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

Cell Rep. 2021 Aug 31;36(9):109627. doi: 10.1016/j.celrep.2021.109627. Epub 2021 Aug 10.


The potential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) escape mutants is a threat to 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 coronavirus disease 2019 (COVID-19) infection. Escape mutations predominantly mapped to the periphery of the angiotensin-converting enzyme 2 (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.

Keywords: S RBD; SARS-CoV-2; deep mutational scanning; escape mutants; neutralizing antibodies; yeast surface display.