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2006.29: Timing the Ancestor of the HIV-1 Pandemic Strains

2006.29: B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinsky and T. Bhattacharya (2000) Timing the Ancestor of the HIV-1 Pandemic Strains. Science, 288 (5472). pp. 1786-1796. ISSN 0036-8075

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DOI: 10.1126/science.288.5472.1789

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 2000 > 92 Biology and other natural sciences
MIMS number:2006.29
Deposited By:Dr Mark Muldoon
Deposited On:10 March 2006

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