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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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“V1 variant, where evidence indicates that the mutations do not impact vaccine efficacy [3-6].”
Early insight into antibody-dependent enhancement after SARS-CoV-2 mRNA vaccination
Hasan, A., Al-Mulla, M. R., Abubaker, J. A., & Al‐Mulla, F. (2021) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2021.1969855 · Cited by 6
Ghosh, A., Kar, P. K., Gautam, A., Gupta, R. K., Singh, R., Chakravarti, R., Ravichandiran, V., Dastidar, S. G., Ghosh, D., & Roy, S. (2022) · RSC Medicinal Chemistry · doi:10.1039/d2md00009a · Cited by 8
Longitudinal Analysis of Coronavirus-Neutralizing Activity in COVID-19 Patients
Hastert, F. D., Henß, L., von Rhein, C., Gerbeth, J., Wieters, I., Borgans, F., Khodamoradi, Y., Zacharowski, K. D., Rohde, G. G. U., Vehreschild, M. J. G. T., et al. (2022) · Viruses · doi:10.3390/v14050882 · Cited by 6
Sun, Z., Kim, A., Sobolewski, M. D., Enick, N., Chen, C., Adams, C., Jacobs, J. L., McCormick, K. D., Mellors, J. W., Dimitrov, D. S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.22.436481 · Cited by 6
SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2Preprint
Weekley, C. M., Purcell, D. F. J., & Parker, M. W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.16.434488 · Cited by 6
How unequal vaccine distribution promotes the evolution of vaccine escapePreprint
Gerrish, P. J., Saldaña, F., Galeota-Sprung, B., Colato, A., Rodríguez‐Torres, E. E., & Velasco‐Hernández, J. X. (2021) · medRxiv · doi:10.1101/2021.03.27.21254453 · Cited by 8
Tran, T. T., Vaage, E. B., Mehta, A., Chopra, A., Kolderup, A., Anthi, A. K., König, M. S. S., Nygaard, G. O., Lind, A., Müller, F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.26.484261 · Cited by 6
“RBDACE2 interaction assays, however, detect antibodies that bind to epitopes that undergo mutations driven by immune escape (9-12).”
BackgroundOng, Y. C., Tejo, B. A., & Yap, W. B. (2024) · Biomedicines · doi:10.3390/biomedicines12112530 · Cited by 6
Rahman, M. A., Becerra‐Flores, M., Patskovsky, Y., de Castro, I. S., Bissa, M., Basu, S., Shen, X., Williams, L. D., Sarkis, S., N’Guessan, K. F., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1139402 · Cited by 5
An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021
Loconsole, D., Sallustio, A., Centrone, F., Casulli, D., Ferrara, M. M., Sanguedolce, A., Accogli, M., & Chironna, M. (2021) · Tropical Medicine and Infectious Disease · doi:10.3390/tropicalmed6030151 · Cited by 5
A SARS‐CoV‐2 Neutralization Assay Using Single Molecule Arrays
Gilboa, T., Cohen, L., Cheng, C., Lazarovits, R., Uwamanzu‐Nna, A., Han, I., Griswold, K., Barry, N., Thompson, D. B., Kohman, R. E., et al. (2021) · Angewandte Chemie · doi:10.1002/ange.202110702 · Cited by 5
Hussen, B. M., Sabir, D. K., Karim, Y., Karim, K. K., & Hidayat, H. J. (2022) · Applied Nanoscience · doi:10.1007/s13204-021-02300-w · Cited by 5
RetractedVerkhivker, G. M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031646 · Cited by 5
Diversidad genómica en SARS-CoV-2: Mutaciones y variantes
Aguilar–Gamboa, F. R., Suclupe-Campos, D. O., Vega-Fernández, J. A., & Silva-Díaz, H. (2021) · Revista del Cuerpo Médico Hospital Nacional Almanzor Aguinaga Asenjo · doi:10.35434/rcmhnaaa.2021.144.1465 · Cited by 5
Kumar, A., Ladha, A., Choudhury, A., Ikbal, A. M. A., Bhattacharjee, B., Das, T., Gupta, G., Sharma, C., Sarbajna, A., Mandal, S. C., et al. (2022) · Expert Review of Vaccines · doi:10.1080/14760584.2022.2081156 · Cited by 5
Çubuk, H., & Özbil, M. (2022) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2022.108260 · Cited by 5
“Furthermore, several mutations on the SARS-CoV-2 spike protein changed the SARS-CoV-2-hACE2 binding affinities and also transmissivity as well [14,16,17].”
Walker, M. R., Podlekareva, D. N., Johnsen, S., Leerhøy, B., Fougeroux, C. E., Søgaard, M., Salanti, A., Ditlev, S. B., & Barfod, L. K. (2022) · Viruses · doi:10.3390/v14091861 · Cited by 5
Di, Y., Lew, J. M., Goncin, U., Radomska, A., Rout, S. S., Gray, B. E. T., Machtaler, S., Falzarano, D., & Lavender, K. J. (2022) · Viruses · doi:10.3390/v14102272 · Cited by 6
Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13
Lamothe, G., Carbonneau, J., Beauparlant, C. J., Vincent, T., Quessy, P., Guedon, A., Kobinger, G., Lemay, J.-F., Boivin, G., Droit, A., et al. (2023) · The CRISPR Journal · doi:10.1089/crispr.2023.0007 · Cited by 5
Schöfbänker, M., Neddermeyer, R., Günther, T., Mueller, M., Romberg, M.-L., Classen, N., Hennies, M. T., Hrincius, E. R., Ludwig, S., Kühn, J., et al. (2023) · Vaccines · doi:10.3390/vaccines11121832 · Cited by 5
“Viral variants frequently evade neutralising immune responses or therapeutic monoclonal antibodies through mutations within immunodominant epitopes such as E484 of the RBD, with Omicron and its subvariants accumulating more than 30 mutations within spike [11,19–23].”
BackgroundKetaren, N. E., Mast, F. D., Fridy, P. C., Olivier, J. P., Sanyal, T., Sali, A., Chait, B. T., Rout, M. P., & Aitchison, J. D. (2024) · eLife · doi:10.7554/elife.89423.3 · Cited by 5
“Importantly, the L452R mutation seems to be a key substitution that contributes to reduced or abolished neutralizing abilities of many mAbs ( Laurini, Marson et al. 2021 , Starr, Greaney et al. 2021 , Starr, Greaney et al. 2021 ).”
BackgroundRepeat offenders: PRRSV-2 clinical re-breaks from a whole genome perspective
Baker, J. P., Rovira, A., & VanderWaal, K. L. (2025) · Veterinary Microbiology · doi:10.1016/j.vetmic.2025.110411 · Cited by 5
Searching for escape-resistant anti–SARS-CoV-2 neutralizing antibodies
Mahla, R. S., & Dustin, L. B. (2022) · Journal of Clinical Investigation · doi:10.1172/jci157416 · Cited by 5
Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France
Colson, P., Fantini, J., Yahi, N., Delerce, J., Levasseur, A., Fournier, P., Lagier, J., Raoult, D., & Scola, B. L. (2022) · Archives of Virology · doi:10.1007/s00705-021-05331-4 · Cited by 4
Martinell, M., Andersson, T., Mannsverk, S., Bergholm, J., Ellström, P., Hill, A., Lindh, J. G., & Kaden, R. (2022) · Viruses · doi:10.3390/v14030504 · Cited by 5
Host–pathogen dynamics in longitudinal clinical specimens from patients with COVID-19
Lin, M. J., Rachleff, V. M., Xie, H. J., Shrestha, L., Lieberman, N. A. P., Peddu, V., Addetia, A., Casto, A. M., Breit, N., Mathias, P. C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-09752-2 · Cited by 6
Pseudovirus-Based Assays for the Measurement of Antibody-Mediated Neutralization of SARS-CoV-2
Balinsky, C. A., Jani, V., Sun, P., Williams, M., Defang, G. N., & Porter, K. R. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2111-0_21 · Cited by 5
Tang, H., Ke, Y., Wang, L., Wu, M., Sun, T., & Zhu, J. (2022) · Pharmaceuticals · doi:10.3390/ph15081002 · Cited by 4
Pohler, A., Abdelfatah, S., Riedl, M., Meesters, C., Hildebrandt, A., & Efferth, T. (2022) · Pharmaceuticals · doi:10.3390/ph15091046 · Cited by 5
Ciuffreda, L., González‐Montelongo, R., Alcoba-Flórez, J., de Artola, D. G.-M., Gil-Campesino, H., Rodríguez‐Pérez, H., Íñigo-Campos, A., de Miguel-Martínez, I., Tosco-Núñez, T., Díez-Gil, O., et al. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.919346 · Cited by 5
Abduljaleel, Z., Melebari, S., Athar, M., Dehlawi, S., Kumar, S., Aziz, S. A. A., Dannoun, A., Malik, S. M., Thasleem, J., & Doss, C. (2023) · Cellular Signalling · doi:10.1016/j.cellsig.2023.110798 · Cited by 5
Hajj-Hassan, H., Hamze, K., Abdel‐Sater, F., Kizilbash, N., & Khachfe, H. M. (2021) · Cureus · doi:10.7759/cureus.16905 · Cited by 5
Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India
Sarkar, R., Saha, R., Mallick, P., Sharma, R. P., Kaur, A., Dutta, S., & Chawla‐Sarkar, M. (2021) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.11.020 · Cited by 6
Baros‐Steyl, S. S., Heialy, S. A., Semreen, A. H., Semreen, M. H., Blackburn, J. M., & Soares, N. C. (2022) · PROTEOMICS · doi:10.1002/pmic.202200118 · Cited by 4
Kumar, A., Asghar, A., Singh, H. N., Faiq, M. A., Kumar, S., Narayan, R. K., Kumar, G., Dwivedi, P., Sahni, C., Jha, R. K., et al. (2022) · JMIR Bioinformatics and Biotechnology · doi:10.2196/42700 · Cited by 5
Gasparo, R. D., Pedotti, M., Simonelli, L., Nickl, P., Muecksch, F., Cassaniti, I., Percivalle, E., Lorenzi, J. C. C., Mazzola, F., Magrì, D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.22.427567 · Cited by 5
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A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in BrazilPreprint
Naveca, F. G., do Nascimento, V. A., Nascimento, F., Ogrzewalska, M., Pauvolid‐Corrêa, A., de Araújo, M. F., Arantes, I., Batista, É. L. R., Magalhães, A. L. Á., Vinhal, F. A., et al. (2021) · medRxiv · doi:10.1101/2021.11.29.21266109 · Cited by 5
Mutations of SARS-CoV-2 variants of concern escaping Spike-specific T cellsPreprint
Bert, N. L., Tan, A. T., Kunasegaran, K., Chia, A., Tan, N., Chen, Q., Hang, S. K., Qui, M., Chan, B. S.-W., Low, J. G. H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.20.477163 · Cited by 5
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Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxisPreprint
Yogev, O., Weissbrod, O., Battistoni, G., Bressan, D., Naamti, A., Falciatori, I., Berkyurek, A. C., Rasnic, R., Hosmillo, M. D. T., Ilan, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.12.488010 · Cited by 5
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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