Journal
NATURE COMMUNICATIONS
Volume 10, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-019-09139-4
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Funding
- National Institute of Mental Health [K23MH086338, R01MH107275]
- National Institute of Allergy and Infectious Diseases [R01AI110324, U01AI100031, R01AI102939]
- National Institute of Child Health and Development [RO1HD070769, R01HD050180]
- Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health
- Bill & Melinda Gates Foundation [22006.02, OPP1084362]
- Johns Hopkins University Center for AIDS Research [P30AI094189]
- European Research Council [PBDR-339251]
- Bill and Melinda Gates Foundation [OPP1084362] Funding Source: Bill and Melinda Gates Foundation
- NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES [ZIAAI000361, ZIAAI001040] Funding Source: NIH RePORTER
- MRC [MR/R015600/1] Funding Source: UKRI
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To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.
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