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

Jessica M. Fogel, David Bonsall, Vanessa Cummings, Rory Bowden, Tanya Golubchik, Mariateresa De Cesare, Ethan A. Wilson, Theresa Gamble, Carlos Del Rio, D. Scott Batey, Kenneth H. Mayer, Jason E. Farley, James P. Hughes, Robert H. Remien, Chris Beyrer, Christophe Fraser, Susan H. Eshleman

Research output: Contribution to journalArticlepeer-review

Abstract

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 <FOR VERIFICATION>copies/mL; 50.0% for 26 samples with 1000-5000 <FOR VERIFICATION>copies/mL; 0% for 23 samples with <1000 <FOR VERIFICATION>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.

Original languageEnglish (US)
Pages (from-to)3510-3516
Number of pages7
JournalJournal of Antimicrobial Chemotherapy
Volume75
Issue number12
DOIs
StatePublished - Dec 1 2020

ASJC Scopus subject areas

  • Pharmacology
  • Microbiology (medical)
  • Infectious Diseases
  • Pharmacology (medical)

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