Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

• Published in: Cell host & microbe Vol. 29; no. 1; pp. 44 - 57.e9
• Main Authors: Greaney, Allison J., Starr, Tyler N., Gilchuk, Pavlo, Zost, Seth J., Binshtein, Elad, Loes, Andrea N., Hilton, Sarah K., Huddleston, John, Eguia, Rachel, Crawford, Katharine H.D., Dingens, Adam S., Nargi, Rachel S., Sutton, Rachel E., Suryadevara, Naveenchandra, Rothlauf, Paul W., Liu, Zhuoming, Whelan, Sean P.J., Carnahan, Robert H., Crowe, James E., Bloom, Jesse D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 13.01.2021; Cell Press
• Subjects: Angiotensin-Converting Enzyme 2 - chemistry; Angiotensin-Converting Enzyme 2 - metabolism; Antibodies, Monoclonal - immunology; Antibodies, Neutralizing - immunology; antibody escape; antigenic evolution; Binding Sites; deep mutational scanning; Epitopes - immunology; Gene Library; High-Throughput Nucleotide Sequencing; Humans; Protein Domains; Saccharomyces cerevisiae - genetics; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - immunology; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - immunology; Spike Glycoprotein, Coronavirus - metabolism; antibody escape; SARS-CoV-2; deep mutational scanning; antigenic evolution
• ISSN: 1931-3128; 1934-6069; 1934-6069
• DOI: 10.1016/j.chom.2020.11.007

Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing antibody responses elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies. They further enable the design of escape-resistant antibody cocktails—including cocktails of antibodies that compete for binding to the same RBD surface but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution. [Display omitted] •Develop system to map all SARS-CoV-2 RBD mutations that escape antibody binding•Escape maps predict which mutations emerge when virus grown in presence of antibody•Escape maps inform surveillance for possible antigenic evolution Greaney et al. develop a method to map all mutations to the SARS-CoV-2 RBD that escape antibody binding and apply this method to 10 antibodies. The resulting escape maps predict which mutations arise when virus is grown in the presence of antibody and can inform the design of antibody therapeutics.