HIV Drug Resistance Mutations in Proviral DNA from a Community Treatment Program

Abstract

BackgroundDrug resistance mutations archived in resting memory CD4+ cells may persist despite suppression of HIV RNA to <50 copies/ml. We sequenced pol gene from proviral DNA among viremic and suppressed patients to identify drug resistance mutations.MethodsThe Peninsula AIDS Research Cohort study enrolled and followed over 2 years 120 HIV infected patients from San Mateo and San Francisco Counties. HIV-1 pol genotyping by bulk sequencing was performed on 38 DNA and RNA from viremic patients and DNA only among 82 suppressed patients at baseline. Antiretroviral susceptibility was predicted by HIVDB.stanford.edu.ResultsAmong 120 subjects, 81% were on antiretroviral therapy and had been treated for a median time of 7 years. Thirty-two viremic patients showed concordant RNA and DNA genotypes (84%); the discordant profiles were mainly observed in patients with low-level viremia. Among suppressed patients, 21 had drug resistance mutations in proviral DNA (26%) with potential resistance to one, two or three ARV classes in 16, 4 and 1 samples respectively.ConclusionsThe high level of genotype concordance between DNA and RNA in viremic patients suggested that DNA genotyping might be used to assess drug resistance in resource-limited settings, and further investigation of extracted DNA from dried blood spots is needed. Drug resistance mutations in proviral DNA in 26% of subjects with less than 50 copies/ml pose a risk for the transmission of drug resistant virus with virologic failure, treatment interruption or decreased adherence.

Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments

“…The discrepancy between CF and CA may result from the low viral load in the sample 267966 as demonstrated by others [30,31,32]. The nucleoside reverse transcriptase inhibitor (NRTI) mutation M184V causes high resistance to lamivudine (3TC) and emtricitabine (FTC), meanwhile, the non-nucleoside reverse transcriptase inhibitor mutation E138EA causes low-level of resistance to rilpivirine (RPV) [33,34,35].…”

Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots

“…Retrospective virus load information was collected to ensure that specimens were selected that spanned the assays' linear ranges. Ninety-five paired DBS and EDTA plasma specimens were obtained from participants in the Peninsula AIDS Research Cohort Study (PARC) (31) and were archived at Ϫ80°C prior to testing. DBS were composed of 50 l of EDTA whole blood collected on Whatman 903 sample collection cards.…”

“…The Aptima was then used to evaluate 95 paired DBS and EDTA plasma samples archived from HIV-infected patients on therapy (31). Applying the WHO-recommended threshold of 1,000 copies/ml threshold for treatment failure, DBS and plasma demonstrated an overall agreement of 94.7% (90/95) ( Table 2).…”

Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults

“…The clinical utility of these assays has not yet been established, but they may be useful in detecting mutations that have been archived in resting CD4 cells but that are no longer detectable by standard commercial resistance assays. 104,105 Results must be interpreted with caution because they can sometimes fail to detect existing mutations. 106 Some switches in the setting of viral suppression may be safe regardless of resistance (eg, TDF to TAF, efavirenz to rilpivirine or etravirine, raltegravir or elvitegravir to dolutegravir, or lopinavir/r to boosted darunavir).…”