Nature Communications (Mar 2019)
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis
- Oliver Ratmann,
- M. Kate Grabowski,
- Matthew Hall,
- Tanya Golubchik,
- Chris Wymant,
- Lucie Abeler-Dörner,
- David Bonsall,
- Anne Hoppe,
- Andrew Leigh Brown,
- Tulio de Oliveira,
- Astrid Gall,
- Paul Kellam,
- Deenan Pillay,
- Joseph Kagaayi,
- Godfrey Kigozi,
- Thomas C. Quinn,
- Maria J. Wawer,
- Oliver Laeyendecker,
- David Serwadda,
- Ronald H. Gray,
- Christophe Fraser,
- PANGEA Consortium and Rakai Health Sciences Program
Affiliations
- Oliver Ratmann
- Department of Mathematics, Imperial College London
- M. Kate Grabowski
- Department of Medicine, Johns Hopkins School of Medicine
- Matthew Hall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford
- Tanya Golubchik
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford
- Chris Wymant
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London
- Lucie Abeler-Dörner
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford
- David Bonsall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford
- Anne Hoppe
- Division of Infection and Immunity, University College London
- Andrew Leigh Brown
- School of Biological Sciences, University of Edinburgh
- Tulio de Oliveira
- College of Health Sciences, University of KwaZulu-Natal
- Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus
- Paul Kellam
- Department of Medicine, Imperial College London
- Deenan Pillay
- Division of Infection and Immunity, University College London
- Joseph Kagaayi
- Rakai Health Sciences Program
- Godfrey Kigozi
- Rakai Health Sciences Program
- Thomas C. Quinn
- Department of Medicine, Johns Hopkins School of Medicine
- Maria J. Wawer
- Rakai Health Sciences Program
- Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine
- David Serwadda
- Rakai Health Sciences Program
- Ronald H. Gray
- Department of Medicine, Johns Hopkins School of Medicine
- Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford
- PANGEA Consortium and Rakai Health Sciences Program
- DOI
- https://doi.org/10.1038/s41467-019-09139-4
- Journal volume & issue
-
Vol. 10,
no. 1
pp. 1 – 13
Abstract
Here, Ratmann et al. show how viral deep sequencing data can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks.
