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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

Authors :
Golubchik, Tanya
Abeler-Dörner, Lucie
Hall, Matthew
Wymant, Chris
Bonsall, David
Macintyre-Cockett, George
Thomson, Laura
Baeten, Jared
Celum, Connie
Galiwango, Ronald
Kosloff, Barry
Limbada, Mohammed
Mujugira, Andrew
Mugo, Nelly
Gall, Astrid
Blanquart, François
Bakker, Margreet
Bezemer, Daniela
Ong, Swee Hoe
Albert, Jan
Bannert, Norbert
Fellay, Jacques
Gunsenheimer-Bartmeyer, Barbara
Günthard, Huldrych
Kivelä, Pia
Kouyos, Roger
Meyer, Laurence
Porter, Kholoud
van Sighem, Ard
van der Valk, Mark
Berkhout, Ben
Kellam, Paul
Cornelissen, Marion
Reiss, Peter
Ayles, Helen
Burns, David
Fidler, Sarah
Grabowski, Mary Kate
Hayes, Richard
Herbeck, Joshua
Kagaayi, Joseph
Kaleebu, Pontiano
Lingappa, Jairam
Ssemwanga, Deogratius
Eshleman, Susan
Cohen, Myron
Ratmann, Oliver
Laeyendecker, Oliver
Fraser, Christophe
Blanquart, François
Centre interdisciplinaire de recherche en biologie (CIRB)
Labex MemoLife
École normale supérieure - Paris (ENS-PSL)
Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris)
Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL)
Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137))
Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord
Centre de recherche en épidémiologie et santé des populations (CESP)
Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay
On behalf of the HPTN 071 (PopART) Phylogenetics protocol team, the BEEHIVE collaboration and the PANGEA consortium
Publication Year :
2022
Publisher :
Cold Spring Harbor Laboratory, 2022.

Abstract

Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining duration of infection classify samples into recent and non-recent and are unable to give more granular TSI estimates. These binary classifications have a limited recency time window of several months, therefore requiring large sample sizes, and cannot assess the cumulative impact of an intervention. We developed a Random Forest Regression model, HIV-phyloTSI, that combines measures of within-host diversity and divergence to generate TSI estimates 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 performed equally well for all major HIV subtypes based on data from African and European cohorts. We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.

Details

Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....6249f6cfe28eed588aaf3d22e3c866b2
Full Text :
https://doi.org/10.1101/2022.05.15.22275117