ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2024
Portable Nanopore sequencing solution for next-generation HIV drug resistance testing.
Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The trial behind it
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- Lassa virus live tracking and lineage assignment: how nextstrain can enhance surveillance and public health in Africa and beyond.Emerging microbes & infections · 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
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- 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
- 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
- Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundTackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care.
methodsWe developed a HIV genotype testing pipeline that centers on a cost-efficient portable Nanopore sequencer. Accuracy verification was conducted through comparison with parallel data obtained via fixed-site Pacbio sequencing. Our complete pol-gene sequencing strategy coupled with portable high-throughput sequencing was applied to identify drug resistance mutations across 58 samples sourced from the ART-treated Los Angeles General Medical Center Rand Schrader Clinic (LARSC) cohort (7 samples from 7 individuals) and the ART-naïve Center for HIV/AIDS Vaccine Immunology (CHAVI) cohort (51 samples from 38 individuals).
resultsA total of 472 HIV consensus sequences, each tagged with a unique molecular identifier, were produced from over 1.4 million bases acquired through portable Nanopore sequencing, which matched those obtained independently via Pacbio sequencing. With this desirable accuracy, we first documented the linkage of multidrug cross-resistance mutations across Integrase Strand Transfer inhibitors (INSTIs) and Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from an individual failing a second-generation INSTI regimen. By producing more than 500 full-length HIV pol gene sequences in a single portable sequencing run, we detected Protease Inhibitor (PI), Nucleoside Reverse Transcriptase Inhibitor (NRTI), NNRTI and INSTI resistance mutations. All drug resistance mutations identified through portable sequencing were cross-validated using fixed-site Pacbio sequencing.
conclusionsOur accurate and affordable HIV drug resistance testing solution is adaptable for both individual patient care and large-scale surveillance initiatives.
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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.