Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition

Cell Rep. 2021 Oct 5;37(1):109784. doi: 10.1016/j.celrep.2021.109784. Epub 2021 Sep 16.

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable challenge to the clinical treatment of coronavirus disease (COVID-19). Therefore, the need for ongoing discovery efforts to identify broadly reactive monoclonal antibodies to SARS-CoV-2 is of utmost importance. Here, we report a panel of SARS-CoV-2 antibodies isolated using the linking B cell receptor to antigen specificity through sequencing (LIBRA-seq) technology from an individual who recovered from COVID-19. Of these antibodies, 54042-4 shows potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs). A cryoelectron microscopy (cryo-EM) structure of 54042-4 in complex with the SARS-CoV-2 spike reveals an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages. Further, 54042-4 possesses uncommon genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings provide motivation for the development of 54042-4 as a lead candidate to counteract current and future SARS-CoV-2 VOCs.

Keywords: COVID-19; Delta variant; LIBRA-seq; SARS-CoV-2; antibody discovery; cryo-EM; monoclonal antibodies biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Angiotensin-Converting Enzyme 2 / chemistry
  • Angiotensin-Converting Enzyme 2 / immunology*
  • Animals
  • Antibodies, Monoclonal / immunology*
  • Antibodies, Neutralizing / immunology*
  • Antibodies, Viral / immunology
  • Antibody Formation
  • COVID-19 / genetics
  • COVID-19 / immunology*
  • COVID-19 / virology
  • Cell Line
  • Chlorocebus aethiops
  • Cryoelectron Microscopy
  • Epitope Mapping / methods
  • Epitopes / chemistry
  • Epitopes / immunology
  • High-Throughput Screening Assays / methods
  • Humans
  • Male
  • Middle Aged
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Receptors, Antigen, B-Cell / chemistry
  • Receptors, Antigen, B-Cell / immunology
  • SARS-CoV-2 / chemistry*
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / immunology*
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / immunology*
  • Vero Cells

Substances

  • Antibodies, Monoclonal
  • Antibodies, Neutralizing
  • Antibodies, Viral
  • Epitopes
  • Receptors, Antigen, B-Cell
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2