Drug resistance mutations in a population prior to antiretroviral therapy initiation in Northern South Africa

AIDS Res Hum Retroviruses. 2021 Jun 9. doi: 10.1089/AID.2021.0026. Online ahead of print.ABSTRACTSouth Africa introduced the "diagnose and treat" HIV treatment programme in September 2016. The programme enables diagnosed HIV positive patients to start treatment. However, the presence of drug resistant (DR) viruses in the drug naïve population complicates the choice of ART. We used next generation sequencing (NGS) to determine the prevalence and diversity of HIV DR mutations in patients entering HIV treatment programmes in northern South Africa. RNA was isolated from the plasma of drug naive HIV-1 infected patients. The HIV-1-pol gene comprising the complete protease (PR) and the first 900bp of reverse transcriptase (RT) was amplified and sequenced on an Illumina MiniSeq platform. Consensus sequences were derived at >20% threshold and at >5% threshold using Geneious PRIME® software version 2020.1.2. HIV-1 surveillance drug resistance mutations (SDRM) were inferred using Calibrated Population Resistance (CPR) tool in HIV Drug Resistance Database. Viral subtypes were determined using REGA and RIP genotyping tools. The HIV PR/RT region was successfully sequenced from 241 patients. From these, 23 (9.5%) had at least one SDRM detected at >20% threshold, with a prevalence of 9.5% (n=18), 3% (n=7) and 0.4% (n=1) for NNRTI, NRTI and PI respectively. The number of patients with SDRM increased to 31 (12.9%) when minority variants were accounted for at >5% threshold. The mo...
Source: Biomed Res - Category: Research Authors: Source Type: research