One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening

Abstract

The potential emergence of SARS-CoV-2 Spike (S) escape mutants is a threat to reduce the efficacy of existing vaccines and neutralizing antibody (nAb) therapies. An understanding of the antibody/S escape mutation landscape is urgently needed to preemptively address this threat. Here we describe a rapid method to identify escape mutants for nAbs targeting the S receptor binding site. We identified escape mutants for five nAbs, including three from the public germline class VH3-53 elicited by natural COVID-19 infection. Escape mutations predominantly mapped to the periphery of the ACE2 recognition site on the RBD with K417, D420, Y421, F486, and Q493 as notable hotspots. We provide libraries, methods, and software as an openly available community resource to accelerate new therapeutic strategies against SARS-CoV-2.

Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies

“…6 B, 7 B, and Fig. S12 , Table 2 and Table S20 ), in line with recent findings 78 . Finally, and in full agreement with Lilly’s data, LY-CoV016 is also found to be escaped by all spike N460 variations (N460I/K/S/T) (Figs.…”

“…Concerning the alternative LY-CoV016 mAb, the official Lilly’s fact sheet 58 reports that SARS-CoV-2 spike mutants showing reduced susceptibility to etesevimab include substitutions K417N, D420N, and N460K/S/T. In agreement with this and other evidences 71 – 78 , our current computational alanine/mutagenesis study marks K417 and all its reported variants (K417E/N/R/T) as the strongest hot spots in eliciting potential escape to the LY-CoV016 mAb (Figs. 5 B, 6 A, 7 A, and Fig.…”

“…S2 , S3 , Table 2 and Tables S6 , S7 ). In line with these predictions, three new studies highlighted all these mutants as viral proteins that may hinder the efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine-induced seroprevalence 64 , 77 , 78 . Remarkably, the spike S494P mutation is a component of the B.1.17 + S494P VOC 51 /VUM 53 identified in United Kingdom in January 2021.…”

An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

“… 1 Understanding the structural, functional, and mechanistic basis of such noncovalent protein–protein interactions can help rationalize emergent cellular behavior, 1 can be exploited for design of biologics like antibodies 2 and can also be used to map and predict the next moves in the trench warfare between humoral immunity and pathogen evasion and evolution. 3 …”

“… 26,61,62 Finally, the Whitehead group has developed a method to determine the set of mutations on S RBD which can escape monoclonal antibody neutralization. 3 …”