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

Abstract

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-naïve 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-naïve 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 case-control study of the impact of minority drug resistance on treatment response. For the cross-sectional analysis, we examined viral RNA from newly diagnosed ART-naïve 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-naïve 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-naïve persons, the findings suggest an important role for sensitive baseline drug resistance testing.

Figure 1. STROBE-Type Flow Diagram for the Retrospective Cross-Sectional (Newly Diagnosed Surveillance) Study Illustrating Drug Resistance in the Parent Cohorts and the Sample Selection for Real-Time PCR Resistance Testing

Additional details are provided in Table 1.

Figure 2. STROBE-Type Flow Diagram for the Retrospective Case-Control Treatment Study Illustrating the Parent Cohort (Blue) Outcomes and Sample Selection for Real-Time PCR Resistance Testing

Figure 3. Real-Time PCR Mutation Test Results (ΔCT) for the Cross-Sectional Group

The samples positive for minority resistance are emphasized (ΔCT results above 13 cycles are not shown). The wild-type and mutant groups were tested for eight key resistance mutations. Horizontal bar (—) denotes the assay cutoff for the mutation. Samples falling below this bar are positive for the mutation. The clonal frequencies are shown for encircled data points.

Figure 4. Real-Time PCR Mutation Test Results (ΔCT) for Three Treatment-Relevant Mutations in the Case-Control Study Group

Horizontal bar (—) denotes the assay cutoff for the mutation. Samples falling below this bar are positive for the mutation.