Background
Ensitrelvir, an oral main protease inhibitor targeting SARS-CoV-2, demonstrated robust antiviral activity in the phase 3 SCORPIO-HR/ACTIV-2d trial with a significant reduction in viral RNA levels and a higher percentage of negative viral cultures at Day 4 compared to placebo. In this exploratory analysis, we investigated emergence of resistance-associated mutations with ensitrelvir treatment.
Methods
A total of 1,888 mITT participants (945 in the ensitrelvir group and 943 in the placebo group, all with Omicron infection) from the SCORPIO-HR/ACTIV-2d trial who received ≥1 dose of study intervention within 3 days of symptom onset were included. Nasopharyngeal (NP) swabs were collected on days 1, 4, 8, and 16 for SARS-CoV-2 RNA levels by quantitative RT-PCR. Whole viral genome and targeted nsp5 gene sequencing were performed. Ensitrelvir resistance-associated mutations were defined as changes that reduced susceptibility by three-fold or more, or if found within 5 Angstroms of the active site. For the calculation of the frequency of treatment-emergent mutations, the denominator included all mITT participants regardless of sequence availability. Comparisons were by Wilcoxon rank sum tests.
Results
Treatment-emergent mutations were more frequent in the ensitrelvir-treated group compared to the placebo group (T25A/N: 0.4% (4/945) vs. 0% (0/943), p=0.12; M49L/I: 1.5% (14/945) vs. 0% (0/943), p<0.001). We also compared pre- and post-treatment SARS-CoV-2 RNA levels in those with successful sequencing at baseline and at least one follow-up time point. Ensitrelvir-treated participants with emergent mutations (n=18) showed higher RNA levels than ensitrelvir-treated participants without emergent mutations (n=255) both before treatment and on days 4 and 8: median (Q1, Q3) SARS-CoV-2 RNA levels pre-treatment: 8.2 (7.2, 8.3) vs. 7.3 (6.1, 8.1) log10 copies/mL; day 4: 5.1 (4.4, 5.8) vs. 4.6 (3.9, 5.4) log10 copies/mL; day 8: 5.4 (4.0, 6.1) vs. 1.7 log10 copies/mL (detected below lower limit of quantification [LLoQ]) (0.0, 2.7).
Conclusions
Resistance-associated mutations emerged with ensitrelvir treatment, but was relatively infrequent and associated with higher pre-treatment RNA levels. Protease inhibitors represent an important treatment modality for COVID-19, but can be vulnerable to treatment-emergent mutations and additional monitoring is warranted.
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