{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T20:12:07Z","timestamp":1789503127956,"version":"build-2803163510"},"reference-count":12,"publisher":"Microbiology Society","issue":"7","license":[{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"PHA4GE","award":["INV-038071"],"award-info":[{"award-number":["INV-038071"]}]},{"name":"CAGE-TB Project"},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"crossref","award":["U2RTW012116"],"award-info":[{"award-number":["U2RTW012116"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"crossref","award":["U2RTW010672"],"award-info":[{"award-number":["U2RTW010672"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001713","name":"EDCTP","doi-asserted-by":"crossref","award":["TMA2020CDF-3159"],"award-info":[{"award-number":["TMA2020CDF-3159"]}],"id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"crossref"}]},{"name":"African Doctoral Dissertation Research Fellowship"},{"name":"Eastern Africa Network of Bioinformatics Training (EANBiT) project"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:p>\n                    The global prevalence of resistance to antiviral drugs combined with antiretroviral therapy (cART) emphasizes the need for continuous monitoring to better understand the dynamics of drug-resistant mutations to guide treatment optimization and patient management as well as check the spread of resistant viral strains. We have recently integrated next-generation sequencing (NGS) into routine HIV drug resistance (HIVDR) monitoring, with key challenges in the bioinformatic analysis and interpretation of the complex data generated, while ensuring data security and privacy for patient information. To address these challenges, here we present HIV-DRIVES (HIV Drug Resistance Identification, Variant Evaluation, and Surveillance), an NGS-HIVDR bioinformatics pipeline that has been developed and validated using Illumina short reads, FASTA, and Sanger\n                    <jats:italic>ab1<\/jats:italic>\n                    .seq files.\n                  <\/jats:p>","DOI":"10.1099\/acmi.0.000815.v3","type":"journal-article","created":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T10:16:50Z","timestamp":1721211410000},"source":"Crossref","is-referenced-by-count":4,"title":["HIV-DRIVES: HIV drug resistance identification, variant evaluation, and surveillance pipeline"],"prefix":"10.1099","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2439-939X","authenticated-orcid":false,"given":"Stephen","family":"Kanyerezi","sequence":"first","affiliation":[{"name":"Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O Box 7072 Kampala, Uganda"},{"name":"The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, the Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O Box 22418 Kampala, Uganda"},{"name":"National Health Laboratories and Diagnostics Services, Central Public Health Laboratories, Ministry of Health, P.O Box 7272 Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7785-7297","authenticated-orcid":false,"given":"Ivan","family":"Sserwadda","sequence":"additional","affiliation":[{"name":"Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center, Amsterdam, Netherlands"},{"name":"Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O Box 7072 Kampala, Uganda"},{"name":"National Health Laboratories and Diagnostics Services, Central Public Health Laboratories, Ministry of Health, P.O Box 7272 Kampala, Uganda"},{"name":"The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, the Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O Box 22418 Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4377-5220","authenticated-orcid":false,"given":"Aloysious","family":"Ssemaganda","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada"},{"name":"National Health Laboratories and Diagnostics Services, Central Public Health Laboratories, Ministry of Health, P.O Box 7272 Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julius","family":"Seruyange","sequence":"additional","affiliation":[{"name":"National Health Laboratories and Diagnostics Services, Central Public Health 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