Favipiravir therapy on SARS-CoV-2

Several clinical studies have reported efficacy of favipiravir in reducing viral load and shortening duration of symptoms, but its effect on viability of SARS-CoV-2 and potential for resistance development is unclear. We conducted genome sequencing of SARS-CoV-2 in nasopharyngeal specimens collected from patients who participated in a randomized clinical trial of favipiravir at hospitals across Japan between March and May 2020. Paired genomes were also sequenced from a subset of patients who remained RT-PCR-positive with low Cp values 5-8 days into favipiravir therapy or 6 days into supportive therapy. Daily nasopharyngeal specimens were examined for cytopathic effect to detect viable virus and compared with RT-PCR results. The SARS-CoV-2 genome distribution in this clinical trial reflected the early influx of clades from China followed by replacement by clades from Europe. We observed a trend towards lower virus viability with favipiravir therapy, but the association was not statistically significant. There was no evidence of resistance development on therapy.