{"doi":"10.1093/nar/gkad790","title":"HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization","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.","journal":"Nucleic Acids Research","year":2023,"id":345116,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":13,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9445,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":643958,"name":"Noah Bonine","orcid":"0000-0002-4456-0347","position":1,"is_corresponding":false},{"id":1084513,"name":"Rita Verstraeten","orcid":"0000-0002-6669-2703","position":2,"is_corresponding":false},{"id":643960,"name":"Marion Pardons","orcid":"0000-0002-9921-8207","position":3,"is_corresponding":false},{"id":410252,"name":"Ytse Noppe","orcid":null,"position":4,"is_corresponding":false},{"id":408656,"name":"Sofie Rutsaert","orcid":"0000-0003-4623-0939","position":5,"is_corresponding":false},{"id":678527,"name":"Filip Van Nieuwerburgh","orcid":"0000-0001-8815-5485","position":6,"is_corresponding":false},{"id":411951,"name":"Wim Van Criekinge","orcid":"0000-0003-2971-5539","position":7,"is_corresponding":false},{"id":643955,"name":"Basiel Cole","orcid":"0000-0001-5899-5598","position":8,"is_corresponding":false},{"id":408658,"name":"Linos Vandekerckhove","orcid":"0000-0002-8600-1631","position":9,"is_corresponding":false},{"id":643956,"name":"Laurens Lambrechts","orcid":"0000-0002-1415-4591","position":0,"is_corresponding":true}],"reference_count":59,"raw_metadata":null,"created_at":"2026-07-19T01:11:39.484741Z","pmid":"37819007","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}