ArticleJournal of clinical microbiology2012
Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.
Article in Journal of clinical microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
- Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART.The Journal of antimicrobial chemotherapy · 2019Trial
- 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
- Protocol for the identification of recent HIV infection in newly diagnosed individuals.STAR protocols · 2026Article
- Analysis of temporal virus evolution and intra-host diversity in long-term non-progressors by bulk next-generation sequencing.Microbiology spectrum · 2026Article
- Article
- HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012-19: a population-based, longitudinal study.The Lancet. Microbe · 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
- Newly designed amplicons-based method for near-full-length genome (NFLG) sequencing of HIV-1 group M recombinant forms.Molecular biology reports · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Prevalence of Naturally Occurring HIV-1 Capsid Inhibitor Resistance-Related Mutations in Antiretroviral Therapy-Naïve and -Experienced Individuals in Taiwan.Open forum infectious diseases · 2025Article
- PacBio high-fidelity near full-length genome sequencing for HIV-1 quasispecies: methodological framework and validation.Frontiers in microbiology · 2025Article
- The genetic architecture of HIV-1 virulence.Virus evolution · 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
- HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre study (DTG RESIST).BMJ open · 2024Article
- Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.medRxiv : the preprint server for health sciences · 2024Article
- Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.Nature microbiology · 2024Article
- Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.Virus evolution · 2024Article
- Development of a multiassay algorithm (MAA) to identify recent HIV infection in newly diagnosed individuals in Indonesia.iScience · 2023Article
- Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.The Journal of general virology · 2023Article
- Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018.The Journal of antimicrobial chemotherapy · 2023Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Whole HIV-1 genome sequences are pivotal for large-scale studies of inter- and intrahost evolution, including the acquisition of drug resistance mutations. The ability to rapidly and cost-effectively generate large numbers of HIV-1 genome sequences from different populations and geographical locations and determine the effect of minority genetic variants is, however, a limiting factor. Next-generation sequencing promises to bridge this gap but is hindered by the lack of methods for the enrichment of virus genomes across the phylogenetic breadth of HIV-1 and methods for the robust assembly of the virus genomes from short-read data. Here we report a method for the amplification, next-generation sequencing, and unbiased de novo assembly of HIV-1 genomes of groups M, N, and O, as well as recombinants, that does not require prior knowledge of the sequence or subtype. A sensitivity of at least 3,000 copies/ml was determined by using plasma virus samples of known copy numbers. We applied our novel method to compare the genome diversities of HIV-1 groups, subtypes, and genes. The highest level of diversity was found in the env, nef, vpr, tat, and rev genes and parts of the gag gene. Furthermore, we used our method to investigate mutations associated with HIV-1 drug resistance in clinical samples at the level of the complete genome. Drug resistance mutations were detected as both major variant and minor species. In conclusion, we demonstrate the feasibility of our method for large-scale HIV-1 genome sequencing. This will enable the phylogenetic and phylodynamic resolution of the ongoing pandemic and efficient monitoring of complex HIV-1 drug resistance genotypes.
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