Virological and genomic analysis of SARS-CoV-2 from a favipiravir clinical trial cohort

Abstract

Introduction: Several clinical studies have reported the efficacy of favipiravir in reducing viral load and shortening the duration of symptoms. However, the viability of SARS-CoV-2 in the context of favipiravir therapy and the potential for resistance development is unclear.

Methods: We sequenced 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 sequenced from those who remained RT-PCR-positive 5-8 days into favipiravir therapy. Daily nasopharyngeal specimens from 69 patients who were RT-PCR-positive at randomization were examined for a cytopathic effect (CPE).

Results: Some strains early in the trial belonged to clade 19 B, whereas the majority belonged to clade 20 B. The median time from the disease onset to negative CPE was 9 days. CPE was strongly correlated with the time from disease onset, viral load, age, and male sex. Among 23 patients for whom paired genomes were available, all except one had identical genomes. Two mutations were observed in one patient who received favipiravir, neither in the RdRp gene.

Conclusions: The SARS-CoV-2 genome distribution in this clinical trial conducted in Japan reflected the early influx of strains from China followed by replacement by strains from Europe. CPE was significantly associated with age, male sex, and viral loads but not with favipiravir therapy. There was no evidence of resistance development during favipiravir therapy.

Keywords: Cytopathic effect; Genome epidemiology; Pharmacotherapy; SARS-CoV-2.

Fig. 1

Phylogenetic tree of SARS-CoV-2 genomes generated by Nextstrain. Strains from this trial and those worldwide, including those collected between December 2019 and August 2020, are shown. Red: This study, Blue: Japan, Yellow: Europe, Green: the USA, and Pale blue: China.

Fig. 2

Kaplan-Meier product-limit estimates for the cumulative probability of being free of negative CPE or RT-PCR negativity over time from the time of randomization and the time of disease onset. The gray shaded area corresponds to pointwise 95% confidence intervals. (a) Cumulative proportion of patients with CPE positive against days from randomization. (b) Cumulative proportion of patients with RT-PCR positive against days from randomization. (c) Cumulative proportion of patients with CPE positive against days from onset. (c) Cumulative proportion of patients with RT-PCR positive against days from onset.

Fig. 3

Kaplan-Meier product-limit estimates for the cumulative probability of being free of negative CPE over time from the time of randomization stratified by treatment group.

Fig. 4

The CPE positive probabilities quantified by the function of age, sex, viral loads. (a) CPE positive probability against log10 (Viral loads) for patients with age 30 or 60, male sex, and 9 days from onset. (b) CPE positive probability against log10 (Viral loads) for patients with age 30 or 60, female sex, and 9 days from onset. (c) CPE positive probability against age for patients with log10 (Viral loads) = 6, male sex, and 9 days from onset. (d) CPE positive probability against age for patients with log10 (Viral loads) = 6, female sex, and 9 days from onset. For patients with age 30 at 9 days from onset, viral loads around 10⁶ copies/mL corresponded to CPE positive probability nearly 0, and viral loads around 10⁷ copies/mL corresponded to CPE positive probability nearly 1. For patients with age 60 at 9 days from onset, viral loads around 10⁴ copies/mL corresponded to CPE positive probability of nearly 0, and viral loads around 10⁸ copies/mL corresponded to CPE positive probability of 50% or more. The association between CPE positive probability and viral loads was more marked in younger patients.