ArticleNucleic acids research2023
HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 12 citations in OpenAlex.
- HIV-1 virome profiling using HIV-PULSE to guide therapeutic and curative interventions.EBioMedicine · 2026Article
- Development and Evaluation of a Novel Relatively Low-Cost Method to Derive HIV-1 Integration Sites and Proviral Sequences.Viruses · 2026Article
- NanoHIVSeq: A Long-Read Bioinformatics Pipeline for High-Throughput Processing of HIV Env Sequences.bioRxiv : the preprint server for biology · 2026Article
- Tools to Quantify and Characterize the Persistent Reservoir in People with HIV-1: Focus on Non-B Subtypes.Viruses · 2026Review
- Aberrant strand transfer events across multiple stages of reverse transcription shape the heterogeneous landscape of the HIV-1 reservoir.Communications biology · 2025Article
- T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.PLoS computational biology · 2025Article
- Blood and tissue HIV-1 reservoirs display plasticity and lack of compartmentalization in virally suppressed people.Nature communications · 2025Article
- Molecular characterization of HIV-1 near-full-length proviral quasispecies in monocytes from patients across different virological responses.Frontiers in microbiology · 2025Article
- Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies.Virus evolution · 2024Article
- Current methods for detecting and assessing HIV-1 antibody resistance.Frontiers in immunology · 2024Review
- Genomic Exploration of the Brain in People Infected with HIV-Recent Progress and the Road Ahead.Current HIV/AIDS reports · 2023Review
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11 vs 18%) and overall good concordance, although at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
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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.