Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
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Abstract
Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasmas, including plasmas from individuals from whom some of the antibodies were isolated. While the binding of polyclonal plasma antibodies are affected by mutations across multiple RBD epitopes, the plasma-escape maps most resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
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Mutations at position 452 have been associated with a reduction in neutralization by monoclonal antibodies (particularly class 2 antibodies) and polyclonal sera.
“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 [9]
Mutations at F486 are associated with a reduction in neutralizing activity by class 1 (and some class 2) neutralizing antibodies and by polyclonal sera.
“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 [9]
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- Authors
- Greaney, A. J., Starr, T. N., Barnes, C. O., Weisblum, Y., Schmidt, F., Caskey, M., Gaebler, C., Cho, A., Agudelo, M., Finkin, S., Wang, Z., Poston, D., Muecksch, F., Hatziioannou, T., Bieniasz, P. D., Robbiani, D. F., Nussenzweig, M. C., Bjorkman, P. J., & Bloom, J. D.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- California Institute of Technology (US)
- Rockefeller University (US)
- Institute for Research in Biomedicine (CH)
- Corresponding author
- Bloom, Jesse D.
- ORCID
- Greaney, Allison J.
- Starr, Tyler N.
- Barnes, Christopher O.
- Weisblum, Yiska
- Schmidt, Fabian
- Caskey, Marina
- Gaebler, Christian
- Cho, Alice
- Agudelo, Marianna
- Finkin, Shlomo
- Wang, Zijun
- Poston, Daniel
- Muecksch, Frauke
- Hatziioannou, Theodora
- Bieniasz, Paul D.
- Robbiani, Davide F.
- Nussenzweig, Michel C.
- Bjorkman, Pamela J.
- Bloom, Jesse D.
- Venue
- Nature Communications
- Published
- 2021-07-07
- Volume
- 12
- Issue
- 1
- Pages
- 4196-4196
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7987015
- OpenAlex
- W3179259355
- Cited by
- 433
- References
- 64
- Citations by year
- 2026: 34 · 2025: 39 · 2024: 56 · 2023: 83 · 2022: 157 · 2021: 64
- FWCI
- 29.43
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- Burroughs Wellcome Fund
- Bill and Melinda Gates Foundation (INV-004949)
- Damon Runyon Cancer Research Foundation (DRG-2381-19)
- Washington Research Foundation
- Fred Hutchinson Cancer Research Center
- George Mason University
- California Institute of Technology
- University of Washington
- National Institutes of Health (1s10od028685-01, P01-AI138398-S1, AI111825)
- Beckman Institute, California Institute of Technology
- National Institute of Allergy and Infectious Diseases (U01AI151698, P01 AI138398-S1, R01AI127893, T32AI083203, U19AI111825, R01AI141707, AI151698, F30AI157898)
- 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 › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- SARS-CoV-2, spike protein receptor-binding domain, antibody escape mutations, neutralizing antibodies, monoclonal antibodies, convalescent plasma, antibody-antigen binding, epitope evolution
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