Initial Virologic Response and HIV Drug Resistance Among HIV-Infected Individuals Initiating First-line Antiretroviral Therapy at 2 Clinics in Chennai and Mumbai, India

Human immunodeficiency virus drug resistance (HIVDR) in cohorts of patients initiating antiretroviral therapy (ART) at clinics in Chennai and Mumbai, India, was assessed following World Health Organization (WHO) guidelines. Twelve months after ART initiation, 75% and 64.6% of participants at the Chennai and Mumbai clinics, respectively, achieved viral load suppression of <1000 copies/mL (HIVDR prevention). HIVDR at initiation of ART (P <.05) and 12-month CD4 cell counts <200 cells/μL (P <.05) were associated with HIVDR at 12 months. HIVDR prevention exceeded WHO guidelines (≥70%) at the Chennai clinic but was below the target in Mumbai due to high rates of loss to follow-up. Findings highlight the need for defaulter tracing and scale-up of routine viral load testing to identify patients failing first-line AR

Evaluation of a Cost Effective In-House Method for HIV-1 Drug Resistance Genotyping Using Plasma Samples

<div><p>Objectives</p><p>Validation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples.</p><p>Design</p><p>The validation includes the establishment of analytical performance characteristics such as accuracy, reproducibility, precision and sensitivity.</p><p>Methods</p><p>The accuracy was assessed by comparing 26 paired Virological Quality Assessment (VQA) proficiency testing panel sequences generated by in-house and ViroSeq Genotyping System 2.0 (Celera Diagnostics, US) as a gold standard. The reproducibility and precision were carried out on five samples with five replicates representing multiple HIV-1 subtypes (A, B, C) and resistance patterns. The amplification sensitivity was evaluated on HIV-1 positive plasma samples (n = 88) with known viral loads ranges from 1000–1.8 million RNA copies/ml.</p><p>Results</p><p>Comparison of the nucleotide sequences generated by ViroSeq and in-house method showed 99.41±0.46 and 99.68±0.35% mean nucleotide and amino acid identity respectively. Out of 135 Stanford HIVdb listed HIV-1 drug resistance mutations, partial discordance was observed at 15 positions and complete discordance was absent. The reproducibility and precision study showed high nucleotide sequence identities i.e. 99.88±0.10 and 99.82±0.20 respectively. The in-house method showed 100% analytical sensitivity on the samples with HIV-1 viral load >1000 RNA copies/ml. The cost of running the in-house method is only 50% of that for ViroSeq method (112$vs 300$), thus making it cost effective.</p><p>Conclusions</p><p>The validated cost effective in-house method may be used to collect surveillance data on the emergence and transmission of HIV-1 drug resistance in resource limited countries. Moreover, the wide applications of a cost effective and validated in-house method for HIV-1 drug resistance testing will facilitate the decision making for the appropriate management of HIV infected patients.</p></div

Drug resistance-associated amino acid positions in protease and reverse transcriptase from 26 proficiency testing panel plasma samples genotyped by the in-house and the ViroSeq methods.

<p>Note: Partial discordant positions are shown in bold.</p

Pairwise sequence identity analysis between the in-house and the ViroSeq method.

<p>Pairwise sequence identity analysis between the in-house and the ViroSeq method.</p

Primers used in the In-house method for HIV-1 drug resistance genotyping.

<p>Primers used in the In-house method for HIV-1 drug resistance genotyping.</p

Reproducibility and Precision of an in-house method.

<p>Reproducibility and Precision of an in-house method.</p

Phylogenetic analysis of the sequences generated during the evaluation of an in-house method.

<p>The phylogenetic tree was generated by using the PhyML software to create a maximum likelihood tree <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087441#pone.0087441-Chaturbhuj1" target="_blank">[13]</a>. The reference sequences were obtained from the Los Alamos HIV Database (<a href="http://www.hiv.lanl.gov" target="_blank">www.hiv.lanl.gov</a>). IHDR- sequences generated by an in-house method; VSQ- sequences generated by the ViroSeq method; R1 to R5- sample used in the reproducibility study (hilighted in blue); P1 to P5- sample used in the precision study (hilighted in red); A, B, C, D, E are the replicates of the same sample.</p

HIV drug resistance following a decade of the free antiretroviral therapy programme in India: A review

Objective: The objective of this review was to assess the burden of HIV drug resistance mutations (DRM) in Indian adults exposed to first-line antiretroviral therapy (ART) as per national guidelines. Methods: An advanced search of the published literature on HIV drug resistance in India was performed in the PubMed and Scopus databases. Data pertaining to age, sex, CD4 count, viral load, and prevalence of nucleoside reverse transcriptase inhibitor (NRTI)/non-nucleoside reverse transcriptase inhibitor (NNRTI) DRM were extracted from each publication. Year-wise Indian HIV-1 reverse transcriptase (RT) sequences were retrieved from the Los Alamos HIV database and mutation analyses were performed. A time trend analysis of the proportion of sequences showing NRTI resistance mutations among individuals exposed to first-line ART was conducted. Results: Overall, 23 studies (1046 unique RT sequences) were identified indicating a prevalence of drug resistance to NRTI and NNRTI. The proportion of RT sequences with any DRM, any NRTI DRM, and any NNRTI DRM was 78.39%, 68.83%, and 73.13%, respectively. The temporal trend analysis of individual DRM from sequences retrieved during 2004–2014 indicated a rising trend in K65R mutations (p = 0.013). Conclusions: Although the overall burden of resistance against first-line ART agents remained steady over the study decade, periodic monitoring is essential. There is the need to develop an HIV-1 subtype C-specific resistance database in India