Rapid characterization of spike variants via mammalian cell surface display

The SARS-CoV-2 spike (S) protein is a critical component of subunit vaccines and a target for neutralizing antibodies. Spike is also undergoing immunogenic selection with clinical variants that increase infectivity and partially escape convalescent plasma. Here, we describe spike display, a high-thr...

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Bibliographic Details
Published in:bioRxiv 2021-03
Main Authors: Kamyab Javanmardi, Chia-Wei, Chou, Terrace, Cynthia, Annapareddy, Ankur, Kaoud, Tamer S, Guo, Qingqing, Lutgens, Josh, Zorkic, Hayley, Horton, Andrew P, Gardner, Elizabeth C, Nguyen, Giaochau, Boutz, Daniel R, Goike, Jule, Voss, Will N, Hung-Che Kuo, Dalby, Kevin N, Gollihar, Jimmy D, Finkelstein, Ilya J
Format: Article
Language:English
Subjects:
ACE2
Alanine
Angiotensin-converting enzyme 2
Antibodies
Cell surface
Coronaviruses
Epitope mapping
Immunogenicity
Infectivity
Monoclonal antibodies
Mutation
Patent applications
Scanning mutagenesis
Severe acute respiratory syndrome coronavirus 2
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Summary:The SARS-CoV-2 spike (S) protein is a critical component of subunit vaccines and a target for neutralizing antibodies. Spike is also undergoing immunogenic selection with clinical 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 thirteen neutralizing antibodies (nAbs). An alanine scan of the N-terminal domain (NTD) highlights a public class of epitopes in the N3 and N5 loops that are recognized by most of the NTD-binding nAbs assayed in this study. Some clinical NTD substitutions abrogate binding to these epitopes but are circulating at low frequencies around the globe. NTD mutations in variants of concern B.1.1.7 (United Kingdom), B.1.351 (South Africa), B.1.1.248 (Brazil), and B.1.427/B.1.429 (California) impact spike expression and escape most NTD-targeting nAbs. However, two classes of NTD nAbs still bind B.1.1.7 spikes and neutralize in pseudoviral assays. B.1.1351 and B.1.1.248 include compensatory mutations that either increase spike expression or increase ACE2 binding affinity. Finally, B.1.351 and B.1.1.248 completely escape a potent ACE2 peptide mimic. We anticipate that spike display will be useful for rapid antigen design, deep scanning mutagenesis, and epitope mapping of antibody interactions for SARS-CoV-2 and other emerging viral threats. Competing Interest Statement The authors declare competing financial interests. K.J., C.-W.C., H.-C.K., and I.J.F. have filed patent applications on spike-6p (HexaPro). A patent application submitted by The University of Texas Board of Regents is pending for anti-SARS-CoV-2 monoclonal antibodies described in the manuscript (W.N.V.). The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare no competing non-financial interests.
DOI:10.1101/2021.03.30.437622