PANGEA-HIV/PANGEA-Sequences: v1.0.0

HIV Consensus Sequence Repositoryof the PANGEA-HIV consortium This repository provides HIV consensus sequences of the PANGEA-HIV consortium. HIV sequence data were obtained from participants from multiple cohorts across Africa and generated following deep-sequencing by the PANGEA-HIV consortium. PANGEA-HIV stands for "Phylogenetics And Networks for Generalised Epidemics in Africa". The overarching goal of the PANGEA consortium is to identify individual and population level factors that drive the epidemic using HIV-1 phylogenetic data, analyse the dynamics of the epidemic, and translate these findings into information that can be used to design more efficient interventions. About the project: PANGEA-HIV 2 is a collaboration between scientists from the Africa Health Research Institute (South Africa), Rakai Health Sciences Program (Uganda), Johns Hopkins University (USA), Medical Research Council/Uganda Virus Research Institute (Uganda), Zambart Project (Zambia), London School of Hygiene and Tropical Medicine (UK), Imperial College London (UK), Partners in Prevention Project at the University of Washington (USA), Botswana Harvard AIDS Institute Partnership (Botswana/USA), University of Edinburgh (UK), and the University of Oxford (UK). Members of the PANGEA-HIV-2 steering commitee are: Fraser, C. (PI), Abeler-Dörner, L., Ayles, H., Bonsall, D., Bowden, R., Calvez, V., Essex, M., Fidler, S., Grabowski, K., Golubchik, T., Gupta, R., Hayes, R., Herbeck, J., Kagaayi, J., Kaleebu, P., Lingappa, J., Moyo, S., Novitsky, V., Ndung'u, T., Pillay, D., Quinn, T., Rambaut, A., Ratmann, O., Seeley, J., Ssemwanga, D., Tanser, F., Wawer, M. Members of the PANGEA-HIV-1 steering commitee were: Pillay, D. (PI), Cohen, M., D'Oliveira, T., Dennis, A., Essex, M., Fidler, S., Frampton, D., Fraser, C., Golubchik, T., Hayes, R., Herbeck, J., Hoppe, A., Kaleebu, P., Kellam, P., Kityo, C., Leigh-Brown, A., Lingappa, J., Novitsky, V., Paton, N., Quinn, T., Ratmann, O., Ssemwanga, D., Tanser, F., Wawer, M. Available HIV consensus sequences: HIV consensus sequences are provided aligned in fasta file format for each cohort site from which the sequences were sampled: Africa Health Research Institute (AHRI), South Africa Rakai Health Sciences Program (RHSP), Uganda Medical Research Council/Uganda Virus Research Institute (MRC), Uganda Zambart Project (Popart), Zambia Botswana Harvard AIDS Institute Partnership (BHP), Botswana Partners in Prevention (Partners), Uganda/Kenya/South Africa/Botswana Further meta-data associated with the participants from which the pathogen sequences were sampled are available, please follow this link. The publications folder contains list of PANGEA Sequence IDs as used in specific research publications. License The data in this repository are licensed under CC-BY-4.0 by PANGEA-HIV. Warranty PANGEA-HIV makes no representation or warranty about the accuracy or completeness of the data. PANGEA-HIV accepts no liability or responsibility for any use which may be made of any data, for results derived from these data, nor for any reliance which may be placed on any such work or results. Funding PANGEA-HIV is supported by the following organizations: Bill & Melinda Gates Foundation (OPP1175094, OPP1084362) Acknowledgements PANGEA-HIV thanks all contributors, program staff and participants across all contributing cohorts; and all members of the consortium.