ArticleThe Journal of antimicrobial chemotherapy2020
Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load.
Article in The Journal of antimicrobial chemotherapy, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Patterns of HIV-1 Viral Load Suppression and Drug Resistance During the Dolutegravir Transition: A Population-based Longitudinal Study.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Article
- Patterns of HIV-1 viral load suppression and drug resistance during the dolutegravir transition: a population-based longitudinal study.medRxiv : the preprint server for health sciences · 2025Article
- HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.BMC bioinformatics · 2025Article
- The utility of integrating nanopore sequencing into routine HIV-1 drug resistance surveillance.Microbial genomics · 2025Review
- Prevalence of primary HIV-1 drug resistance among antiretroviral-naïve individuals in Togo in 2023: a national study.Frontiers in public health · 2025Article
- Population dynamics of HIV drug resistance during treatment scale-up in Uganda: a population-based longitudinal study.medRxiv : the preprint server for health sciences · 2024Article
- Article
- Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory.Journal of medical virology · 2023Article
- Drug Resistance to HIV-1 Integrase Inhibitors Among Treatment-Naive Patients in Beijing, China.Pharmacogenomics and personalized medicine · 2022Article
- HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China.Pathogens (Basel, Switzerland) · 2021Article
- A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings.Journal of clinical microbiology · 2020Article
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Authors and funding
17 authors at 12 institutions in 2 countries.
Funding
Abstract
objectivesTo 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.
methodsPlasma 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).
resultsHIV 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).
conclusionsThe 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.
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