Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain
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Abstract
Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short complementarity-determining region (CDR) H3. Germline-encoded sequence motifs in heavy chain CDRs H1 and H2 have a major function, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, is not clear. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that seem to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. These results advance understanding of the antibody response to SARS-CoV-2.
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VH3-53 and VH3-66 are known to be enriched in RBD-binding B cells.
“Notably, both of these IGHV genes are known to be enriched in RBD-binding B cells (45, 46).”
From mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern (2021) · cites this paper as [45]
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SARS-CoV-2 escape <i>in vitro</i> from a highly neutralizing COVID-19 convalescent plasma
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mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern
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- Authors
- Tan, T. J. C., Yuan, M., Kuzelka, K., Padron, G. C., Beal, J. R., Chen, X., Wang, Y., Rivera-Cardona, J., Zhu, X., Stadtmueller, B. M., Brooke, C. B., Wilson, I. A., & Wu, N. C.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Scripps Research Institute (US)
- Corresponding author
- Wilson, Ian A.
- Wu, Nicholas C.
- ORCID
- Venue
- Nature Communications
- Published
- 2021-06-21
- Volume
- 12
- Issue
- 1
- Pages
- 3815-3815
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC8217500
- OpenAlex
- W3176441117
- Cited by
- 75
- References
- 81
- Citations by year
- 2026: 7 · 2025: 14 · 2024: 7 · 2023: 18 · 2022: 19 · 2021: 10
- FWCI
- 4.26
- 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)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Bill and Melinda Gates Foundation (INV-004923)
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (AI139445)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2, receptor binding domain, spike protein, neutralizing antibodies, CDR-H3, somatic hypermutation, antibody affinity
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