Timing the Ancestor of the HIV-1 Pandemic Strains

Korber, B. and Muldoon, M. and Theiler, J. and Gao, F. and Gupta, R. and Lapedes, A. and Hahn, B. H. and Wolinsky, S. and Bhattacharya, T. (2000) Timing the Ancestor of the HIV-1 Pandemic Strains. Science, 288 (5472). pp. 1786-1796. ISSN 0036-8075

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Abstract

HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.

Item Type:	Article
Additional Information:	The DOI link above points to the publisher's online version of the article. Further details of this work are available at http://www.santafe.edu/~btk/science-paper/bette.html
Uncontrolled Keywords:	immunodeficiency-virus type-1; deficiency syndrome aids; maximum-likelihood; dna-sequences; transmission history; interspecies transmission; antiretroviral therapy; phylogenetic methods; population-dynamics; genetic diversity
Subjects:	MSC 2010, the AMS's Mathematics Subject Classification > 92 Biology and other natural sciences
Depositing User:	Dr Mark Muldoon
Date Deposited:	10 Mar 2006
Last Modified:	20 Oct 2017 14:12
URI:	https://eprints.maths.manchester.ac.uk/id/eprint/179

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