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.
“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]
The B.1.351 variant is characterized by three deleterious mutations at key antigenic sites in the RBD, including N501Y, K417N, and E484K.
“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]
Breakthrough cases observed might be due to immune evasion mediated by particular alterations present in these strains.
“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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BackgroundStudies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail
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Self-citationPotent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability
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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 1,113 · see citing works
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× · see citing works
“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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“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 727 · cited 1× · see citing works
“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 · see citing works
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× · see citing works
“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× · see citing works
“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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“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 · see citing works
Inferring the shape of global epistasis
Otwinowski, J., McCandlish, D. M., & Plotkin, J. B. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1804015115 · Cited by 243 · cited 1× · see citing works
“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
Rodda, L., Netland, J., Shehata, L., Pruner, K., Morawski, P., Thouvenel, C., Takehara, K., Eggenberger, J., Hemann, E. A., Waterman, H., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-57112/v1 · Cited by 237 · see citing works
Human 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 236 · see citing works
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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× · see citing works
“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-citationZost, S. J., Gilchuk, P., Chen, R. E., et al. (2020) · bioRxiv · doi:10.1101/2020.05.12.091462 · Cited by 201 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Production of complex human glycoproteins in yeast.
Hamilton, S., Bobrowicz, P., Bobrowicz, B., et al. (2003) · Science · doi:10.1007/0-387-25515-x_24 · Cited by 165
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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× · see citing works
“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 · see citing works
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 109 · see citing works
Thomson, E., Rosen, L. E., Shepherd, J., et al. (2020) · bioRxiv · doi:10.1101/2020.11.04.355842 · Cited by 104 · cited 10× · see citing works
“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 68 · see citing works
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× · see citing works
“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 · see citing works
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× · see citing works
“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 29 · see citing works
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× · see citing works
“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× · see citing works
“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× · see citing works
“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× · see citing works
“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 · see citing works
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× · see citing works
“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 · see citing works
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 · see citing works
SARS-CoV-2 escape <i>in vitro</i> 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
Flagged first, then by citations
Research works printed but not linked: 1
- Kemp, S.A., Collier, D.A., Datir, R., Ferreira, I.A., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I.U., et al. (2020b). Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion (medRxiv).
Cited by
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Mechanisms of SARS-CoV-2 entry into cells
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Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
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Detection of a SARS-CoV-2 variant of concern in South Africa
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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 1,653 · see citing works
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 · see citing works
“Moreover, E484K is associated with reduced antibody neutralisation (6, 56-58).”
BackgroundMultiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity
Garcia-Beltran, W. F., Lam, E. C., St. Denis, K., Nitido, A. D., Garcia, Z. H., Hauser, B. M., Feldman, J., Pavlovic, M. N., Gregory, D. J., Poznansky, M. C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.013 · Cited by 1,353 · see citing works
“The P.2. variant, which contains an E484K mutation within the RBD region, was capable of significantly reducing neutralization potency of fully vaccinated individuals, in line with what has been suggested by deep mutational scanning (Greaney et al., 2021a; Jangra et al., 2021).”
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343 · see citing works
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Self-citationSARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147 · see citing works
SARS-CoV-2 variant biology: immune escape, transmission and fitness
Carabelli, A. M., Peacock, T. P., Thorne, L., Harvey, W. T., Hughes, J., de Silva, T. I., Peacock, S. J., Barclay, W., de Silva, T. I., Towers, G. J., et al. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00841-7 · Cited by 1,293 · see citing works
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
Cameroni, E., Bowen, J. E., Rosen, L. E., Saliba, C., Zepeda, S. K., Culap, K., Pinto, D., VanBlargan, L. A., Marco, A. D., di Iulio, J., et al. (2021) · Nature · doi:10.1038/s41586-021-04386-2 · Cited by 1,043 · see citing works
Self-citationThe biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009 · see citing works
Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence
Sabino, E. C., Buss, L. F., Carvalho, M. P. S., Prete, C. A., Crispim, M. A. E., Fraiji, N. A., Pereira, R. H. M., Parag, K. V., da Silva Peixoto, P., Kraemer, M. U. G., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00183-5 · Cited by 758 · see citing works
Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies
Planas, D., Bruel, T., Grzelak, L., Guivel-Benhassine, F., Staropoli, I., Porrot, F., Planchais, C., Buchrieser, J., Rajah, M. M., Bishop, E., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01318-5 · Cited by 697 · see citing works
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., Cantoni, D., Scott, S., Logan, N., Ashraf, S., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01143-7 · Cited by 785 · see citing works
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., et al. (2021) · doi:10.1101/2021.01.19.21249840 · Cited by 729 · see citing works
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Network for Genomic Surveillance in South Africa, Cele, S., COMMIT-KZN Team, Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03471-w · Cited by 651 · see citing works
“Using a deep mutation scanning approach 36 to determine the effect of individual mutations on neutralization by polyclonal sera, mutations at E484 37 were associated with the largest drops in neutralization [11].”
MethodSensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., et al. (2021) · Nature · doi:10.1038/s41586-021-03412-7 · Cited by 728 · see citing works
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01911-2 · Cited by 707 · see citing works
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606 · see citing works
“…of a few neutralizing mAbs to mutations at positions 417 and 439 have also been reported in other studies (Baum et al., 2020; Gaebler et al., 2021; Greaney et al., 2021; Li et al., 2020a; Starr et al., 2020a; Weisblum et al., 2020), although combinations of mutations have typically not been…”
BackgroundInfluentialPreliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant
Shinde, V., Bhikha, S., Hoosain, Z., Archary, M., Bhorat, Q., Fairlie, L., Lalloo, U., Masilela, M. S. L., Moodley, D., Hanley, S., et al. (2021) · doi:10.1101/2021.02.25.21252477 · Cited by 625 · see citing works
“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.(12,14,16,17) The N501Y mutation is known to increase binding affinity of the spike protein to the human angiotensin-converting enzym…”
BackgroundInfluentialEfficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant
Shinde, V., Bhikha, S., Hoosain, Z., Archary, M., Bhorat, Q., Fairlie, L., Lalloo, U., Masilela, M. S. L., Moodley, D., Hanley, S., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2103055 · Cited by 625 · see citing works
Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021
Galloway, S. E., Paul, P., MacCannell, D., Johansson, M. A., Brooks, J. T., MacNeil, A., Slayton, R. B., Tong, S., Silk, B. J., Armstrong, G. L., et al. (2021) · MMWR Morbidity and Mortality Weekly Report · doi:10.15585/mmwr.mm7003e2 · Cited by 609 · see citing works
“A recent case report documented the first case of SARS-CoV-2 reinfection in Brazil with a SARS-CoV-2 variant that contained the E484K mutation,** which has been shown to reduce neutralization by convalescent sera and monoclonal antibodies (9,10).”
BackgroundReduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera
Supasa, P., Zhou, D., Dejnirattisai, W., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Nutalai, R., Tuekprakhon, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.033 · Cited by 460 · see citing works
“These mutations also fall within the footprint of a number of potent neutralizing antibodies likely to afford vaccine-induced protection and of several candidate therapeutic mAbs (Cheng et al., 2021; Greaney et al., 2021; Nelson et al., 2021), thus potentially affording mutant viruses greater fitness to infect new hos…”
Wu, K., Werner, A. P., Moliva, J. I., Koch, M., Choi, A., Stewart-Jones, G. B. E., Bennett, H., Boyoglu-Barnum, S., Shi, W., Graham, B. S., et al. (2021) · doi:10.1101/2021.01.25.427948 · Cited by 419 · see citing works
“…target for neutralizing antibodies, these mutations could impact the effectiveness of monoclonal antibodies already approved and in advanced development as well as of polyclonal antibody elicited by infection or vaccination in neutralizing the virus (Greaney et al., 2021, Wibmer et al, 2021).”
BackgroundRöltgen, K., Nielsen, S. C. A., Silva, O., Younes, S. F., Zaslavsky, M., Costales, C., Yang, F., Wirz, O. F., Solis, D., Hoh, R. A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.01.018 · Cited by 459 · see citing works
SARS-CoV-2 spike E484K mutation reduces antibody neutralisation
Jangra, S., Ye, C., Rathnasinghe, R., Stadlbauer, D., Alshammary, H., Amoako, A. A., Awawda, M. H., Beach, K. F., Bermúdez-González, M. C., Chernet, R. L., et al. (2021) · The Lancet Microbe · doi:10.1016/s2666-5247(21)00068-9 · Cited by 385 · see citing works
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Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Greaney, A. J., Starr, T. N., Barnes, C. O., Weisblum, Y., Schmidt, F., Caskey, M., Gaebler, C., Cho, A., Agudelo, M., Finkin, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24435-8 · Cited by 433 · see citing works
Self-citationPrior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose
Reynolds, C. J., Pade, C., Gibbons, J. M., Butler, D. K., Otter, A. D., Menacho, K., Fontana, M., Smit, A., Sackville-West, J. E., Cutino-Moguel, T., et al. (2021) · Science · doi:10.1126/science.abh1282 · Cited by 338 · see citing works
The emergence, genomic diversity and global spread of SARS-CoV-2
Li, J., Lai, S., Gao, G. F., & Shi, W. (2021) · Nature · doi:10.1038/s41586-021-04188-6 · Cited by 408 · see citing works
SARS-CoV-2 within-host diversity and transmission
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“We did not observe N501Y or E484K, both mutations of concern, in any of our samples (48).”
BackgroundStructural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
Yuan, M., Huang, D., Lee, C.-C. D., Wu, N. C., Jackson, A. M., Zhu, X., Liu, H., Peng, L., van Gils, M. J., Sanders, R. W., et al. (2021) · doi:10.1101/2021.02.16.430500 · Cited by 364 · see citing works
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Covid‐19 vaccines and variants of concern: A review
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“As a consequence, it could alter the effectiveness of current vaccines.(38)”
BackgroundSARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · doi:10.1101/2021.01.18.427166
Greaney, A. J., Loes, A. N., Gentles, L. E., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abi9915 · Cited by 244 · see citing works
Self-citationLectins enhance SARS-CoV-2 infection and influence neutralizing antibodies
Lempp, F. A., Soriaga, L. B., Montiel-Ruiz, M., Benigni, F., Noack, J., Park, Y., Bianchi, S., Walls, A. C., Bowen, J. E., Zhou, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03925-1 · Cited by 292 · see citing works
N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2
Tian, F., Tong, B., Sun, L., Shi, S., Zheng, B., Wang, Z., Dong, X., & Zheng, P. (2021) · eLife · doi:10.7554/elife.69091 · Cited by 380 · see citing works
“351 lineage, beta) was first detected in October 2020 in the Republic of South Africa (Rahimi and Talebi Bezmin Abadi, 2021; Greaney et al., 2021; CNBC, 2021).”
BackgroundInfluentialSARS-CoV-2 Variants, Vaccines, and Host Immunity
Mistry, P., Barmania, F., Mellet, J., Peta, K. T., Strydom, A., Viljoen, I. M., James, W., Gordon, S., & Pepper, M. S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.809244 · Cited by 293 · see citing works
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“Affinity matured antibodies exhibit activity against SARS-CoV-2 VOC Selection for rVSV/SARS-CoV-2 resistance to class 1, 2, and 3 antibodies in cell culture has repeatedly identified K417, E484, and N501 substitutions, with E484K giving the most pervasive effects against polyclonal plasma (Baum et al., 2020; Greaney e…”
BackgroundBroad sarbecovirus neutralization by a human monoclonal antibody
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) · Nature · doi:10.1038/s41586-021-03817-4 · Cited by 251 · see citing works
Self-citationA human coronavirus evolves antigenically to escape antibody immunity
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“In this respect, it is worth noting that while the neutralizing activity of SARS-CoV-2 immunity elicited by infection primarily targets the RBD [36,54], mutations to the NTD also reduce neutralization by some antibodies and sera [55–62]—and some regions of the NTD undergo significant sequence evolution in 229E (Fig 4A…”
BackgroundSelf-citationEmerging SARS-CoV-2 Variants and Impact in Global Vaccination Programs against SARS-CoV-2/COVID-19
Gómez, C. E., Perdiguero, B., & Estéban, M. (2021) · Vaccines · doi:10.3390/vaccines9030243 · Cited by 262 · see citing works
Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models
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“351 strain do impair neutralization (Greaney et al., 2021; Wibmer et al., 2021).”
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“One of the mutations in this variant, N501Y, is located in the important receptor-binding domain (RBD) of spike protein, and is predicted to increase binding to human cells and reduce viral neutralization by the monoclonal antibody LY-CoV016 (Greaney et al., 2021; Starr et al., 2020).”
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“[14] Allison J Greaney, Andrea N Loes, Katharine HD Crawford, Tyler N Starr, Keara D Malone, He406 len Y Chu, and Jesse D Bloom.”
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Moulana, A., Dupic, T., Phillips, A. M., Chang, J., Nieves, S., Roffler, A. A., Greaney, A. J., Starr, T. N., Bloom, J. D., & Desai, M. M. (2022) · Nature Communications · doi:10.1038/s41467-022-34506-z · Cited by 156 · see citing works
Self-citationEmerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy
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- 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 · 2020: 3 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1
- 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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