HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.
Golubchik T, Abeler-Dörner L, Hall M, Wymant C, Bonsall D, Macintyre-Cockett G, Thomson L, Baeten JM, Celum CL, Galiwango RM, Kosloff B, Limbada M, Mujugira A, Mugo NR, Gall A, Blanquart F, Bakker M, Bezemer D, Ong SH, Albert J, Bannert N, Fellay J, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Ayles H, Burns DN, Fidler S, Grabowski MK, Hayes R, Herbeck JT, Kagaayi J, Kaleebu P, Lingappa JR, Ssemwanga D, Eshleman SH, Cohen MS, Ratmann O, Laeyendecker O, Fraser C; HPTN 071 (PopART) Phylogenetics protocol team, the BEEHIVE consortium and the PANGEA consortium.
Golubchik T, et al. Among authors: fellay j.
BMC Bioinformatics. 2025 Aug 14;26(1):212. doi: 10.1186/s12859-025-06189-y.
BMC Bioinformatics. 2025.
PMID: 40813968
Free PMC article.
BACKGROUND: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. ...It performs equally well for all major HIV subtypes based on data from African and European cohorts. CONCLUSIONS: We …
BACKGROUND: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV …