Imperial College London
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ProfessorPaulKellam

Faculty of Medicine, Department of Infectious Disease

Professor of Virus Genomics
 
 
 
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Contact

 

p.kellam

 
 
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Location

 

460Wright Fleming WingSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Ratmann:2019:10.1038/s41467-019-09139-4,
author = {Ratmann, O and Grabowski, MK and Hall, M and Golubchik, T and Wymant, C and Abeler-Dörner, L and Bonsall, D and Hoppe, A and Brown, AL and de, Oliveira T and Gall, A and Kellam, P and Pillay, D and Kagaayi, J and Kigozi, G and Quinn, TC and Wawer, MJ and Laeyendecker, O and Serwadda, D and Gray, RH and Fraser, C},
doi = {10.1038/s41467-019-09139-4},
journal = {Nature Communications},
title = {Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis},
url = {http://dx.doi.org/10.1038/s41467-019-09139-4},
volume = {10},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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.
AU  - Ratmann,O
AU  - Grabowski,MK
AU  - Hall,M
AU  - Golubchik,T
AU  - Wymant,C
AU  - Abeler-Dörner,L
AU  - Bonsall,D
AU  - Hoppe,A
AU  - Brown,AL
AU  - de,Oliveira T
AU  - Gall,A
AU  - Kellam,P
AU  - Pillay,D
AU  - Kagaayi,J
AU  - Kigozi,G
AU  - Quinn,TC
AU  - Wawer,MJ
AU  - Laeyendecker,O
AU  - Serwadda,D
AU  - Gray,RH
AU  - Fraser,C
DO  - 10.1038/s41467-019-09139-4
PY  - 2019///
SN  - 2041-1723
TI  - Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis
T2  - Nature Communications
UR  - http://dx.doi.org/10.1038/s41467-019-09139-4
UR  - http://hdl.handle.net/10044/1/68242
VL  - 10
ER  -
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