca, M., Bustamante, E. I., Tapia, C. V., Sarda, A. G., Sepúlveda, F., et al. (2021) · eLife · doi:10.7554/elife.70333 · Cited by 9
Miyakawa, K., Kubo, S., Jeremiah, S. S., Go, H., Yamaoka, Y., Ohtake, N., Kato, H., Ikeda, S., Mihara, T., Matsuba, I., et al. (2021) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofab626 · Cited by 10
Abdulnoor, M., Eshaghi, A., Perusini, S. J., Broukhanski, G., Corbeil, A., Cronin, K. I., Fittipaldi, N., Forbes, J. D., Guthrie, J. L., Kus, J. V., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00681-21 · Cited by 9
Cia, G., Pucci, F., & Rooman, M. J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042078 · Cited by 9
Morris, C. P., Luo, C. H., Sachithanandham, J., Li, M., Schwartz, M. C., Gaston, D. C., Gniazdowski, V., Giraldo, N. A., Amadi, A., Norton, J. M., et al. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.809407 · Cited by 10
Ding, Z., Chen, T., Lan, J., & Wong, G. (2022) · Biosafety and Health · doi:10.1016/j.bsheal.2022.05.001 · Cited by 9
Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS
Forte, E., Soye, B. J. D., Melani, R. D., Hollas, M. A. R., Kafader, J. O., Sha, B. E., Schneider, J. R., & Kelleher, N. L. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00514 · Cited by 8
Egia‐Mendikute, L., Bosch, A., Prieto‐Fernández, E., Vila-Vecilla, L., Zanetti, S. R., Lee, S. Y., Jiménez-Lasheras, B., Río, A. G.-D., Antoñana-Vildosola, A., de Blas, A., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1014309 · Cited by 9
Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater
Conway, M. J., Yang, H., Revord, L. A., Novay, M. P., Lee, R. J., Ward, A. S., Abel, J. D., Williams, M. R., Uzarski, R. L., & Alm, E. W. (2024) · BMC Genomics · doi:10.1186/s12864-024-09977-7 · Cited by 9
Acute Actions of Natriuretic Peptides in Coronary Vasculature and Ischaemic Myocardium
Rautureau, Y., & Baxter, G. F. (2004) · Current Pharmaceutical Design · doi:10.2174/1381612043383854 · Cited by 9
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Umair, M., Ikram, A., Salman, M., Badar, N., Haider, S. A., Rehman, Z., Ammar, M., Rana, M. S., & Ali, Q. (2021) · medRxiv · doi:10.1101/2021.07.14.21259909 · Cited by 9
Modeling viral evolution: A novel SIRSVIDE framework with application to SARS-CoV-2 dynamics
Jin, K., Tang, X., Qian, Z., Wú, Z., Yang, Z., Qian, T., Hon, C., & Lü, J. (2024) · hLife · doi:10.1016/j.hlife.2024.03.006 · Cited by 9
“The Spike protein facilitates host cell receptor recognition and contains antigenic sites crucial for antibody-antigen neutralization [60,106], making mutations in the Spike gene in fl uential on transmissibility, pathogenicity, and immune escape.”
Broad-spectrum coronavirus inhibitors discovered by modeling viral fusion dynamics
Reilly, C. B., Moore, J., Lightbown, S. L., Paul, A., Bernier, S. G., Carlson, K. E., & Ingber, D. E. (2025) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2025.1575747 · Cited by 9
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“Most of the sites where mutations have the most impact on serum neutralization are in the RBD, as expected from prior work showing that RBD-directed antibodies are usually responsible for most serum neutralizing activity (55–57), although mutations at some NTD sites also have a substantial effect.”
Self-citationAn Overview of the Epidemiologic, Diagnostic and Treatment Approaches of COVID-19: What do We Know?
Beyrampour-Basmenj, H., Milani, M., Kalan, A. E., Taleb, Z. B., Ward, K. D., Abbasabad, G. D., Serej, Z. A., & Kalan, M. E. (2021) · Public health reviews · doi:10.3389/phrs.2021.1604061 · Cited by 9
Characteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates
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“The occurrence of highly transmission and pathogenicity of Delta relied on the critical mutations in its spike protein, which were partially shared with other VOC (Deng et al., 2021; Greaney et al., 2021).”
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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