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Journal of Virology, December 2007, p. 13050-13056, Vol. 81, No. 23
0022-538X/07/$08.00+0     doi:10.1128/JVI.00889-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1

Robert J. Gifford,^1,2*, Tulio de Oliveira,^3,4, Andrew Rambaut,⁵ Oliver G. Pybus,³ David Dunn,⁶ Anne-Mieke Vandamme,⁷ Paul Kellam,¹ Deenan Pillay,^1,8 on Behalf of the UK Collaborative Group on HIV Drug Resistance

Department of Infection, University College London, London, United Kingdom,¹ Division of Infectious Diseases, Stanford University, Stanford, California,² Department of Zoology, University of Oxford, Oxford, United Kingdom,³ The South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa,⁴ Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland,⁵ Medical Research Council Clinical Trials Unit, London, United Kingdom,⁶ Rega Institute for Medical Research, K.U. Leuven, Belgium,⁷ Centres for Infection, Health Protection Agency, Colindale, United Kingdom⁸

Received 25 April 2007/ Accepted 17 September 2007

With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods.

Published ahead of print on 26 September 2007.

These authors contributed equally.

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