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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.

Original publication

DOI

10.1038/s41467-019-09139-4

Type

Journal article

Journal

Nature communications

Publication Date

29/03/2019

Volume

10

Addresses

Department of Mathematics, Imperial College London, London, SW72AZ, UK. oliver.ratmann@imperial.ac.uk.

Keywords

PANGEA Consortium and Rakai Health Sciences Program, Humans, HIV-1, HIV Infections, Phylogeny, Base Sequence, Adolescent, Adult, Middle Aged, Africa, Young Adult, Epidemics, High-Throughput Nucleotide Sequencing