Cited by 285SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesMonoclonal and Polyclonal Antibodies Research

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Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail

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Dong, Jinhui, Zost, Seth J., Greaney, Allison J., Starr, Tyler N., Dingens, Adam S., Chen, Elaine C., Chen, Rita E., Case, James Brett, Sutton, Rachel E., Gilchuk, Pavlo, Rodriguez, Jessica, Armstrong, Erica, Gainza, Christopher, Nargi, Rachel S., Binshtein, Elad, Xie, Xuping, Zhang, Xianwen, Shi, Pei-Yong, Logue, James, Weston, Stuart, McGrath, Marisa E., Frieman, Matthew B., Brady, Tyler, Tuffy, Kevin M., Bright, Helen, Loo, Yueh-Ming, McTamney, Patrick M., Esser, Mark T., Carnahan, Robert H., Diamond, Michael S., Bloom, Jesse D., Crowe, James E.·2021·Nature Microbiology

DOI 10.1038/s41564-021-00972-2PMC PMC8543371

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Abstract

Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization. AZD8895 forms an 'aromatic cage' at the heavy/light chain interface using germ line-encoded residues in complementarity-determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1; the HCDR3 makes interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germ line-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.

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Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots
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“The simulated RBD–antibody complexes included: group A: CB6/LY-CoV016 (etesevimab) [91]; group B: AZD8895 [92] and REGN1033 [93]; group C: LY-CoV555 [94]; and group D: CoV2-2130/AZD1061 [92], REGN10987 [93], and LY-CoV1404 [95].”
Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding
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Influential
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“AZD7442 is a combination of two fully human SARS-CoV-2-neutralising mAbs—tixagevimab (AZD8895) and cilgavimab (AZD1061)—derived from potent antibodies isolated from B cells of individuals with prior SARS-CoV-2 infection [14].”
BackgroundSelf-citation
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“…was derived from the IGHV1-58 and IGKV3-20 genes; this combination of germline sequences was reported previously for several other CoV2 neutralizing antibodies, including Tixagevimab (AZD8895 or COV2-2196), and BD-836 (Cao et al., 2022b; Dong et al., 2021; Du et al., 2021; Hansen et al., 2020a).”
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BackgroundInfluential
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“Furthermore, we showed the utility of the recombinant chimeric viruses we generated carrying GFP for the evaluation of the neutralizing activities against the licensed anti-SARS-CoV-2 monoclonal antibody combination AZD7442 (tixagevimab/cilgavimab) (13).”
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“In addition to being solvent accessible (a requirement for efficient glycosylation), K444 is an important contact residue for many previously described class 3 mAbs, including COV2-2130 (the parental mAb of cilgavimab) and LY-CoV1404 (the parental mAb of bebtelovimab) 7,9 .”
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Background
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Background
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Background
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Background
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Background
Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its VariantsPreprint
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“This critical role of N487 in interaction with ACE2 and attenuated binding between N487T RBD and ACE2 were also reported in two research using yeast surface display RBD mutant libraries [18,25], according to which nearly all the mutation on N487 including N487T attenuated ACE2 binding.”
BackgroundResultSelf-citation
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BackgroundInfluential
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iThenticate Report for version 1
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SciScore Report for version 1
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Editor response for version 1
Allen, D. (2023) · doi:10.1099/acmi.0.000573.v1.5
Reviewer response for version 1
Peronace, C. (2023) · doi:10.1099/acmi.0.000573.v1.3
Reviewer response for version 1
Bamford, C. (2023) · doi:10.1099/acmi.0.000573.v1.4
Editor response for version 2
Allen, D. (2023) · doi:10.1099/acmi.0.000573.v2.3
Editor response for version 3
Allen, D. (2023) · doi:10.1099/acmi.0.000573.v3.3
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Self-citation

Authors: Dong, J., Zost, S. J., Greaney, A. J., Starr, T. N., Dingens, A. S., Chen, E. C., Chen, R. E., Case, J. B., Sutton, R. E., Gilchuk, P., Rodriguez, J., Armstrong, E., Gainza, C., Nargi, R. S., Binshtein, E., Xie, X., Zhang, X., Shi, P.-Y., Logue, J., Weston, S., McGrath, M. E., Frieman, M. B., Brady, T., Tuffy, K. M., Bright, H., Loo, Y.-M., McTamney, P. M., Esser, M. T., Carnahan, R. H., Diamond, M. S., Bloom, J. D., & Crowe, J. E.
Affiliations: Vanderbilt University Medical Center (US)
University of Washington (US)
Fred Hutch Cancer Center (US)
Washington University in St. Louis (US)
The University of Texas Medical Branch at Galveston (US)
University of Maryland, College Park (US)
AstraZeneca (United States) (US)
Howard Hughes Medical Institute (US)
Corresponding author: Crowe, James E.
ORCID: Dong, Jinhui
Zost, Seth J.
Greaney, Allison J.
Starr, Tyler N.
Dingens, Adam S.
Chen, Elaine C.
Chen, Rita E.
Case, James Brett
Gilchuk, Pavlo
Rodriguez, Jessica
Binshtein, Elad
Xie, Xuping
Zhang, Xianwen
Shi, Pei-Yong
Logue, James
Weston, Stuart
McGrath, Marisa E.
Frieman, Matthew B.
Brady, Tyler
Tuffy, Kevin M.
Bright, Helen
Loo, Yueh-Ming
Esser, Mark T.
Carnahan, Robert H.
Diamond, Michael S.
Bloom, Jesse D.
Crowe, James E.
Venue: Nature Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2021-09-21
Volume: 6
Issue: 10
Pages: 1233-1244
ISSN: 2058-5276 (ISSN-L)
DOI: 10.1038/s41564-021-00972-2
PMC: PMC8543371
OpenAlex: W3199394546
Cited by: 285
References: 84
Citations by year: 2026: 12 · 2025: 17 · 2024: 43 · 2023: 72 · 2022: 107 · 2021: 33
FWCI: 20.13
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Microbiology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (AI095202, 75N93019C00062, AI157155, AI141707, 75N93019C00074, AI150739)
U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (UL1TR001439)
United States Department of Defense | Defense Advanced Research Projects Agency (HR0011-18-3-0001, HR0011-18-2-0001)
Merck KGaA (Future Insight Prize 2019)
DOE | LDRD | Argonne National Laboratory (DE-AC02-06CH11357)
Michigan Economic Development Corporation (085P1000817)
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
Life Sciences › Immunology and Microbiology › Immunology › Monoclonal and Polyclonal Antibodies Research
Keywords: SARS-CoV-2, spike protein, receptor binding domain, monoclonal antibodies, antibody neutralization, antibody-antigen complex structure, hypervariable region, HCDR3, neutralization escape, variants of concern, deep mutational scanning
MeSH terms: Protein Domains, COVID-19, SARS-CoV-2, Antibodies, Monoclonal, Antibodies, Viral, Antigenic Variation, Binding Sites, Humans, Mutation, Complementarity Determining Regions, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus

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