Background: The iPrEx study showed that pre–exposure prophylaxis (PrEP) with oral emtricitabine/tenofovir disoproxyl fumarate (FTC/TDF) provides additional protection against HIV–1 infection among men who have sex with men (MSM) receiving standard prevention methods. Selection for drug resistance may occur if PrEP is used inconsistently. Viral population-based drug resistance assays, used in previous reports from iPrEx, are not sensitive for the detection of minor sequence variants. 

Methods:  Among iPrEx participants with HIV-1 seroconversion, reverse transcription mutations K65R, K70E, M184V, and M184I were interrogated in plasma samples obtained at first evidence of seroconversion using a quantitative minor variant assay based on allele-specific PCR (lower limit of quantitation 0.5%). Seronegative participants with pre-existing infection at enrollment were monitored longitudinally for drug resistance using population-based sequencing (TRUGENE).

Results:  Control of primer-binding site heterogeneity proved to be essential for the specificity of the minor variant assay. Of the 100 post-enrollment infections, none showed FTC or TDF resistance by population sequencing. Plasma RNA from 91 subjects were analyzed for minor variant drug resistance. None of the 33 in the active arm showed evidence of minor variant drug resistance, including the 3 active arm seroconverters who had detectable (albeit low) drug levels. Of 58 in the placebo arm, 2 showed minor variant drug resistance, 1 subject at K65R (0.69%), and 1 at M184V (1.26%). Both were infected with subtype B virus. Plasma viral load was high and comparable in the 2 arms (active arm median 5.31 log₁₀ copies/mL, IQR 4.96 to 5.75; placebo arm median 5.22 log₁₀ copies/mL, IQR 4.71 to 5.62). Among those who enrolled with pre-existing HIV-1 infection (RNA positive, seronegative), M184V or I mutants that were detectable at seroconversion became undetectable by population sequencing 9 and 12 weeks after stopping FTC/TDF, and 36 weeks after stopping placebo.

Conclusions:  Minor variant drug resistance was not detected in the active arm of the iPrEx study, consistent with low drug exposure in FTC/TDF PrEP failures. FTC resistance among those who started FTC/TDF with pre-existing infection waned rapidly after FTC/TDF was stopped.