Abstract
SARS-CoV-2 has evolved variants with substitutions in the spike receptor-binding domain (RBD) that impact its affinity for ACE2 receptor and recognition by antibodies. These substitutions could also shape future evolution by modulating the effects of mutations at other sites—a phenomenon called epistasis. To investigate this possibility, we performed deep mutational scans to measure the effects on ACE2 binding of all single amino-acid mutations in the Wuhan-Hu-1, Alpha, Beta, Delta, and Eta variant RBDs. Some substitutions, most prominently N501Y, cause epistatic shifts in the effects of mutations at other sites, thereby shaping subsequent evolutionary change. These epistatic shifts occur despite high conservation of the overall RBD structure. Our data shed light on RBD sequence-function relationships and facilitate interpretation of ongoing SARS-CoV-2 evolution.
Competing Interest Statement
JDB consults for Moderna on viral evolution and epidemiology and Flagship Labs 77 on deep mutational scanning. TNS, AJG, ANL, and JDB may receive a share of IP revenue as inventors on Fred Hutch-optioned technology/patents related to deep mutational scanning of viral proteins. KH, EF, JRD, DC, and GS are employees of Vir Biotechnology and may hold shares in Vir Biotechnology.
Footnotes
↵* Co-first authors