{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T11:04:03Z","timestamp":1788433443683,"version":"build-2803163510"},"reference-count":32,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2024,10,10]],"date-time":"2024-10-10T00:00:00Z","timestamp":1728518400000},"content-version":"vor","delay-in-days":9,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2024,10,1]],"date-time":"2024-10-01T00:00:00Z","timestamp":1727740800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2024,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Accurate HIV\u20101 genome sequencing is necessary to identify drug resistance mutations (DRMs) in people with HIV\u20101 (PWH). Next\u2010generation\u2010sequencing (NGS) allows the detection of minor variants and is now available in many laboratories. Our study aimed to compare two NGS approaches, a \u201cshort read\u201d sequencing protocol using DeepChek\u00ae Whole Genome HIV\u20101 Assay on Illumina, and a \u201clong read\u201d sequencing protocol of HIV\u20101\n                    <jats:italic>pol<\/jats:italic>\n                    and\n                    <jats:italic>env<\/jats:italic>\n                    single\u2010molecule real\u2010time sequencing (SMRT) on Pacific Biosciences (PacBio). We analyzed 16 plasma samples and 13 cellular samples from PWH. HIV\u20101 whole genome was amplified into five amplicons using DeepChek\u00ae Whole Genome HIV\u20101 Assay and sequenced on an iSeq. 100. In parallel, HIV\u20101\n                    <jats:italic>pol<\/jats:italic>\n                    and\n                    <jats:italic>env<\/jats:italic>\n                    genes were separately amplified and sequenced using PacBio SMRT system with the circular consensus sequencing mode on a Sequel IIe. Concordance rates for determining DRMs with both approaches varied depending on the HIV\u20101 region, with higher concordance in the integrase region compared to the reverse transcriptase and protease regions. DeepChek\u00ae Whole Genome HIV\u20101 Assay exhibited better sensitivity in HIV\u20101 RNA sequencing of plasmas with lower viral loads. In cell HIV\u20101 DNA sequencing, the DeepChek\u00ae Whole Genome HIV\u20101 Assay performed better in\n                    <jats:italic>pol<\/jats:italic>\n                    and\n                    <jats:italic>env<\/jats:italic>\n                    sequencing but detected more APOBEC\u2010induced DRMs, which can represent defective proviruses. Our findings indicate that both DeepChek\u00ae Whole Genome HIV\u20101 Assay and PacBio SMRT sequencing exhibit good performance for subtype determination, detection, and quantification of DRMs of the HIV\u20101 genome. However, some discrepancies were found in cellular samples, highlighting the challenges of interpreting HIV\u20101 DNA DRMs.\n                  <\/jats:p>","DOI":"10.1002\/jmv.29951","type":"journal-article","created":{"date-parts":[[2024,10,10]],"date-time":"2024-10-10T09:20:22Z","timestamp":1728552022000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Comparison of short\u2010read and long\u2010read next\u2010generation sequencing technologies for determining HIV\u20101 drug resistance"],"prefix":"10.1002","volume":"96","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8637-6695","authenticated-orcid":false,"given":"Camille","family":"Vellas","sequence":"first","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"},{"name":"INSERM UMR1291\u2010CNRS UMR5051\u2010Universit\u00e9 Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amira","family":"Doudou","sequence":"additional","affiliation":[{"name":"ABL Diagnostics (ABLD) Woippy France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4741-1432","authenticated-orcid":false,"given":"Sofiane","family":"Mohamed","sequence":"additional","affiliation":[{"name":"ABL Diagnostics (ABLD) Woippy France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phanie","family":"Raymond","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"},{"name":"INSERM UMR1291\u2010CNRS UMR5051\u2010Universit\u00e9 Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Jeanne","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justine","family":"Latour","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofia","family":"Demmou","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"No\u00e9mie","family":"Ranger","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitri","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"ABL Diagnostics (ABLD) Woippy France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Delobel","sequence":"additional","affiliation":[{"name":"INSERM UMR1291\u2010CNRS UMR5051\u2010Universit\u00e9 Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases Toulouse France"},{"name":"CHU de Toulouse, Service de Maladies Infectieuses et Tropicales Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Izopet","sequence":"additional","affiliation":[{"name":"CHU de Toulouse, Laboratoire de Virologie Toulouse France"},{"name":"INSERM UMR1291\u2010CNRS UMR5051\u2010Universit\u00e9 Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,10,10]]},"reference":[{"key":"e_1_2_10_2_1","unstructured":"HIV drug resistance report 2019. 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