Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition

Abstract

Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and make a major contribution to the neutralizing antibody response 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 RBD surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies, and enable us to design escape-resistant antibody cocktails–including cocktails of antibodies that compete for binding to the same surface of the RBD 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.

Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies

“…It is important to note that the most significant component of neutralizing epitopes are certain residues that make contacts with interacting mAbs. Even a single residue mutation may result in drastically different mAb neutralization potentials, despite the possibility of maintained binding affinities [ 58 ].…”

“…Moreover, point mutations in a neutralizing epitope can differentially influence the potency of different neutralizing mAbs, even if their epitopes overwhelmingly overlap. Greaney et al developed a deep mutational scanning method to produce viral escape maps induced by specific mAbs [ 58 ]. In contrast to antibody–spike complex structures on their own, these maps can showcase which specific immunogenic residues are important for neutralization.…”

Human endemic coronavirus emergence in the context of past and recent zoonotic outbreaks

“…Whether SARS-CoV-2 will evolve variants that alter its antigenic properties is also, of course, of great interest. Our data on HCoV-229E and HCoV-OC43 suggest that antigenic drift is not a major evolutionary driving force for these viruses and available data on SARS-CoV-2 suggest that variants affecting antigenic properties are present at low frequency in the circulating viral population 112,113 . However, the evolution of the virus is likely to depend on the duration and e cacy of natural immunity.…”

Recurrent independent emergence and transmission of SARS-CoV-2 Spike amino acid H69/V70 deletions

“…4). Based on its location it might be expected to escape antibodies similar to COV2-2499 5 (Fig. 3C, D).…”

“…Despite this critical interaction and the constraints it imposes, it appears the RBD, and particularly the receptor binding motif (RBM), is relatively toleratant to mutations 3,4 , raising the real possibility of virus escape from vaccine-induced immunity and monoclonal antibody treatments. Spike mutants exhibiting reduced susceptibility to monoclonal antibodies have been identi ed in in vitro screens 3,5,6 , and some of these mutations have been found in clinical isolates 7 . Due to the susceptibility of the human population to this virus, the acute nature of infections and limited use of vaccines to date there has been limited selection pressure placed SARS-CoV-2 8 ; as a consequence few mutations that could alter antigenicity have increased signi cantly in frequency.…”