ArticleJournal of clinical microbiology2020
A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings.
Article in Journal of clinical microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
54 citing papers in PubMed, 85 citations in OpenAlex.
- Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.The Lancet. Microbe · 2024Trial
- Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus.Nature communications · 2021Trial
- Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial.Lancet (London, England) · 2021Trial
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- 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
- Evaluation of a HIV-1 drug resistance genotyping method based on high-throughput sequencing (HTS).BMC infectious diseases · 2026Article
- The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study.medRxiv : the preprint server for health sciences · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia.Virus evolution · 2026Article
- Design and Evaluation of Next-Generation HIV Genotyping for Detection of Resistance Mutations to 28 Antiretroviral Drugs Across 5 Major Classes Including Lenacapavir.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2025Article
- 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
- Advancing the course of HIV genomics research in Africa.BMJ global health · 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
- Laboratory Diagnosis of Hendra and Nipah: Two Emerging Zoonotic Diseases with One Health Significance.Viruses · 2025Review
- Distinct neutralization sensitivity between adult and infant transmitted/founder HIV-1 subtype C viruses to broadly neutralizing monoclonal antibodies.PLoS pathogens · 2025Article
- The Case for Genomic Surveillance in Africa.Tropical medicine and infectious disease · 2025Review
- Addressing data management and analysis challenges in viral genomics: The Swiss HIV cohort study viral next generation sequencing database.PLOS digital health · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Characterization of People Living with HIV Who Inject Drugs in Mexico City: Importance for Transmission and Detection.AIDS patient care and STDs · 2025Article
- Estimates of HIV-1 within-host recombination rates across the whole genome.Virus evolution · 2025Article
Corrections and comments
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Authors and funding
23 authors at 7 institutions in 3 countries.
Funding
Abstract
Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method's performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.