{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T03:33:48Z","timestamp":1792899228558,"version":"4.5.0"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T00:00:00Z","timestamp":1773532800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"vor","delay-in-days":39,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["D43 TW011326"],"award-info":[{"award-number":["D43 TW011326"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Virol J"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>HIV drug resistance (HIVDR) testing remains essential for optimizing antiretroviral therapy (ART), yet access remains constrained by high cost, low throughput, and limited availability of Sanger sequencing in resource-limited settings (RLS). Recent improvements in Oxford Nanopore Technologies (ONT) sequencing offer a potential alternative, especially following the expansion of genomic surveillance infrastructure established during the COVID-19 pandemic.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A cross-sectional laboratory validation study was conducted comparing ONT MinION sequencing with Sanger sequencing for HIV-1 protease\/reverse transcriptase (PR\/RT) and integrase (IN) genotyping. Sixty-four stored amplicons from patients with virological failure on second-line protease inhibitor (PI)- or integrase strand transfer inhibitor (INSTI)-based regimens were sequenced on the MinION Mk1C (R10.4.1). ONT-derived consensus sequences were generated using a custom pipeline and compared to Sanger reference sequences to assess nucleotide identity and drug resistance mutation (DRM) concordance using the Stanford HIVdb v9.8. We also evaluated the cost and scalability of ONT to determine its feasibility for broader implementation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>ONT MinION sequencing produced high-quality consensus sequences with a median pairwise identity of 99.4% (IQR: 99.2\u201399.7). After resolving initial discrepancies through chromatogram review and high-depth Nanopore data, high concordance for major DRMs was observed across PR, RT, and IN coding regions. Using a 48-sample multiplexing configuration, the estimated reagent and consumable cost for ONT sequencing was approximately US$23.47 per sample. Published Sanger-based HIV drug resistance assays report per-sample costs in the range of approximately US$43 to US$100, although costs vary depending on laboratory workflow and testing volume. Moreover, ONT provided a substantially shorter turnaround time (~\u20095\u00a0h from library prep to sequence data), offering a more efficient and cost-effective workflow overall.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>ONT MinION sequencing provides an accurate, rapid, and cost-effective alternative to Sanger sequencing for HIVDR genotyping in RLS. Its scalability, ability to detect minority variants, and compatibility with infrastructure setup up in response to the COVID-19 pandemic, make it a viable platform for both national HIVDR surveillance and decentralized clinical testing. Integrating ONT workflows into routine HIVDR monitoring could expand diagnostic access and enable more timely ART optimization in high-burden settings.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12985-026-03134-0","type":"journal-article","created":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T02:53:33Z","timestamp":1773543213000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Leveraging the Oxford Nanopore MinION sequencing platform for HIV-1 drug resistance surveillance in resource-limited settings: a post-COVID implementation opportunity"],"prefix":"10.1186","volume":"23","author":[{"given":"Tendai","family":"Washaya","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Chimukangara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin","family":"Mayini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Bote","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nyasha","family":"Chin\u2019ombe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shungu","family":"Munyati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justen","family":"Manasa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,15]]},"reference":[{"key":"3134_CR1","unstructured":"HIV drug resistance. \u2013 brief report 2024 [Internet]. 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PubMed PMID: 38219684; PubMed Central PMCID: PMC10947882.","journal-title":"J Clin Virol"}],"container-title":["Virology Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12985-026-03134-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12985-026-03134-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12985-026-03134-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T23:05:18Z","timestamp":1776899118000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12985-026-03134-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,15]]},"references-count":25,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["3134"],"URL":"https:\/\/doi.org\/10.1186\/s12985-026-03134-0","relation":{},"ISSN":["1743-422X"],"issn-type":[{"value":"1743-422X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,15]]},"assertion":[{"value":"3 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 March 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 March 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study obtained research ethics approval from the local institutional review board of the University of Zimbabwe Joint Research Ethics Committee. Additional approvals were obtained from the BRTI Ethics Research Board, the Parirenyatwa Group of Hospitals (JREC\/362\/2021), and the Medical Research Council of Zimbabwe (MRCZ\/A\/2847).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"This study did not obtain informed consent from individuals because it used anonymized routine HIVDR samples for genotyping. The Ministry of Health of Zimbabwe approved this study and waived the need for individual participant consent.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"107"}}