Rapid characterization of spike variants via mammalian cell surface display

Mol Cell. 2021 Dec 16;81(24):5099-5111.e8. doi: 10.1016/j.molcel.2021.11.024.


The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.

Keywords: COVID-19; N-terminal domain; cell display; receptor-binding domain; variants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antibodies, Monoclonal / immunology
  • Antibodies, Neutralizing / immunology
  • COVID-19 / immunology
  • COVID-19 / virology
  • Cell Line
  • Epitopes / genetics
  • Epitopes / immunology
  • HEK293 Cells
  • Humans
  • Mammals / immunology
  • Mammals / virology*
  • Protein Binding / genetics
  • Protein Binding / immunology
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / immunology
  • Spike Glycoprotein, Coronavirus / genetics*
  • Spike Glycoprotein, Coronavirus / immunology


  • Antibodies, Monoclonal
  • Antibodies, Neutralizing
  • Epitopes
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Supplementary concepts

  • SARS-CoV-2 variants