Edinburgh Research Explorer

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

Dataset

  • Oliver Ratmann (Creator)
  • Mary K. Grabowski (Creator)
  • Matthew D Hall (Creator)
  • Tanya Golubchik (Creator)
  • Chris Wymant (Creator)
  • Lucie Abeler-Dörner (Creator)
  • David Bonsall (Creator)
  • Anne Hoppe (Creator)
  • Andrew Leigh-Brown (Creator)
  • Tulio de Oliveira (Creator)
  • Astrid Gall (Creator)
  • Paul Kellam (Creator)
  • Deenan Pillay (Creator)
  • Joseph Kagaayi (Creator)
  • Godfrey Kigozi (Creator)
  • Thomas C Quinn (Creator)
  • Maria J Wawer (Creator)
  • Oliver Laeyendecker (Creator)
  • David Serwadda (Creator)
  • Ronald H Gray (Creator)
  • Christophe Fraser (Creator)

Related Edinburgh Organisations

PublisherDryad
Temporal coverage2011 - 2015
Date made available2 Apr 2019
Geographical coverageRakai District Uganda

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.

Data Citation

Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, , (2019) Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. Dryad Digital Repository. https://doi.org/10.5061/dryad.7h46hg2

ID: 104689528