Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. Export

@article{citeulike:6070951, abstract = {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.}, author = {Gifford, Robert J. and de Oliveira, Tulio and Rambaut, Andrew and Pybus, Oliver G. and Dunn, David and Vandamme, Anne-Mieke M. and Kellam, Paul and Pillay, Deenan and {UK Collaborative Group on HIV Drug Resistance}}, citeulike-article-id = {6070951}, citeulike-linkout-0 = {http://dx.doi.org/10.1128/JVI.00889-07}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17898057}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17898057}, doi = {10.1128/JVI.00889-07}, issn = {1098-5514}, journal = {Journal of virology}, keywords = {britain, clustering, genetic-diversity, hiv, migration, phylogenetics, spatial, transmission}, month = {December}, number = {23}, pages = {13050--13056}, posted-at = {2009-11-04 19:05:07}, priority = {0}, title = {Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.}, url = {http://dx.doi.org/10.1128/JVI.00889-07}, volume = {81}, year = {2007} }

TY - JOUR ID - citeulike:6070951 L3 - citeulike-article-id:6070951 N2 - 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. IS - 23 JF - Journal of virology SN - 1098-5514 EP - 13056 TI - Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. VL - 81 SP - 13050 KW - britain KW - clustering KW - genetic-diversity KW - hiv KW - migration KW - phylogenetics KW - spatial KW - transmission AU - Gifford, Robert AU - de Oliveira, Tulio AU - Rambaut, Andrew AU - Pybus, Oliver AU - Dunn, David AU - Vandamme, Anne-Mieke AU - Kellam, Paul AU - Pillay, Deenan PY - 2007/12// UR - http://dx.doi.org/10.1128/JVI.00889-07 ER -