The impact of remdesivir on SARS-CoV-2 evolution in vivo.

The impact of remdesivir on SARS-CoV-2 diversity and evolution in vivo has remained unclear. In this single-center, retrospective cohort study, we assessed SARS-CoV-2 diversification and diversity over time in a cohort of hospitalized patients who did or did not receive remdesivir. Whole genome sequencing was performed on 98 paired specimens collected from 49 patients before and after remdesivir administration. Genetic divergence between paired specimens was not significantly different from what was observed in paired specimens from patients who did not receive the drug. However, when comparing minority variants, several positions showed preferential diversification after remdesivir treatment, several of which were associated with different variants of concern. Most notably, remdesivir administration resulted in strong selection for a nonsynonymous mutation in nsp12, G671S, previously associated with enhanced viral fitness. This same mutation was found enriched in a second cohort of 143 inpatients with specimens collected after remdesivir administration compared to controls. Only one other mutation previously implicated in remdesivir resistance (nsp12:V792I) was found to be preferentially selected for after remdesivir administration. These data suggest that SARS-CoV-2 variants with enhanced replicative fitness may be selected for in the presence of antiviral therapy as an indirect means to overcome this selective pressure.