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

The coronavirus disease 2019 (COVID-19) pandemic underscores the need to better understand animal-to-human transmission of coronaviruses and adaptive evolution within new hosts. We scanned more than 182,000 severe acute respiratory syndrome coronavirus 2 (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 in 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 (wild-type [WT]-SARS-CoV-2) enhanced replication in human lung cells relative to its putative ancestral variant (T372), an effect that was 20 times greater than the well-known D614G mutation. Our findings suggest that this mutation likely contributed to SARS-CoV-2 emergence from animal reservoirs or enabled sustained human-to-human transmission. [Display omitted] •Over 182,000 SARS-CoV-2 genomes were screened for selective sweep signatures•An adaptive change within the spike protein receptor-binding domain was identified•This change was predicted and experimentally confirmed to increase affinity to hACE2•As a result, viral replication is enhanced relative to the putative ancestral variant A non-synonymous change (T372A) within the spike protein RBD of human SARS-CoV-2 shows higher binding affinity to hACE2 and enhanced replication in human lung cells compared with its putative ancestral variant (T372), providing evidence of a viral mutation that is likely to have been necessary to enable human-to-human transmission.