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Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window of several months, and cannot assess the cumulative impact of an intervention.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a Random Forest Regression model, HIV-phyloTSI, which combines measures of within-host diversity and divergence to generate continuous TSI estimates directly from viral deep-sequencing data, with no need for additional variables. HIV-phyloTSI provides a continuous measure of TSI up to 9\u00a0years, with a mean absolute error of less than 12\u00a0months overall and less than 5\u00a0months for infections with a TSI of up to a year. It performs equally well for all major HIV subtypes based on data from African and European cohorts. <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s12859-025-06189-y","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T08:20:38Z","timestamp":1755159638000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence 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Int J Epidemiol. 2018;47:236\u201345.","journal-title":"Int J Epidemiol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06189-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-025-06189-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06189-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T22:21:22Z","timestamp":1757456482000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-025-06189-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,14]]},"references-count":55,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["6189"],"URL":"https:\/\/doi.org\/10.1186\/s12859-025-06189-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,14]]},"assertion":[{"value":"29 August 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 August 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Participants in all studies gave written informed consent. Ethics approvals were granted as follows. Rakai community cohort study: Uganda National Council for Science and Technology (HS450), Uganda Virus Research Institute Ethics Council (GC\/127\/08\/12\/137 and Johns Hopkins School of Medicine (CR00046394\/IRB00217467). MRC Uganda: Uganda National Council for Science and Technology (HS1432 and HS1230). UWP cohorts: Kenya Medical Research Institute (11-06380), Moi University (2004\/3), Kenyatta National Hospital (KNH-ERC\/R\/72), UC San Francisco (065240), Indiana University (0401-29), University of Washington (25582 and 25584), University of Cape Town Research Ethics Committee (213\/400), University of Witwatersrand HREC (40206), Kilimanjaro Christian Medical University College (061), Harvard School of Public Health (P11408-104), London School of Hygiene and Tropical Medicine (5181), Uganda National Council for Science and Technology (HS12 and ARC073), Emory University and the Health Ministry of the Republic of Rwanda (00001497), Emory University (00067994), Republic of Zambia National Ethics Committee (004-05-05), and Botswana Harvard Partnership (PPME-12\/18\/1), PopART HPTN-071\u201302: The University of Zambia Biomedical Research Ethics Committee (004-05-15) and London School of Hygiene and Tropical Medicine (9700). For BEEHIVE, samples in the present study originated from the UK Register of HIV Seroconverters. Ethics approvals were as follows: UK Register of HIV Seroconverters (04\/Q2707\/155), Comit\u00e9 de Protection des Personnes Ile de France III (N EURODRACT: DGS: 9660695; R\u00e9f. CCP Dossier N: Am5617-10-1157), Ministerie van Volksgezondheid, Welzijn en Sport (CZ\/B\/2238-87); Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Germany (EA2\/024\/021); Helsingin ja uudenmaan sairaanhoitopiirin kuntayhtym\u00e4, Finland (565\/E5\/01); Kantonalen Ethikkommission Z\u00fcrich, Switzerland (2023-02080). This study adhered to the Declaration of Helsinki.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval and consent to participate"}},{"value":"Not applicable.","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":"212"}}