A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

Kang, Lin; He, Guijuan; Sharp, Amanda K.; Wang, Xiaofeng; Brown, Anne M.; Michalak, Pawel; Weger-Lucarelli, James

The COVID-19 pandemic underscores the need to understand better animal-to-human transmission of coronaviruses and adaptive evolution within new hosts. We scanned over 182,000 SARS-CoV-2 genomes for selective sweep signatures and found a distinct footprint of positive selection located around a non-synonymous change (A1114G; T372A) within the Spike protein receptor-binding domain (RBD), predicted to remove glycosylation and increase binding to human ACE2 (hACE2), the cellular receptor. This change is present in all human SARS-CoV-2 sequences but not closely related viruses from bats and pangolins. As predicted, T372A RBD bound hACE2 with higher affinity in experimental binding assays. We engineered the reversion mutant (A372T) and found that A372 (WT-SARS-CoV-2) enhanced replication in human lung cells relative to its putative ancestral variant (T372), an effect which was 20x greater than the well-known D614G mutation. Our findings suggest that this mutation likely contributed to SARS-CoV-2’s emergence from animal reservoirs or enabled sustained human-to-human transmission.