DOI: 10.5281/zenodo.7741616
title: Phylogenetic and epidemiologic data relating to age-specific HIV incidence and transmission in Rakai, Uganda, 2003-2018.

description: This repository contains the data for the analyses presented in the paper Growing gender inequity in HIV infection in Africa: sources and policy implications by M. Monod, A. Brizzi, R. Galiwango, R. Ssekubugu, Y. Chen, X. Xi et al. available in the pre-print https://doi.org/10.1101/2023.03.16.23287351 We thank all contributors, program staff and participants to the Rakai Community Cohort Study; all members of the PANGEA-HIV consortium, the Rakai Health Sciences Program, and CDC Uganda for comments on an earlier version of the manuscript. We also extend our gratitude to the Imperial College Research Computing Service and the Biomedical Research Computing Cluster at the University of Oxford for providing the computational resources to perform this study. Additionally, we thank the Office of Cyberinfrastructure and Computational Biology at the National Institute for Allergy and Infectious Diseases for data management support; and Zulip for sponsoring team communications through the Zulip Cloud Standard chat app. All analysis code is available from https://github.com/MLGlobalHealth/phyloSI-RakaiAgeGender.
description: Project leaders: Oliver Ratmann, Kate Grabowski, Joseph Kagaayi Researchers: Mélodie Monod, Andrea Brizzi, Ronald M Galiwango, Robert Ssekubugu, Yu Chen, Xiaoyue Xi, Edward Nelson Kankaka, Victor Ssempijja, Lucie Abeler Dörner, Adam Akullian, Alexandra Blenkinsop, David Bonsall, Larry W Chang, Shozen Dan, Christophe Fraser, Tanya Golubchik, Ronald H Gray, Matthew Hall, Jade C Jackson, Godfrey Kigozi, Oliver Laeyendecker, Lisa A. Mills, Thomas C Quinn, Steven J. Reynolds, John Santelli, Nelson K. Sewankambo, Simon EF Spencer, Joseph Ssekasanvu, Laura Thomson, Maria J Wawer, David Serwadda, Peter Godfrey-Faussett Keywords: HIV prevention; HIV transmission; phylogenetics Grants: Wagman, R01MH099733 to Ned Sacktor and MJW, R01MH107275 to LWC, R01MH115799 to MJW and LWC, U19MH110001 to Dr Mary McKay and Dr Fred Ssewamala); the National Institute of Child Health and Development (R01HD038883 to RHG, R01HD050180 to MJW, R01HD070769 to MJW, R01HD091003 to JS); the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases (K01AA024068 to Dr Jennifer Wagman); the National Heart, Lung, and Blood Institute (R01HL152813 to LWC); the Fogarty International Center (D43TW009578 to RHG, D43TW010557 to LWC); the Doris Duke Charitable Foundation to Dr Aaron Tobian; the Johns Hopkins University Center for AIDS Research (P30AI094189 to Dr Richard Chaisson); the U.S. President's Emergency Plan for AIDS Relief (PEPFAR) through the Centers for Disease Control and Prevention (NU2GGH000817 to RHSP); the Engineering and Physical Sciences Research Council through the EPSRC Centre for Doctoral Training in Modern Statistics and Statistical Machine Learning at Imperial and Oxford (EP/S023151/1 to Prof Axel Gandy); and the Imperial College London President's PhD Scholarship fund to YC. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. OR, MKG, CF, DB report grants from the Bill & Melinda Gates Foundation during the conduct of this study. MKG, MJW, RHG, LCW report grants from the National Institutes of Health during the conduct of this study. ABr, CY, XX report an EPSRC PhD studentship during the conduct of this study. Dr. Wawer and Dr. Gray are paid consultants to the Rakai Health Sciences Program and serves on its Board of Directors. This arrangement has been reviewed and approved by the Johns Hopkins University in accordance with its conflict of interest policies.
description: {"references": ["Golubchik, Tanya et al (2022). HIV-phyloTSI: Subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data", "Wymant, Chris et al (2017). PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity", "Xi, Xiaoyue et al (2022). Inferring the Sources of HIV Infection in Africa from Deep-Sequence Data with Semi-Parametric Bayesian Poisson Flow Models"]}