{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:22:55Z","timestamp":1788225775300,"version":"build-2803163510"},"reference-count":55,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T00:00:00Z","timestamp":1623369600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001713","name":"European and Developing Countries Clinical Trials Partnership","doi-asserted-by":"publisher","award":["TMA2019CDF-2728"],"award-info":[{"award-number":["TMA2019CDF-2728"]}],"id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.<\/jats:p>","DOI":"10.3390\/v13061125","type":"journal-article","created":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T22:26:01Z","timestamp":1623709561000},"page":"1125","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0680-7337","authenticated-orcid":false,"given":"Sontaga","family":"Manyana","sequence":"first","affiliation":[{"name":"National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1060-9170","authenticated-orcid":false,"given":"Lilishia","family":"Gounder","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melendhran","family":"Pillay","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8874-907X","authenticated-orcid":false,"given":"Justen","family":"Manasa","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kogieleum","family":"Naidoo","sequence":"additional","affiliation":[{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa"},{"name":"South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Chimukangara","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa"},{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,6,11]]},"reference":[{"key":"ref_1","unstructured":"UNIADS (2021, May 24). 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