Research Article: Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

Date Published: July 29, 2008

Publisher: Public Library of Science

Author(s): Jeffrey A Johnson, Jin-Fen Li, Xierong Wei, Jonathan Lipscomb, David Irlbeck, Charles Craig, Amanda Smith, Diane E Bennett, Michael Monsour, Paul Sandstrom, E. Randall Lanier, Walid Heneine, Steven G Deeks

Abstract: BackgroundTransmitted 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 FindingsWe 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).ConclusionsThese 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.

Partial Text: Antiretroviral drugs have been remarkably successful in suppressing HIV-1 infection; however, transmitted drug resistance can reduce the efficacy of first-line regimens. Surveys using conventional bulk sequencing in North America and Europe, where the history of ART is extensive, have shown that transmitted or primary HIV-1 drug resistance is present in 8%–20% of ART-naïve persons [1–7]. As antiretroviral drug use expands to cope with the pandemic, adequately assessing the prevalence and transmission of drug resistance mutations will be increasingly important for optimizing treatment efficacy.

Using assays validated for drug resistance mutations in HIV-1 clinical samples, we identified, in ART-naïve persons from the US and Canada, a substantial number of minority mutant viruses at levels above the natural quasispecies frequency of each mutation. The preponderance of minority resistance mutations implies that a considerable proportion of transmitted drug resistance decayed to low levels by the time of HIV-1 diagnosis. The detection of minority resistance mutations in 17% of the wild-type virus group, part of a US cohort of newly diagnosed HIV-1–infected persons that had 20% bulk sequence-detectable primary drug resistance, suggests that bulk sequencing missed 40% of the resistance samples in this population. The frequent occurrence of drug resistance likely reflects a high prevalence of ART in these locations and suggests that transmission of HIV-1 from antiretroviral drug-experienced persons expressing virus is not uncommon.



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