Contribution of human immunodeficiency virus type 1 minority variants to reduced drug susceptibility in patients on an integrase strand transfer inhibitor-based therapy.

Richard M Gibson,Dane Winner,Michael D Miller,Miguel E Quiñones-Mateu,Jan Weber,Nicolas Sluis-Cremer

doi:10.1371/journal.pone.0104512

Abstract

The role of HIV-1 minority variants on transmission, pathogenesis, and virologic failure to antiretroviral regimens has been explored; however, most studies of low-level HIV-1 drug-resistant variants have focused in single target regions. Here we used a novel HIV-1 genotypic assay based on deep sequencing, DEEPGEN (Gibson et al 2014 Antimicrob Agents Chemother 58∶2167) to simultaneously analyze the presence of minority variants carrying mutations associated with reduced susceptibility to protease (PR), reverse transcriptase (RT), and integrase strand transfer integrase inhibitors (INSTIs), as well as HIV-1 coreceptor tropism. gag-p2/NCp7/p1/p6/pol-PR/RT/INT and env/C2V3 PCR products were obtained from twelve heavily treatment-experienced patients experiencing virologic failure while participating in a 48-week dose-ranging study of elvitegravir (GS-US-183-0105). Deep sequencing results were compared with (i) virological response to treatment, (ii) genotyping based on population sequencing, (iii) phenotyping data using PhenoSense and VIRALARTS, and (iv) HIV-1 coreceptor tropism based on the phenotypic test VERITROP. Most patients failed the antiretroviral regimen with numerous pre-existing mutations in the PR and RT, and additionally newly acquired INSTI-resistance mutations as determined by population sequencing (mean 9.4, 5.3, and 1.4 PI- RTI-, and INSTI-resistance mutations, respectively). Interestingly, since DEEPGEN allows the accurate detection of amino acid substitutions at frequencies as low as 1% of the population, a series of additional drug resistance mutations were detected by deep sequencing (mean 2.5, 1.5, and 0.9, respectively). The presence of these low-abundance HIV-1 variants was associated with drug susceptibility, replicative fitness, and coreceptor tropism determined using sensitive phenotypic assays, enhancing the overall burden of resistance to all four antiretroviral drug classes. Further longitudinal studies based on deep sequencing tests will help to clarify (i) the potential impact of minority HIV-1 drug resistant variants in response to antiretroviral therapy and (ii) the importance of the detection of HIV minority variants in the clinical practice.

Highlights

Antiretroviral therapy based on the combination of several antiHIV-1 drugs is the gold standard of care for HIV-1 infected individuals in most developed countries and has been credited with considerable reductions in morbidity and mortality [1,2]
We have recently developed a novel HIV-1 genotyping and coreceptor assay based on deep sequencing (DEEPGEN) that allows the detection of minority HIV-1 variants when present at frequencies as low as 1% of the HIV-1 population [43]
It is possible that the threshold for the identification of significant lowlevel variants may be mutation and/or antiretroviral drug dependent [31]; it is clear that additional studies based on reliable ultrasensitive assays are needed to better understand the clinical relevance of these minority HIV-1 variants

Summary

Introduction

Antiretroviral therapy based on the combination of several antiHIV-1 drugs is the gold standard of care for HIV-1 infected individuals in most developed countries and has been credited with considerable reductions in morbidity and mortality [1,2]. Prescribed antiretroviral regimens include two nucleoside reverse transcriptase inhibitors (NRTIs) in combination with a nonnucleoside reverse transcriptase inhibitor (NNRTI), a protease inhibitor (PI), or an integrase strand transfer inhibitor (INSTI). INSTI is the most recent class of antiretroviral drugs approved by the U.S Food and Drug Administration (FDA) for the treatment of HIV-1 infection. Elvitegravir (EVG, JTK-303/GS-9137, Gilead Sciences)[6] was approved in 2012 in a fixed dose combination with a pharmacokinetic enhancer (cobicistat) and two nucleos(t)ide analog RT inhibitors (emtricitabine and tenofovir) for the treatment of antiretroviral-naıve HIV-infected individuals (QUAD, Stribild, Gilead Sciences) [7].

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Results

Conclusion