High-throughput sequencing of HIV-1 pol region from second line failure patients from South Africa

HIV-1C have been shown to have a greater risk of virological failure and reduced susceptibility towards boosted-protease inhibitors (bPIs), a component of second-line combination antiretroviral therapy (cART) in South Africa. This study aimed at evaluating the HIV-1 drug resistance mutations at the minor viral populations, by high throughput sequencing genotypic resistance testing (HTS-GRT), in patients suspected of failing on South African national second-line cART regimen with bPIs.Plasma was obtained from 75 patients. The complete pol gene was amplified and sequenced with Illumina HiSeq2500, followed by bioinformatics analysis to quantify the resistance associated mutations (RAMs) according to the Stanford HIV drug resistance database.HTS-GRT improved identification of PI and RTI RAMs in second-line cART patients from South Africa, compared to the conventional GRT with ≥20% used in Sanger-based sequencing. Deep sequencing could be of greater value in detecting the acquired resistance mutations early.