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Timing the Ancestor of the HIV-1 Pandemic Strains

Authors: Muldoon, M.; Theiler, J.; Lapedes, A.; Wolinsky, S.; Gao, F.; Gupta, R.; Korber, B.; +2 Authors

Timing the Ancestor of the HIV-1 Pandemic Strains

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.

Keywords

Acquired Immunodeficiency Syndrome, Likelihood Functions, Time Factors, Pan troglodytes, Simian Acquired Immunodeficiency Syndrome, Genes, env, Haiti, United States, Disease Outbreaks, HIV Envelope Protein gp160, Europe, Evolution, Molecular, Africa, Consensus Sequence, Confidence Intervals, HIV-1, Animals, Humans, Simian Immunodeficiency Virus, Phylogeny

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
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788
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119
81
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