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.
Publication types
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, P.H.S.
MeSH terms
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Acquired Immunodeficiency Syndrome / epidemiology*
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Acquired Immunodeficiency Syndrome / transmission
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Acquired Immunodeficiency Syndrome / virology*
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Africa / epidemiology
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Animals
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Confidence Intervals
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Consensus Sequence
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Disease Outbreaks
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Europe / epidemiology
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Evolution, Molecular*
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Genes, env
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HIV Envelope Protein gp160 / genetics
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HIV-1 / classification
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HIV-1 / genetics*
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Haiti / epidemiology
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Humans
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Likelihood Functions
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Pan troglodytes
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Phylogeny
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Simian Acquired Immunodeficiency Syndrome / transmission
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Simian Acquired Immunodeficiency Syndrome / virology
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Simian Immunodeficiency Virus / genetics
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Time Factors
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United States / epidemiology
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Zoonoses
Substances
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HIV Envelope Protein gp160