Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naive populations and associate with reduced treatment efficacy

Background Transmitted HIV-1 drug resistance can compromise initial antiretroviral therapy (ART); therefore, its detection is important for patient management. The absence of drug- associated selection pressure in treatment-naive persons can cause drug- resistant viruses to decline to levels undetectable by conventional bulk sequencing (minority drug-resistant variants). We used sensitive and simple tests to investigate evidence of transmitted drug resistance in antiretroviral drug- naive persons and assess the clinical implications of minority drug- resistant variants. Methods and Findings We performed a cross- sectional analysis of transmitted HIV-1 drug resistance and a casecontrol study of the impact of minority drug resistance on treatment response. For the crosssectional analysis, we examined viral RNA from newly diagnosed ART- naive persons in the US and Canada who had no detectable (wild type, n = 205) or one or more resistance- related mutations (n = 303) by conventional sequencing. Eight validated real- time PCR- based assays were used to test for minority drug resistance mutations ( protease L90M and reverse transcriptase M41L, K70R, K103N, Y181C, M184V, and T215F/Y) above naturally occurring frequencies. The sensitive real- time PCR testing identified one to three minority drug resistance mutation(s) in 34/ 205 (17%) newly diagnosed persons who had wild- type virus by conventional genotyping; four (2%) individuals had mutations associated with resistance to two drug classes. Among 30/ 303 (10%) samples with bulk genotype resistance mutations we found at least one minority variant with a different drug resistance mutation. For the case-control study, we assessed the impact of three treatment- relevant drug resistance mutations at baseline from a separate group of 316 previously ART-naive persons with no evidence of drug resistance on bulk genotype testing who were placed on efavirenz-based regimens. We found that 7/ 95 (7%) persons who experienced virologic failure had minority drug resistance mutations at baseline; however, minority resistance was found in only 2/ 221 (0.9%) treatment successes (Fisher exact test, p = 0.0038). Conclusions These data suggest that a considerable proportion of transmitted HIV-1 drug resistance is undetected by conventional genotyping and that minority mutations can have clinical consequences. With no treatment history to help guide therapies for drug- naive persons, the findings suggest an important role for sensitive baseline drug resistance testing.