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

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.

journal_name

Nat Commun

journal_title

Nature communications

authors

Ratmann O,Grabowski MK,Hall M,Golubchik T,Wymant C,Abeler-Dörner L,Bonsall D,Hoppe A,Brown AL,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

doi

10.1038/s41467-019-09139-4

subject

Has Abstract

pub_date

2019-03-29 00:00:00

pages

1411

issue

1

issn

2041-1723

pii

10.1038/s41467-019-09139-4

journal_volume

10

pub_type

杂志文章

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