Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load.

Journal Article (Journal Article)

OBJECTIVES: 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 <1000 copies/mL). For samples with results from both methods, drug resistance mutations (DRMs) were detected in 33 samples using ViroSeq and 42 samples using veSEQ-HIV (detection threshold: 5.0%). Overall, 146 major DRMs were detected; 107 were detected by both methods, 37 were detected by veSEQ-HIV only (frequency range: 5.0%-30.6%) and two were detected by ViroSeq only. HIV viral loads estimated by veSEQ-HIV strongly correlated with results from the Abbott RealTime Viral Load assay (R2 = 0.85; n = 142). CONCLUSIONS: The NGS-based veSEQ-HIV method provided results for most samples with higher viral loads, was accurate for detecting major DRMs, and detected mutations at lower levels compared with a method based on population sequencing. The veSEQ-HIV method also provided HIV viral load data.

Full Text

Duke Authors

Cited Authors

  • 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

Published Date

  • December 1, 2020

Published In

Volume / Issue

  • 75 / 12

Start / End Page

  • 3510 - 3516

PubMed ID

  • 32772080

Pubmed Central ID

  • PMC7662169

Electronic International Standard Serial Number (EISSN)

  • 1460-2091

Digital Object Identifier (DOI)

  • 10.1093/jac/dkaa352


  • eng

Conference Location

  • England