Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

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dc.contributor.authorRatmann, Oliver tophe Fraser
dc.contributor.authorGrabowski, M. Kate
dc.contributor.authorHall, Matthew
dc.contributor.authorGolubchik, Tanya
dc.contributor.authorWymant, Chris
dc.contributor.authorAbeler-Dörner, Lucie
dc.contributor.authorBonsall, David
dc.contributor.authorHoppe, Anne
dc.contributor.authorLeigh Brown, Andrew
dc.contributor.authorOliveira, Tulio de
dc.contributor.authorGall, Astrid
dc.contributor.authorKellam, Paul
dc.contributor.authorPillay, Deenan
dc.contributor.authorKagaayi, Joseph
dc.contributor.authorKigozi, Godfrey
dc.contributor.authorQuinn, Thomas C.
dc.contributor.authorWawer, Maria J.
dc.contributor.authorLaeyendecker, Oliver
dc.contributor.authorSerwadda, David
dc.contributor.authorGray, Ronald H.
dc.date.accessioned2022-08-18T20:59:33Z
dc.date.available2022-08-18T20:59:33Z
dc.date.issued2019
dc.description.abstractTo 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.en_US
dc.identifier.citationRatmann, 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/s41467-019-09139-4en_US
dc.identifier.urihttps://doi.org/10.1038/s41467-019-09139-4
dc.identifier.urihttps://nru.uncst.go.ug/handle/123456789/4315
dc.language.isoenen_US
dc.publisherNature communicationsen_US
dc.subjectHIV-1 transmission networksen_US
dc.subjectEpidemic spreaden_US
dc.subjectAfricaen_US
dc.subjectPhylogenetic analysisen_US
dc.titleInferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysisen_US
dc.typeArticleen_US
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