Background: Doravirine (DOR) is a novel human immunodeficiency type 1 virus (HIV-1) non-nucleoside reverse transcriptase inhibitor (NNRTI), with improved potency against prevalent NNRTI resistance-associated mutations, including RT K103N, Y181C, G190A, and E138K, at clinically relevant concentrations. This study aimed to characterize the mutant viruses selected in treatment-naïve participants through Week 48 from DRIVE-FORWARD and DRIVE-AHEAD, and to assess the impact of selected mutations on NNRTI susceptibility and viral fitness.
Methods: Plasma samples from the trials were tested for genotypic and phenotypic NNRTI susceptibility using a Monogram Biosciences resistance assay. Additionally, laboratory mutant isolates were generated via a site-directed mutagenesis (SDM) method with gene synthesis and subcloning into plasmid RT112. The resulting mutants were tested for their susceptibility to DOR and other NNRTIs in MT4-GFP cells to assess potential cross-resistance. The relative replication capacity of the mutants was measured by mixing various ratios of wild-type (WT) and mutant infected cells. The resulting cultures were incubated for 4 weeks with medium change every 3-4 days. At each passage, supernatant was harvested for clonal sequencing analysis to quantitate the relative abundance of WT and mutant viruses.
Results: Seven of 747 (0.9%) participants developed NNRTI resistance-associated mutations from 2 DOR phase 3 clinical trials (Table 1). SDMs were generated for the substitutions Y188L, V106I/F227C, A98G/F227C, V106I/H221Y/F227C, A98G/V106I/H221Y/F227C, V106A/P225H/Y318F, and V106M/F227C and their susceptibility to NNRTIs was evaluated. Most of the mutants conferred high level of resistance to DOR with a fold change (FC) >100 (FC: mutantEC50 versus WTEC50). Among the 7 mutants, V106I/F227C, V106I/H221Y/F227C, V106M/F227C, and Y188L mutants displayed FC < 10 against etravirine and rilpivirine, which is consistent with the phenotypic data from Monogram Biosciences. In addition, mutants containing F227C substitution were shown to be hypersensitive to some NRTIs such as AZT, TDF/TAF, and d4T. The replication capacity (RC) of Y188L, V106I/F227C, and A98G/V106I/H221Y/F227C was < 10% of WT virus and the RC of A98G/F227C and V106M/F227C was approximately 20% of WT virus.
Conclusions: The majority of DOR-selected viruses identified in the treatment-naive participants in clinical trials to date may retain susceptibility to etravirine and hypersensitivity to some NRTIs with low replication capacity.

Table 1. Doravirine-selected NNRTI resistance in treatment-naïve participants in clinical trials
[Table 1. Doravirine-selected NNRTI resistance in treatment-naïve participants in clinical trials]