Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1)

Abstract

Background: Remdesivir is approved for treatment of coronavirus disease 2019 (COVID-19) in nonhospitalized and hospitalized adult and pediatric patients. Here we present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance analyses from the phase 3 ACTT-1 randomized placebo-controlled trial conducted in adult participants hospitalized with COVID-19.

Methods: Swab samples were collected at baseline and longitudinally through day 29. SARS-CoV-2 genomes were sequenced using next-generation sequencing. Phenotypic analysis was conducted directly on participant virus isolates and/or using SARS-CoV-2 subgenomic replicons expressing mutations identified in the Nsp12 target gene.

Results: Among participants with both baseline and postbaseline sequencing data, emergent Nsp12 substitutions were observed in 12 of 31 (38.7%) and 12 of 30 (40.0%) participants in the remdesivir and placebo arms, respectively. No emergent Nsp12 substitutions in the remdesivir arm were observed in more than 1 participant. Phenotyping showed low to no change in susceptibility to remdesivir relative to wild-type Nsp12 reference for the substitutions tested: A16V (0.8-fold change in EC50), P323L + V792I (2.2-fold), C799F (2.5-fold), K59N (1.0-fold), and K59N + V792I (3.4-fold).

Conclusions: The similar rate of emerging Nsp12 substitutions in the remdesivir and placebo arms and the minimal change in remdesivir susceptibility among tested substitutions support a high barrier to remdesivir resistance development in COVID-19 patients. Clinical Trials Registration. NCT04280705.

Keywords: COVID-19; RNA-dependent RNA polymerase; SARS-CoV-2; remdesivir; resistance.

Figure 1.

ACTT-1 study design. Abbreviations: ACTT-1, Adaptive COVID-19 Treatment Trial-1; IV, intravenous; RDV, remdesivir.

Figure 2.

Clinical recovery in participants treated with remdesivir with or without emergent Nsp12 amino acid substitutions. Recovery was defined as either discharged from the hospital or hospitalized but not requiring supplemental oxygen and no longer requiring ongoing medical care at day 28.

Figure 3.

Emergent Nsp12 amino acid substitutions in participants treated with remdesivir relatively (A) distant and (B) nearer to the RdRp active site or RNA. The structure is a model of RDV-TP incorporation in the SARS-CoV-2 polymerase active site based on the 6XEZ Cryo-EM structure [30]. A, Map of the observed postbaseline amino acid substitutions on Cryo-EM structure of SARS-CoV-2 polymerase complex in rotated view. Full Nsp12 protein (in green) with the locations of the observed postbaseline amino acid substitutions located in this view of the structure are shown in magenta. For context, all substitutions not highlighted in this particular view are shown in light pink. White is Nsp7, yellow is Nsp8 (2 subunits), and orange is Nsp13 (2 subunits). The template RNA strand is shown in blue and the nascent RNA strand is shown in red. B, Map of observed postbaseline amino acid substitutions closest to the active site of Nsp12 and on Cryo-EM structure of the SARS-CoV-2 polymerase complex. Abbreviations: Cryo-EM, cryoelectron microscopy; RdRp, RNA-dependent RNA polymerase; RDV-TP, triphosphate form of remdesivir; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.