Tanya Golubchik, Lucie Abeler-Dörner, Matthew Hall, Chris Wymant, David Bonsall, George Macintyre-Cockett, Laura Thomson, Jared M Baeten, Connie L Celum, Ronald M Galiwango, Barry Kosloff, Mohammed Limbada, Andrew Mujugira, Nelly R Mugo, Astrid Gall, François Blanquart, Margreet Bakker, Daniela Bezemer, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, Barbara Gunsenheimer-Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger D Kouyos, Laurence Meyer, Kholoud Porter, Ard van Sighem, Mark van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Helen Ayles, David N Burns, Sarah Fidler, Mary Kate Grabowski, Richard Hayes, Joshua T Herbeck, Joseph Kagaayi, Pontiano Kaleebu, Jairam R Lingappa, Deogratius Ssemwanga, Susan H Eshleman, Myron S Cohen, Oliver Ratmann, Oliver Laeyendecker, Christophe Fraser
{"title":"HIV-phyloTSI：自HIV-1感染以来的亚型独立估计时间，用于使用深度序列数据的人口发病率的横截面测量。","authors":"Tanya Golubchik, Lucie Abeler-Dörner, Matthew Hall, Chris Wymant, David Bonsall, George Macintyre-Cockett, Laura Thomson, Jared M Baeten, Connie L Celum, Ronald M Galiwango, Barry Kosloff, Mohammed Limbada, Andrew Mujugira, Nelly R Mugo, Astrid Gall, François Blanquart, Margreet Bakker, Daniela Bezemer, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, Barbara Gunsenheimer-Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger D Kouyos, Laurence Meyer, Kholoud Porter, Ard van Sighem, Mark van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Helen Ayles, David N Burns, Sarah Fidler, Mary Kate Grabowski, Richard Hayes, Joshua T Herbeck, Joseph Kagaayi, Pontiano Kaleebu, Jairam R Lingappa, Deogratius Ssemwanga, Susan H Eshleman, Myron S Cohen, Oliver Ratmann, Oliver Laeyendecker, Christophe Fraser","doi":"10.1186/s12859-025-06189-y","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. 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.</p><p><strong>Results: </strong>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 years, with a mean absolute error of less than 12 months overall and less than 5 months 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.</p><p><strong>Conclusions: </strong>We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.</p>","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":"26 1","pages":"212"},"PeriodicalIF":3.3000,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12351810/pdf/","citationCount":"0","resultStr":"{\"title\":\"HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.\",\"authors\":\"Tanya Golubchik, Lucie Abeler-Dörner, Matthew Hall, Chris Wymant, David Bonsall, George Macintyre-Cockett, Laura Thomson, Jared M Baeten, Connie L Celum, Ronald M Galiwango, Barry Kosloff, Mohammed Limbada, Andrew Mujugira, Nelly R Mugo, Astrid Gall, François Blanquart, Margreet Bakker, Daniela Bezemer, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, Barbara Gunsenheimer-Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger D Kouyos, Laurence Meyer, Kholoud Porter, Ard van Sighem, Mark van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Helen Ayles, David N Burns, Sarah Fidler, Mary Kate Grabowski, Richard Hayes, Joshua T Herbeck, Joseph Kagaayi, Pontiano Kaleebu, Jairam R Lingappa, Deogratius Ssemwanga, Susan H Eshleman, Myron S Cohen, Oliver Ratmann, Oliver Laeyendecker, Christophe Fraser\",\"doi\":\"10.1186/s12859-025-06189-y\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. 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HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.
Background: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. 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.
Results: 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 years, with a mean absolute error of less than 12 months overall and less than 5 months 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.
Conclusions: We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.
期刊介绍：
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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