Rapid characterization of spike variants via mammalian cell surface display

Kamyab Javanmardi†, Chia-Wei Chou, Cynthia Terrace, Ankur Annapareddy, Tamer S. Kaoud, Qingqing Guo, Josh Lutgens, Hayley Zorkic, Andrew P. Horton, Elizabeth C. Gardner, Giaochau Nguyen, Daniel R. Boutz, Jule Goike, Will N. Voss, Hung-Che Kuo, Kevin N. Dalby, Jimmy D. Gollihar & Ilya J. Finkelstein† († co-corresponding), Mol. Cell 81 (24) :5099-5111.e8 (2021).
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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.