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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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BepiTBR: T-B reciprocity enhances B cell epitope prediction
Zhu, J. J., Gouru, A., Wu, F., Berzofsky, J. A., Xie, Y., & Wang, T. (2022) · iScience · doi:10.1016/j.isci.2022.103764 · Cited by 21
Organoid Models of SARS-CoV-2 Infection: What Have We Learned about COVID-19?
Tran, B. M., Deliyannis, G., Hachani, A., Earnest, L., Torresi, J., & Vincan, E. (2022) · Organoids · doi:10.3390/organoids1010002 · Cited by 21
Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy
Damavandi, A. R., Dowran, R., Sharif, S. A., Kashanchi, F., & Jafari, R. (2022) · Medical Microbiology and Immunology · doi:10.1007/s00430-022-00729-6 · Cited by 21
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Makowski, E. K., Schardt, J. S., Smith, M. D., & Tessier, P. M. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010160 · Cited by 20
“Experimentally, multiple studies have reported impressive progress characterizing the impact of RBD mutations on ACE2 and human serum antibody affinity [2, 6].”
InfluentialSpinicci, M., Mazzoni, A., Coppi, M., Antonelli, A., Salvati, L., Maggi, L., Basile, G., Graziani, L., Lauria, N. D., Pilato, V. D., et al. (2022) · Journal of Clinical Immunology · doi:10.1007/s10875-022-01313-6 · Cited by 19
A tale of three SARS-CoV-2 variants with independently acquired P681H mutations in New York StatePreprint
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Structural basis for broad sarbecovirus neutralization by a human monoclonal antibodyPreprint
Tortorici, M. A., Czudnochowski, N., Starr, T. N., Marzi, R., Walls, A. C., Zatta, F., Bowen, J. E., Jaconi, S., di Iulio, J., Wang, Z., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.07.438818 · Cited by 22
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Self-citationEpitope mapping via in vitro deep mutational scanning methods and its applications
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“Similarly, the RBD epitopes are characterised as the ridge (residues 455 – 456, 471 – 491), loop (residues 443 – 453, 494 – 502), and core (residues 365 – 373, 382 – 387) (Greaney et al., 2021).”
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COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development
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Genetic differentiation and diversity of SARS-CoV-2 Omicron variant in its early outbreak
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Yeast Surface Display: New Opportunities for a Time-Tested Protein Engineering System
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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
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Spread of endemic SARS-CoV-2 lineages in Russia before April 2021
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A spatial vaccination strategy to reduce the risk of vaccine-resistant variants
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“(Mutant binding data of the type produced in [13,31] may be used to assess the existence and sign of potential correlation between, for example, antibody and receptor binding.)”
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Vaccination boosts protective responses and counters SARS-CoV-2-induced pathogenic memory B cellsPreprint
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Richard, D., Shaw, L. P., Lanfear, R., Corbett-Detig, R. B., Hinrichs, A. S., McBroome, J., Turakhia, Y., Acman, M., Owen, C. J., Tan, C. C. S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.06.442903 · Cited by 20
Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape StrategiesPreprint
Lan, S., Neilsen, G., Slack, R. L., Cantara, W. A., Castaner, A. E., Lorson, Z. C., Lulkin, N., Zhang, H., Lee, J., Cilento, M. E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.31.522389 · Cited by 22
“Among the new strains, multiple versions of Omicron have been reported with more than 500 Omicron sublineages in existence [49-53][61].”
BackgroundSelvavinayagam, S. T., Karishma, S. J., Hemashree, K., Yong, Y. K., Suvaithenamudhan, S., Rajeshkumar, M., Aswathy, B., Kalaivani, V., Priyanka, J., Kumaresan, A., et al. (2023) · The Lancet Regional Health - Southeast Asia · doi:10.1016/j.lansea.2023.100272 · Cited by 19
“17,18 The S477N and P681H mutations play an essential role in SARS-CoV-2 infectivity by enhancing its binding af fi nity for ACE2, 19 and by augmenting furin cleavage of the S protein, 20 respectively.”
BackgroundMise‐Omata, S., Ikeda, M., Takeshita, M., Uwamino, Y., Wakui, M., Arai, T., Yoshifuji, A., Murano, K., Siomi, H., Nakagawara, K., et al. (2022) · The Journal of Immunology · doi:10.4049/jimmunol.2200525 · Cited by 20
Mutational fitness landscape of human influenza H3N2 neuraminidase
Lei, R., Garcia, A. H., Tan, T. J. C., Teo, Q. W., Wang, Y., Zhang, X., Luo, S., Nair, S. K., Peng, J., & Wu, N. C. (2023) · Cell Reports · doi:10.1016/j.celrep.2022.111951 · Cited by 19
“14 Recent deep mutational scanning studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor-binding domain have provided critical insights into the evolution and antibody escape of SARS-CoV-2 15–17 as well as COVID-19 vaccine design.”
Adams, L. J., VanBlargan, L. A., Liu, Z., Gilchuk, P., Zhao, H., Chen, R. E., Raju, S., Chong, Z., Whitener, B. M., Shrihari, S., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101305 · Cited by 18
Adjuvanted SARS-CoV-2 spike protein vaccination elicits long-lived plasma cells in nonhuman primates
Prabhakaran, M. S., Matassoli, F. L., Leggat, D. J., Hoover, A., Srikanth, A., Wu, W., Henry, A. R., Wang, J. P., Lin, B. C., Teng, I., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.add5960 · Cited by 19
“We also screened for binding to RBD residues harboring single, dual, or triple mutations associated with increased transmission or attenuation of neutralization of convalescent plasma and monoclonal antibodies ( 23 – 26 ).”
BackgroundPharmaceutical Aspects and Clinical Evaluation of COVID-19 Vaccines
Hofman, K., Shenoy, G. N., Chak, V., & Balu‐Iyer, S. V. (2021) · Immunological Investigations · doi:10.1080/08820139.2021.1904977 · Cited by 20
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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