Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing

Abstract

Objectives: It is still debated if pre-existing minority drug-resistant HIV-1 variants (MVs) affect the virological outcomes of first-line NNRTI-containing ART.

Methods: This Europe-wide case-control study included ART-naive subjects infected with drug-susceptible HIV-1 as revealed by population sequencing, who achieved virological suppression on first-line ART including one NNRTI. Cases experienced virological failure and controls were subjects from the same cohort whose viraemia remained suppressed at a matched time since initiation of ART. Blinded, centralized 454 pyrosequencing with parallel bioinformatic analysis in two laboratories was used to identify MVs in the 1%-25% frequency range. ORs of virological failure according to MV detection were estimated by logistic regression.

Results: Two hundred and sixty samples (76 cases and 184 controls), mostly subtype B (73.5%), were used for the analysis. Identical MVs were detected in the two laboratories. 31.6% of cases and 16.8% of controls harboured pre-existing MVs. Detection of at least one MV versus no MVs was associated with an increased risk of virological failure (OR = 2.75, 95% CI = 1.35-5.60, P = 0.005); similar associations were observed for at least one MV versus no NRTI MVs (OR = 2.27, 95% CI = 0.76-6.77, P = 0.140) and at least one MV versus no NNRTI MVs (OR = 2.41, 95% CI = 1.12-5.18, P = 0.024). A dose-effect relationship between virological failure and mutational load was found.

Conclusions: Pre-existing MVs more than double the risk of virological failure to first-line NNRTI-based ART.

Keywords: CHAIN; European multicentre study; antiretroviral therapy; minority drug-resistant HIV-1 variants.

Figure 1.

Subject disposition and scheme of the study design. MVs were analysed by next-generation sequencing in plasma samples with HIV-1 RNA levels ≥10 000 copies/mL collected within 6 months prior to ART initiation. *ART-naive patients in the cohorts starting ART containing two NRTIs and one NNRTI (efavirenz or nevirapine), achieving viral suppression ≤50 HIV-1 RNA copies/mL plasma and providing a genotypic HIV-1 drug resistance test prior to first-line ART. **Three hundred and sixty-six samples from 366 different patients were extracted from the different cohorts. Since several patients were matched controls in more than one case–control set, the total number of samples was 422. ***The main analyses were performed on 260 samples; a sensitivity analysis was performed on 245 unique samples. ****The exclusion of 61 patients due to technical challenges, NNRTI or NRTI mutations representing ≥25% of the virus population or missing demographic data led to the exclusion of an additional 60 samples since certain case–control sets were subsequently incomplete.

Figure 2.

IAS-USA 2013 mutations detected as minority drug resistance mutations by case–control status. Only P values <0.2 are reported. Two hundred and forty-five unique samples were included.