Performance of a High-Throughput Next-Generation Sequencing Method for Analysis of Hiv Drug Resistance and Viral Load. [HPTN 078]
Citation
Fogel JM, Bonsall D, Cummings V, Bowden R, Golubchik T, de Cesare M, Wilson EA, Gamble T, Del Rio C, Batey DS, Mayer KH, Farley JE, Hughes JP, Remien RH, Beyrer C, Fraser C, Eshleman SH. Performance of a High-Throughput Next-Generation Sequencing Method for Analysis of Hiv Drug Resistance and Viral Load. [HPTN 078]. J Antimicrob Chemother. 2020, 75: 3510-3516. PMC7662169
Abstract
To evaluate the performance of a high-throughput research assay for HIV drug resistance testing based on whole genome next-generation sequencing (NGS) that also quantifies HIV viral load. METHODS: Plasma samples (n = 145) were obtained from HIV-positive MSM (HPTN 078). Samples were analysed using clinical assays (the ViroSeq HIV-1 Genotyping System and the Abbott RealTime HIV-1 Viral Load assay) and a research assay based on whole-genome NGS (veSEQ-HIV). RESULTS: HIV protease and reverse transcriptase sequences (n = 142) and integrase sequences (n = 138) were obtained using ViroSeq. Sequences from all three regions were obtained for 100 (70.4%) of the 142 samples using veSEQ-HIV; results were obtained more frequently for samples with higher viral loads (93.5% for 93 samples with >5000 copies/mL; 50.0% for 26 samples with 1000-5000 copies/mL; 0% for 23 samples with