{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:12:13Z","timestamp":1772118733993,"version":"3.50.1"},"reference-count":25,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2023,12,5]],"date-time":"2023-12-05T00:00:00Z","timestamp":1701734400000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2023,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Detection of HIV drug resistance (HIVDR) is vital to successful anti\u2010retroviral therapy (ART). HIVDR testing to determine drug\u2010resistance mutations is routinely performed in Australia to guide ART choice in newly diagnosed people living with HIV or in cases of treatment failure. In 2022, our clinical microbiology laboratory sought to validate a next\u2010generation sequencing (NGS)\u2010based HIVDR assay to replace the previous Sanger\u2010sequencing (SS)\u2010based ViroSeq. NGS solutions for HIVDR offer higher throughput, lower costs and higher sensitivity for variant detection. We sought to validate the previously described low\u2010cost probe\u2010based NGS method (veSEQ\u2010HIV) for whole\u2010genome recovery and HIVDR\u2010testing in a diagnostic setting. veSEQ\u2010HIV displayed 100% and 98% accuracy in major and minor mutation detection, respectively, and 100% accuracy of subtyping (provided\u2009&gt;\u20091000 mapped reads were obtained). Pairwise comparison exhibited low inter\u2010and intrarun variability across the whole\u2010genome (Jaccard index [\n                    <jats:italic>J<\/jats:italic>\n                    ]\u2009=\u20090.993; J\u2009=\u20090.972) and the\n                    <jats:italic>Pol<\/jats:italic>\n                    gene (\n                    <jats:italic>J<\/jats:italic>\n                    \u2009=\u20090.999;\n                    <jats:italic>J<\/jats:italic>\n                    \u2009=\u20090.999), respectively. veSEQ\u2010HIV met all our pre\u2010set criteria based on WHO recommendations and successfully replaced ViroSeq in our laboratory. Scaling\u2010down veSEQ\u2010HIV to a limited batch size and sequencing on Illumina iSeq. 100, allowed easy implementation of the assay into the workflow of a small sequencing laboratory with minimal staff and equipment and the ability to meet clinically relevant test turn\u2010around times. As HIVDR\u2010testing moves from SS\u2010 to NGS\u2010based methods and new ART drugs come to market (particularly those with targets outside the\n                    <jats:italic>Pol<\/jats:italic>\n                    region), whole\u2010genome recovery using veSEQ\u2010HIV provides a robust, cost\u2010effective and \u201cfuture\u2010proof\u201d NGS method for HIVDR\u2010testing.\n                  <\/jats:p>","DOI":"10.1002\/jmv.29273","type":"journal-article","created":{"date-parts":[[2023,12,5]],"date-time":"2023-12-05T06:29:20Z","timestamp":1701757760000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory"],"prefix":"10.1002","volume":"95","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-3285-7170","authenticated-orcid":false,"given":"Frances","family":"Jenkins","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases and Microbiology Royal Prince Alfred Hospital  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Le","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Microbiology Royal Prince Alfred Hospital  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rima","family":"Farhat","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Microbiology Royal Prince Alfred Hospital  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angie","family":"Pinto","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Microbiology Royal Prince Alfred Hospital  Sydney Australia"},{"name":"The Kirby Institute, UNSW Australia  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Azim","family":"Anzari","sequence":"additional","affiliation":[{"name":"Wellcome Centre for Human Genetics University of Oxford  Oxford UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Bonsall","sequence":"additional","affiliation":[{"name":"Wellcome Centre for Human Genetics University of Oxford  Oxford UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tanya","family":"Golubchik","sequence":"additional","affiliation":[{"name":"Department of Medical Sciences, Faculty of Medicine and Health University of Sydney  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rory","family":"Bowden","sequence":"additional","affiliation":[{"name":"The Walter and Eliza Hall Institute of Medical Research, Advanced Genomics Facility  Melbourne Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederick J.","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Clinical Immunology and Allergy Royal Prince Alfred Hospital  Sydney Australia"},{"name":"Sydney Medical School University of Sydney  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5852-4155","authenticated-orcid":false,"given":"Sebastiaan J.","family":"van Hal","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Microbiology Royal Prince Alfred Hospital  Sydney Australia"},{"name":"Sydney Medical School University of Sydney  Sydney Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,12,5]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.5694\/j.1326-5377.2007.tb01353.x"},{"key":"e_1_2_11_3_1","volume-title":"HIV, viral hepatitis 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