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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies
Open accessPreprint — published as 10.1016/j.chom.2021.02.003 · Paper page
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 serum antibodies are impacted by all mutations to the spike’s receptor-binding domain (RBD), the main target of serum neutralizing activity. Binding by polyclonal serum antibodies is affected by mutations in three main epitopes in the RBD, but there is substantial variation in the impact of mutations 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 sera is reduced >10-fold by several mutations, including one in emerging viral lineages in South Africa and Brazil. Going forward, these serum escape maps can inform surveillance of SARS-CoV-2 evolution.
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“The E484K mutation has been reported to abolish or substantially reduce neutralization by multiple potent monoclonal antibodies and polyclonal convalescent sera in both wild-type and pseudo-virus neutralization assays.12,13,17,18,22”
From Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant (2021) · cites this paper as [13]
In the citing paper
“The B.1.351 variant is characterized by three deleterious mutations at key antigenic sites in the RBD, including N501Y, K417N, and E484K, with the latter two having particular functional impact.”
From Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant (2021) · cites this paper as [13]
In the citing paper
“From a biological point of view, the breakthrough cases observed in this study might be due to immune evasion, mediated by particular alterations present in these strains 9,[23][24][25][26][27] .”
From Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals (2021) · cites this paper as [23]
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Cites
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BackgroundInfluentialEscape from neutralizing antibodies by SARS-CoV-2 spike protein variants
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“This lack of concordance between the epitopes of serum and monoclonal antibodies is consistent with other studies reporting that the specificities of potent monoclonal antibodies often do not recapitulate the sera from which they were isolated (Barnes et al., 2020b; Weisblum et al., 2020).”
BackgroundResultInfluentialA human neutralizing antibody targets the receptor-binding site of SARS-CoV-2
Shi, R., Shan, C., Duan, X., Chen, Z., Liu, P., Song, J., Song, T., Bi, X., Han, C., Wu, L., et al. (2020) · Nature · doi:10.1038/s41586-020-2381-y · Cited by 1,286
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“Because the RBD is usually in the “down” conformation (Cai et al., 2020; Ke et al., 2020; Walls et al., 2020), we speculate that while sites accessible in this conformation can be targeted by neutralizing antibodies, they may be subdominant in the context of polyclonal serum binding to full spike even if they are do…”
BackgroundStudies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail
Hansen, J., Baum, A., Pascal, K. E., Russo, V., Giordano, S., Wloga, E., Fulton, B. O., Yan, Y., Koon, K., Patel, K., et al. (2020) · Science · doi:10.1126/science.abd0827 · Cited by 1,210 · cited 4×
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Self-citationPotent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability
Brouwer, P. J. M., Caniels, T. G., van der Straten, K., Snitselaar, J. L., Aldon, Y., Bangaru, S., Torres, J. L., Okba, N. M. A., Claireaux, M., Kerster, G., et al. (2020) · Science · doi:10.1126/science.abc5902 · Cited by 1,140 · cited 2×
“This result suggests that RBD-binding antibodies comprise a relatively modest proportion of all spike-binding IgG serum antibodies in naturally infected individuals, consistent with studies reporting that less than half of spike-reactive B cells and monoclonal antibodies bind to RBD (Brouwer et al., 2020; Huang et al…”
ResultStructures and distributions of SARS-CoV-2 spike proteins on intact virions
Ke, Z., Otón, J., Qu, K., Cortese, M., Žíla, V., McKeane, L., Nakane, T., Zivanov, J., Neufeldt, C. J., Cerikan, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2665-2 · Cited by 1,140
Potently neutralizing and protective human antibodies against SARS-CoV-2
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Self-citationAntibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers
Lumley, S. F., O’Donnell, D., Stoesser, N. E., Matthews, P. C., Howarth, A., Hatch, S. B., Marsden, B. D., Cox, S., James, T., Warren, F., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2034545 · Cited by 940 · cited 1×
“Introduction Neutralizing antibodies against the SARS-CoV-2 spike are associated with protection against infection in both humans (Addetia et al., 2020; Lumley et al., 2020) and animal models (Alsoussi et al.”
BackgroundEvolution of Antibody Immunity to SARS-CoV-2Preprint
Gaebler, C., Wang, Z., Lorenzi, J. C. C., et al. (2020) · bioRxiv · doi:10.1101/2020.11.03.367391 · Cited by 810 · cited 2×
“We speculated that such changes might occur because other studies have shown that anti-SARS-CoV-2 antibodies become more somatically hypermutated and less clonal in the months following recovery from infection (Gaebler et al., 2020; Nielsen et al., 2020; Rodda et al., 2020).”
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“For instance, mutations in the S309 epitope footprint (Pinto et al., 2020) and at sites of escape from antibody C135 (e.g., R346 and N440) (Barnes et al., 2020a; Weisblum et al., 2020) had minimal effects on serum antibody binding ( Figures 3, S3 ).”
InfluentialCrawford, K. H. D., Eguia, R. T., Dingens, A. S., Loes, A. N., Malone, K. D., Wolf, C. R., Chu, H. Y., Tortorici, M. A., Veesler, D., Murphy, M., et al. (2020) · Viruses · doi:10.3390/v12050513 · Cited by 744 · cited 1×
“For most of the 17 individuals, both the RBD binding and the neutralizing activity decreased moderately from one to four months post-infection (Crawford et al., 2020a) (Supplementary Table 1).”
BackgroundSelf-citationFunctional SARS-CoV-2-Specific Immune Memory Persists after Mild COVID-19
Rodda, L. B., Netland, J., Shehata, L., Pruner, K. B., Morawski, P. A., Thouvenel, C. D., Takehara, K. K., Eggenberger, J., Hemann, E. A., Waterman, H. R., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.029 · Cited by 647
Prospective mapping of viral mutations that escape antibodies used to treat COVID-19Preprint
Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. W., Choudhary, M., Dingens, A. S., Li, J. Z., & Bloom, J. (2020) · bioRxiv · doi:10.1101/2020.11.30.405472 · Cited by 633 · cited 19×
“The library covered nearly all possible single amino-acid mutations to the RBD (Starr et al., 2020b) .”
BackgroundMethodInfluentialSelf-citationStructural basis of a shared antibody response to SARS-CoV-2
Yuan, M., Liu, H., Wu, N. C., Lee, C.-C. D., Zhu, X., Zhao, F., Huang, D., Yu, W., Hua, Y., Tien, H., et al. (2020) · Science · doi:10.1126/science.abd2321 · Cited by 589 · cited 2×
“In particular, E484 is the site in the RBD where mutations usually have the largest effect on binding and neutralization—possibly because E484 is often targeted by antibodies that utilize heavy-chain germline genes that are common among anti-SARS-CoV-2 RBD antibodies, IGHV3-53 and IGHV3-66 (Barnes et al., 2020a; Grean…”
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Self-citationZost, S. J., Gilchuk, P., Chen, R. E., Case, J. B., Reidy, J. X., Trivette, A., Nargi, R. S., Sutton, R. E., Suryadevara, N., Chen, E. C., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0998-x · Cited by 429
Self-citationFree fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein
Toelzer, C., Gupta, K., Yadav, S. K. N., Borucu, U., Davidson, A. D., Williamson, M. K., Shoemark, D. K., Garzoni, F., Staufer, O., Milligan, R., et al. (2020) · Science · doi:10.1126/science.abd3255 · Cited by 427 · cited 1×
“The sites where mutations reduced binding by these core-RBD targeting sera clustered around the lipid-binding pocket in the RBD, where binding of free fatty acids may contribute to locking spike into a “closed” conformation (Carrique et al., 2020; Toelzer et al., 2020).”
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“The site where mutations tend to have the largest effect on binding and neutralization is E484, which unfortunately is a site where mutations are present in several emerging SARS-CoV-2 lineages (Tegally et al., 2020; Voloch et al., 2020).”
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“Introduction Neutralizing antibodies against the SARS-CoV-2 spike are associated with protection against infection in both humans (Addetia et al., 2020; Lumley et al., 2020) and animal models (Alsoussi et al.”
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Self-citationA human coronavirus evolves antigenically to escape antibody immunity
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“However, other human coronaviruses undergo antigenic evolution that erodes neutralizing antibody immunity (Eguia et al., 2020).”
BackgroundSelf-citationRecurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp, S. A., Meng, B., Ferriera, I. A., Datir, R., Harvey, W. T., Papa, G., Lytras, S., Collier, D. A., Mohamed, A., Gallo, G., et al. (2020) · doi:10.1101/2020.12.14.422555 · Cited by 252
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“We next deconvolved variant-level escape scores into escape fraction estimates for single mutations using global epistasis models (Otwinowski et al., 2018) implemented in the dms_variants package, as detailed at (https://jbloomlab.”
MethodFunctional SARS-CoV-2-sperific immune memory persists after mild COVID-19Preprint
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Self-citationDynamics of neutralizing antibody titers in the months after SARS-CoV-2 infectionPreprint
Crawford, K. H., Dingens, A., Eguia, R. T., et al. (2020) · medRxiv · doi:10.1101/2020.08.06.20169367 · Cited by 229 · cited 6×
“We used spike-pseudotyped lentiviral particles that were generated essentially as described in (Crawford et al., 2020b) , using a codon-optimized SARS-CoV-2 spike from Wuhan-Hu-1 that contains a 21-amino-acid deletion at the end of the cytoplasmic tail (Crawford et al., 2020a) and the D614G…”
InfluentialSelf-citationHuman B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2
Nielsen, S. C. A., Yang, F., Jackson, K., Hoh, R. A., Röltgen, K., Jean, G. H., Stevens, B., Lee, J.-Y., Rustagi, A., Rogers, A. J., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.09.002 · Cited by 229
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Self-citationHuman B cell clonal expansion and convergent antibody responses to SARS CoV-2Preprint
Nielsen, S. C. A., Yang, F., Jackson, K., et al. (2020) · bioRxiv · doi:10.1101/2020.07.08.194456 · Cited by 197
A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection
Alsoussi, W. B., Turner, J. S., Case, J. B., Zhao, H., Schmitz, A. J., Zhou, J. Q., Chen, R. E., Lei, T., Rizk, A. A., McIntire, K. M., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.2000583 · Cited by 181
Neutralising antibodies in Spike mediated SARS-CoV-2 adaptationPreprint
Kemp, S. A., Collier, D. A., Datir, R. P., et al. (2020) · medRxiv · doi:10.1101/2020.12.05.20241927 · Cited by 180
Production of complex human glycoproteins in yeast.
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“…escape mutants with reduced neutralization sensitivity (Andreano et al., 2020; Weisblum et al., 2020) , or characterizing the antigenic effects of specific mutations such as those observed in circulating viral isolates (Kemp et al., 2020b; Li et al., 2020; Liu et al., 2020b; Thomson et al., 2020) .”
BackgroundInfluentialNatural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escapePreprint
McCarthy, K. R., Rennick, L., Nambulli, S., et al. (2020) · bioRxiv · doi:10.1101/2020.11.19.389916 · Cited by 117 · cited 2×
“For example, mutations and deletions in the NTD can affect serum antibody neutralization (Andreano et al., 2020; Kemp et al., 2020b; Liu et al., 2020a; McCarthy et al., 2020; Voss et al., 2020), and are certainly of great importance.”
BackgroundLee, J. M., Eguia, R. T., Zost, S. J., Choudhary, S., Wilson, P. C., Bedford, T., Stevens‐Ayers, T., Boeckh, M., Hurt, A. C., Lakdawala, S. S., et al. (2019) · eLife · doi:10.7554/elife.49324 · Cited by 112
Self-citationReceptor-binding loops in alphacoronavirus adaptation and evolution
Wong, A. H. M., Tomlinson, A. C. A., Zhou, D., Satkunarajah, M., Chen, K., Sharon, C., Desforges, M., Talbot, P. J., & Rini, J. M. (2017) · Nature Communications · doi:10.1038/s41467-017-01706-x · Cited by 110
Thomson, E., Rosen, L. E., Shepherd, J., et al. (2020) · bioRxiv · doi:10.1101/2020.11.04.355842 · Cited by 104 · cited 10×
“ACE2 is shown as a dark gray cartoon.”
BackgroundInfluentialDingens, A. S., Crawford, K. H. D., Adler, A., Steele, S. L., Lacombe, K., Eguia, R. T., Amanat, F., Walls, A. C., Wolf, C. R., Murphy, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18178-1 · Cited by 69
Self-citationVoss, W. N., Hou, Y., Johnson, N., Kim, J. E., Delidakis, G., Horton, A. P., Bartzoka, F., Paresi, C. J., Tanno, Y., Abbasi, S. A., et al. (2020) · bioRxiv · doi:10.1101/2020.12.20.423708 · Cited by 57 · cited 2×
“For example, mutations and deletions in the NTD can affect serum antibody neutralization (Andreano et al., 2020; Kemp et al., 2020b; Liu et al., 2020a; McCarthy et al., 2020; Voss et al., 2020), and are certainly of great importance.”
BackgroundResultAuthor response: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., et al. (2020) · eLife · doi:10.7554/elife.61312.sa2 · Cited by 53
dms-view: Interactive visualization tool for deep mutational scanning data
Hilton, S. K., Huddleston, J., Black, A., et al. (2020) · bioRxiv · doi:10.1101/2020.05.14.096842 · Cited by 39
Self-citationKidd, M., Richter, A., Best, A., et al. (2020) · medRxiv · doi:10.1101/2020.12.24.20248834 · Cited by 36 · cited 1×
“lineage is unlikely to greatly affect neutralization by most human sera, although it could contribute to increased viral titer or enhanced transmissibility (Kidd et al., 2020; Public Health England, 2020).”
Backgrounddms-view: Interactive visualization tool for deep mutational scanning data
Hilton, S. K., Huddleston, J., Black, A., North, K., Dingens, A. S., Bedford, T., & Bloom, J. D. (2020) · The Journal of Open Source Software · doi:10.21105/joss.02353 · Cited by 26
Self-citationSteffen, T. L., Stone, E. T., Hassert, M., Geerling, E., Grimberg, B. T., Espino, A. M., Pantoja, P., Climent, C., Hoft, D. F., George, S. L., et al. (2020) · doi:10.1101/2020.08.21.261727 · Cited by 25 · cited 3×
“Several recent studies have reported that RBD-binding antibodies contribute the majority of the neutralizing activity in most convalescent human sera (Piccoli et al., 2020; Steffen et al., 2020).”
BackgroundInfluentialPlasmablast-derived antibody response to acute SARS-CoV-2 infection in humansPreprint
Huang, K.-Y. A., Tan, T., Chen, T.-H., et al. (2020) · bioRxiv · doi:10.1101/2020.08.28.267526 · Cited by 23 · cited 1×
“This result suggests that RBD-binding antibodies comprise a relatively modest proportion of all spike-binding IgG serum antibodies in naturally infected individuals, consistent with studies reporting that less than half of spike-reactive B cells and monoclonal antibodies bind to RBD (Brouwer et al., 2020; Huang et al…”
ResultCarrique, L., Duyvesteyn, H. M. E., Malinauskas, T., Zhao, Y., Ren, J., Zhou, D., Walter, T. S., Radecke, J., Huo, J., Ruza, R. R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.13.249177 · Cited by 18 · cited 1×
“The sites where mutations reduced binding by these core-RBD targeting sera clustered around the lipid-binding pocket in the RBD, where binding of free fatty acids may contribute to locking spike into a “closed” conformation (Carrique et al., 2020; Toelzer et al., 2020).”
BackgroundKistler, K. E., & Bedford, T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.30.352914 · Cited by 14 · cited 1×
“This antigenic evolution is driven by positive selection for mutations in the viral spike, particularly in regions involved in receptor binding (Kistler and Bedford, 2020; Wong et al., 2017).”
BackgroundCarrique, L., Duyvesteyn, H. M. E., Malinauskas, T., et al. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3656643 · Cited by 10
Lee, J. M., Eguia, R. T., Zost, S. J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/670497 · Cited by 10 · cited 1×
“One reason that influenza virus undergoes such rapid antigenic evolution is that neutralizing human immunity often focuses on just a few residues in hemagglutinin, such that a single mutation can dramatically reduce neutralization (Lee et al., 2019).”
BackgroundSelf-citationLee, J. M., Eguia, R. T., Zost, S. J., Choudhary, S., Wilson, P. C., Bedford, T., Stevens‐Ayers, T., Boeckh, M., Hurt, A. C., Lakdawala, S. S., et al. (2019) · eLife · doi:10.7554/elife.49324.049 · Cited by 4
Self-citationPathogenic measles viruses cannot evolve to bypass vaccine-induced neutralizing antibodiesPreprint
Muñoz-Alía, M., Nace, R. A., Zhang, L., et al. (2020) · bioRxiv · doi:10.1101/2020.10.22.351189 · Cited by 4
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
Andreano, E., Piccini, G., Licastro, D., Casalino, L., Johnson, N. V., Paciello, I., Monego, S. D., Pantano, E., Manganaro, N., Manenti, A., et al. (2020) · doi:10.1101/2020.12.28.424451 · cited 6×
“Notably, E484 is a site at which mutations have recently been demonstrated to reduce neutralization by several monoclonal antibodies and sera (Andreano et al., 2020; Greaney et al., 2020; Starr et al., 2020a; Weisblum et al., 2020).”
BackgroundResultInfluential
Cited by
Sorted by citations
Mechanisms of SARS-CoV-2 entry into cells
Jackson, C. B., Farzan, M., Chen, B., & Choe, H. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00418-x · Cited by 3,022
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Wang, P., Nair, M. S., Liu, L., Iketani, S., Luo, Y., Guo, Y., Wang, M., Yu, J., Zhang, B., Kwong, P. D., et al. (2021) · Nature · doi:10.1038/s41586-021-03398-2 · Cited by 2,312
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04411-y · Cited by 1,678
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461
“Moreover, E484K is associated with reduced antibody neutralisation (6, 56-58).”
Background
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
- openRxiv
- Published
- 2021-01-04
- Volume
- 29
- Issue
- 3
- Pages
- 463-476.e6
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC7869748
- OpenAlex
- W3127852352
- Cited by
- 1,178
- References
- 58
- Citations by year
- 2026: 43 · 2025: 64 · 2024: 79 · 2023: 158 · 2022: 361 · 2021: 459
- FWCI
- 83.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cell Host & Microbe (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- Bill and Melinda Gates Foundation (INV-004949)
- Damon Runyon Cancer Research Foundation (DRG-2381-19)
- Washington Research Foundation
- Vanderbilt University
- University of Washington
- National Institutes of Health (1s10od028685-01)
- National Institute of Allergy and Infectious Diseases (R01AI127893, T32AI083203, F30AI149928, R01AI140891, R01AI141707)
- Office of Research Infrastructure Programs, National Institutes of Health (S10OD028685)
- 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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