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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

View ORCID ProfileAllison J. Greaney, View ORCID ProfileAndrea N. Loes, View ORCID ProfileKatharine H.D. Crawford, View ORCID ProfileTyler N. Starr, Keara D. Malone, View ORCID ProfileHelen Y. Chu, View ORCID ProfileJesse D. Bloom
doi: https://doi.org/10.1101/2020.12.31.425021
Allison J. Greaney
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
2Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
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Andrea N. Loes
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
3Howard Hughes Medical Institute, Seattle, WA 98109, USA
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Katharine H.D. Crawford
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
2Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
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Tyler N. Starr
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
3Howard Hughes Medical Institute, Seattle, WA 98109, USA
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Keara D. Malone
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Helen Y. Chu
4Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
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  • ORCID record for Helen Y. Chu
Jesse D. Bloom
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
3Howard Hughes Medical Institute, Seattle, WA 98109, USA
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  • For correspondence: jbloom@fredhutch.org
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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 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.

Competing Interest Statement

H.Y.C. is a consultant for Merck and Pfizer and receives research funds from Cepheid, Ellume, Genentech, and Sanofi-Pasteur. The other authors declare no competing interests.

Footnotes

  • https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_HAARVI_sera

  • https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_HAARVI_sera/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 04, 2021.
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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies
Allison J. Greaney, Andrea N. Loes, Katharine H.D. Crawford, Tyler N. Starr, Keara D. Malone, Helen Y. Chu, Jesse D. Bloom
bioRxiv 2020.12.31.425021; doi: https://doi.org/10.1101/2020.12.31.425021
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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies
Allison J. Greaney, Andrea N. Loes, Katharine H.D. Crawford, Tyler N. Starr, Keara D. Malone, Helen Y. Chu, Jesse D. Bloom
bioRxiv 2020.12.31.425021; doi: https://doi.org/10.1101/2020.12.31.425021

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