Background:  HIV drug resistance is thought to have at least 2 origins:  pre-existing resistant mutants at a low frequency that are selected by therapy; and suboptimal therapy that permits replication, evolution, and selection of resistant mutants. Studying the mechanisms and anatomic origins of HIV drug resistance in humans is constrained by limited blood or tissue sampling and ethical restrictions on therapy. Here we examined the impact of short-course efavirenz (EFV) monotherapy on the evolution of drug resistance in a macaque model of ART.

Methods:  We infected 6 macaques with a pathogenic simian immunodeficiency (SIV)/HIV chimeric virus, RT-SHIV_mne, in which SIV_mne RT is replaced with HIV-1 RT. Plasma viral loads were allowed to stabilize for 13 weeks before the animals received either 3 days of EFV or no treatment. Starting 4 weeks later, all animals received daily therapy with tenofovir (TDF) + emtricitabine (FTC) + efavirenz (EFV) for 20 weeks, followed by treatment interruption. Resistance was measured by allele-specific polymerase chain reaction (AS-PCR) and single-genome sequencing (SGS).

Results:  Triple-drug therapy reduced plasma viral load to low or undetectable levels for 20 weeks in 5 of the 6 animals. Viral load rebound occurred after only 5 weeks of triple therapy in 1 of 3 animals that had received EFV monotherapy. AS-PCR revealed non-nucleoside reverse transcriptase inhibitor (NNRTI) -resistant variants before triple therapy in 2 of 3 animals who had received EFV monotherapy of >20% frequency. Of note, the animal that failed triple therapy had the highest viral load set-point (>10⁶ copies/mL) before any therapy. SGS analyses revealed linkage of specific K103N and M184I/V resistance alleles during failure. To understand the effects of treatment interruption on selection of drug resistance, therapy was stopped and reinitiated after viral load rebounded to >3000 copies/mL.

Conclusions:  Combination therapy with TDF+FTC+EFV was effective in suppressing RT-SHIV replication in macaques. Brief exposure to EFV monotherapy resulted in selection of NNRTI-resistant variants in 2 of 3 animals and early failure of triple drug therapy in 1 of 3 animals. The effect of interruption and re-initiation of therapy on the selection of resistance is being determined. This new animal model of ART has the flexibility to address many key questions about the selection, tissue origins and persistence of drug resistance that cannot be answered in human studies.