ArticleScientific reports2024
Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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
8 citing papers in PubMed.
- Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.Bioinformatics (Oxford, England) · 2026Article
- Leveraging the Oxford Nanopore MinION sequencing platform for HIV-1 drug resistance surveillance in resource-limited settings: a post-COVID implementation opportunity.Virology journal · 2026Article
- Article
- NanoHIVSeq: A Long-Read Bioinformatics Pipeline for High-Throughput Processing of HIV Env Sequences.bioRxiv : the preprint server for biology · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- HIV-1 RNA in Large and Small Plasma Extracellular Vesicles: A Novel Parameter for Monitoring Immune Activation and Virological Failure.Journal of medical virology · 2025Article
- The utility of integrating nanopore sequencing into routine HIV-1 drug resistance surveillance.Microbial genomics · 2025Review
- HIV-1 diversity and pre-treatment drug resistance in the era of integrase inhibitor among newly diagnosed ART-naïve adult patients in Luanda, Angola.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
HIV-1 drug resistance genotypic tests have primarily been performed by Sanger sequencing of gene segments encoding different drug target proteins. Since the number of targets has increased with the addition of a new class of antiretroviral drugs, a simple high-throughput system for assessing nucleotide sequences throughout the HIV-1 genome is required. Here, we developed a new solution using nanopore sequencing of viral pangenomes amplified by PCR. Benchmark tests using HIV-1 molecular clones demonstrated an accuracy of up to 99.9%. In addition, validation tests of our protocol in 106 clinical samples demonstrated high concordance of drug resistance and tropism genotypes (92.5% and 98.1%, respectively) between the nanopore sequencing-based results and archived clinical determinations made based on Sanger sequencing data. These results suggest that our new approach will be a powerful solution for the comprehensive survey of HIV-1 drug resistance mutations in clinical settings.
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Registered trials
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