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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 SARS-CoV-2 variant with lineage B.1.351 clusters investigation team (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.13.2100333 · Cited by 14
Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity
Tang, H., Gao, L., Wu, Z., Meng, F., Zhao, X., Shao, Y., Shi, X., Qiao, S., An, J., Du, X., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.720357 · Cited by 15
Variantes del SARS-CoV-2: epidemiología, fisiopatología y la importancia de las vacunas
Bedoya-Sommerkamp, M., Medina-Ranilla, J., Rodriguez, V. H. C., Li-Soldevilla, R., Vera-Albújar, Á., & Garcia, P. J. (2021) · Revista Peruana de Medicina Experimental y Salud Pública · doi:10.17843/rpmesp.2021.383.8734 · Cited by 13
Targeting the Fusion Process of SARS-CoV-2 Infection by Small Molecule Inhibitors
Park, S. B., Irvin, P., Hu, Z., Khan, M., Hu, X., Zeng, Q., Chen, C., Xu, M., Leek, M., Zang, R., et al. (2022) · mBio · doi:10.1128/mbio.03238-21 · Cited by 15
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Paul, K., Sibbertsen, F., Weiskopf, D., Lütgehetmann, M., Barroso, M., Danecka, M. K., Glau, L., Hecher, L., Hermann, K., Kohl, A., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.867577 · Cited by 13
Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice
Walls, A. C., VanBlargan, L. A., Wu, K., Choi, A., Navarro, M. J., Lee, D. W., Avena, L. E., Berrueta, D. M., Pham, M. N., Elbashir, S. M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111299 · Cited by 13
“For example, polyclonal neutralizing antibody responses resulting from infection or vaccination with ancestral SARS-CoV-2 isolates in humans and NHPs can be hyperfocused on position 484 in the RBD,which does not appear to be recapitulated in mice (Greaney et al., 2021; Walls et al., 2021).”
Neutralizing and enhancing antibodies against SARS-CoV-2
Liu, Y., & Arase, H. (2022) · Inflammation and Regeneration · doi:10.1186/s41232-022-00233-7 · Cited by 13
Verkhivker, G. M., Alshahrani, M., Gupta, G., Xiao, S., & Tao, P. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24097747 · Cited by 16
Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection
Wang, R., Han, Y., Zhang, R., Zhu, J., Nan, X., Liu, Y., Yang, Z., Zhou, B., Yu, J., Lin, Z., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.10.007 · Cited by 13
mRNA and Synthesis-Based Therapeutic Proteins: A Non-Recombinant Affordable Option
Niazi, S. K., & Magoola, M. (2023) · Biologics · doi:10.3390/biologics3040020 · Cited by 13
Current Updates on Variants of SARS‐CoV‐ 2: Systematic Review
Erkihun, M., Ayele, B., Asmare, Z., & Endalamaw, K. (2024) · Health Science Reports · doi:10.1002/hsr2.70166 · Cited by 16
“The primary K417N, E484K, N501Y, and D614G mutations are covered by the beta variant's mutations; of these, the E484K mutation was able to lessen the variants' susceptibility to the potency of antibodies triggering immune escape [66].”
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Bednarski, E., Estrada, P. M. D. R., DaSilva, J., Boukadida, C., Zhang, F., Luna-Villalobos, Y. A., Rodríguez-Rangel, X., Pitén-Isidro, E., Luna-García, E., Díaz-Rivera, D., et al. (2022) · mBio · doi:10.1128/mbio.00840-22 · Cited by 15
A Complementary Union of SARS-CoV2 Natural and Vaccine Induced Immune Responses
Torresi, J., Edeling, M. A., Nolan, T. M., & Godfrey, D. I. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.914167 · Cited by 15
Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding
Perlinska, A. P., Stasiulewicz, A., Nguyen, M. L., Świderska, K. W., Żmudziński, M., Maksymiuk, A. W., Drąg, M., & Sulkowska, J. I. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010667 · Cited by 14
Miteva, D., Kitanova, M., Batselova, H., Lazova, S., Chervenkov, L., Peshevska-Sekulovska, M., Sekulovski, M., Gulinac, M., Vasilev, G., Tomov, L., et al. (2023) · Vaccines · doi:10.3390/vaccines11071181 · Cited by 16
Targeting Viral Surface Proteins through Structure-Based Design
Narkhede, Y. B., Gonzalez, K. J., & Strauch, E. (2021) · Viruses · doi:10.3390/v13071320 · Cited by 15
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“Specific Omicron RBD mutations linked to neutralizing antibody escape include: G339D [54], S375F [54], K417N [54,56], N440K [54,57,58], G446S [54,58], L452R [20], S477N [20], T478K [20], F486V [20] and Q493R [54,57,58].”
InfluentialTranscriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection
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“Although our measurement of serum antibody levels used an ELISA against the entire S protein (not just the RBD), RBD-specific antibodies account for the vast majority of SARS-CoV-2 neutralization (26), and thus, we focused our analyses on B cells that make these key RBD-specific antibodies.”
MethodQuantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features
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“9 – 12, where due to reduced sample size fewer AA positions were screened in for assessment of differential VE.”
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Highly versatile antibody binding assay for the detection of SARS-CoV-2 infection and vaccination
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Host chitinase 3-like-1 is a universal therapeutic target for SARS-CoV-2 viral variants in COVID-19
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Potent SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models
Takeshita, M., Fukuyama, H., Kamada, K., Matsumoto, T., Makino‐Okamura, C., Uchikubo‐Kamo, T., Tomabechi, Y., Hanada, K., Moriyama, S., Takahashi, Y., et al. (2022) · iScience · doi:10.1016/j.isci.2022.105596 · Cited by 13
“The unevenly distributed epitopes of the selected antibodies are consistent with previous reports 35,36 that antibodies in the sera of patients infected with Wuhan strains mainly target the area around E484.”
Conformational stability of SARS-CoV-2 glycoprotein spike variants
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Vaccine Candidate Against COVID-19 Based on Structurally Modified Plant Virus as an Adjuvant
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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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