Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain

Timothy J.C. Tan, Meng Yuan, Kaylee Kuzelka, Gilberto C. Padron, Jacob R. Beal, Xin Chen, Yiquan Wang, Joel Rivera-Cardona, Xueyong Zhu, Beth M. Stadtmueller, Christopher B. Brooke, Ian A. Wilson, Nicholas C. Wu

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article number3815
JournalNature Communications
Issue number1
StatePublished - Dec 2021


  • Novel coronavirus
  • COVID-19
  • severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
  • Coronavirus
  • 2019-nCoV
  • Pandemic

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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