Imperial College London
Alternate

DrOliverRatmann

Faculty of Natural Sciences, Department of Mathematics

Reader in Statistics and Machine Learning for Public Good
 
 
 
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Contact

 

oliver.ratmann05 Website

 
 
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Location

 

525Huxley BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Wilkinson:2016:10.1016/j.meegid.2016.07.008,
author = {Wilkinson, E and Rasmussen, D and Ratmann, O and Stadler, T and Engelbrecht, S and de, Oliveira T},
doi = {10.1016/j.meegid.2016.07.008},
journal = {Infection, Genetics and Evolution},
pages = {200--208},
title = {Origin, imports and exports of HIV-1 subtype C in South Africa: a historical perspective},
url = {http://dx.doi.org/10.1016/j.meegid.2016.07.008},
volume = {46},
year = {2016}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - BACKGROUND: While the HIV epidemic in South Africa had a later onset than epidemics in other southern African countries, prevalence grew rapidly during the 1990's when the country was going through socio-political changes with the end of Apartheid. South Africa currently has the largest number of people living with HIV in the world and the epidemic is dominated by a unique subtype, HIV-1 subtype C. This large epidemic is also characterized by high level of genetic diversity. We hypothesize that this diversity is due to multiple introductions of the virus during the period of change. In this paper, we apply novel phylogeographic methods to estimate the number of viral imports and exportsfrom the start of the epidemic to the present. METHODS: We assembled 11,289 unique subtype C pol sequences from southern Africa. These represent one of the largest sequence datasets ever analyzed in the region. Sequences were stratified based on country of sampling and levels of genetic diversity were estimated for each country. Sequences were aligned and a maximum-likelihood evolutionary tree was inferred. Least-Squares Dating was then used to obtain a dated phylogeny from which we estimated the number of introductions into and exports out of South Africa using parsimony-based ancestral location reconstructions. RESULTS: Our results identified 189 viral introductions into South Africa with the largest number of introductions attributed to Zambia (n=109), Botswana (n=32), Malawi (n=26) and Zimbabwe (n=13). South Africa also exported many viral lineages to its neighbours. The bulk viral imports and exports appear to have occurred between 1985 and 2000, coincident with the period of socio-political transition. CONCLUSION: The high level of subtype C genetic diversity in South Africa is related to multiple introductions of the virus to the country. While the number of viral imports and exports we identified was highly sensitive to the number of samples included from each country, they mo
AU  - Wilkinson,E
AU  - Rasmussen,D
AU  - Ratmann,O
AU  - Stadler,T
AU  - Engelbrecht,S
AU  - de,Oliveira T
DO  - 10.1016/j.meegid.2016.07.008
EP  - 208
PY  - 2016///
SN  - 1567-7257
SP  - 200
TI  - Origin, imports and exports of HIV-1 subtype C in South Africa: a historical perspective
T2  - Infection, Genetics and Evolution
UR  - http://dx.doi.org/10.1016/j.meegid.2016.07.008
UR  - http://hdl.handle.net/10044/1/38582
VL  - 46
ER  -
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