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

Allison J Greaney,Pavlo Gilchuk,Robert H Carnahan,Katharine H.D Crawford,Rachel Eguia,Elad Binshtein,Zhuoming Liu,Seth J Zost,John Huddleston,Paul W Rothlauf,Adam S Dingens,Rachel S Nargi,Rachel E Sutton,Sarah K Hilton,Naveen Chandra Suryadevara ,Tyler N Starr,Sean P J Whelan ,Andrea N Loes,Jesse D Bloom

doi:10.1016/j.chom.2020.11.007

Abstract

SummaryAntibodies 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.

Highlights

The coronavirus disease 2019 (COVID-19) pandemic has generated urgent interest in antibody therapeutics and vaccines that induce antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Escape mutants can be selected by passaging virus expressing the SARS-CoV-2 spike protein in the presence of anti-receptor-binding domain (RBD) antibodies in the lab (Baum et al, 2020a; Weisblum et al, 2020), and some RBD mutations that alter antibody binding are already present at very low levels in SARS-CoV-2
To eliminate RBD mutants that were completely misfolded or unable to bind angiotensin-converting enzyme 2 (ACE2), we first used fluorescence-activated cell sorting (FACS) to eliminate RBD variants with

Summary

Introduction

The coronavirus disease 2019 (COVID-19) pandemic has generated urgent interest in antibody therapeutics and vaccines that induce antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Anti-RBD antibodies often dominate the neutralizing activity of the polyclonal antibody response elicited by natural infection (Barnes et al, 2020a; Steffen et al, 2020; Weisblum et al, 2020) Both passively administered and vaccine-induced anti-RBD neutralizing antibodies protect against SARS-CoV-2 in animals (Alsoussi et al, 2020; Cao et al, 2020; Hassan et al, 2020; Rogers et al, 2020; Walls et al, 2020a; Wu et al, 2020; Zost et al, 2020a), and preliminary evidence suggests neutralizing antibodies correlate with protection in humans (Addetia et al, 2020). Escape mutants can be selected by passaging virus expressing the SARS-CoV-2 spike protein in the presence of anti-RBD antibodies in the lab (Baum et al, 2020a; Weisblum et al, 2020), and some RBD mutations that alter antibody binding are already present at very low levels in SARS-CoV-2

Results

Discussion

Conclusion