Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis
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Date
2019
Journal Title
Journal ISSN
Volume Title
Publisher
Nature communications
Abstract
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.
Description
Keywords
HIV-1 transmission networks, Epidemic spread, Africa, Phylogenetic analysis
Citation
Ratmann, O., Grabowski, M. K., Hall, M., Golubchik, T., Wymant, C., Abeler-Dörner, L., ... & Fraser, C. (2019). Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. Nature communications, 10(1), 1-13. https://doi.org/10.1038/s41467-019-09139-4