Timing the ancestor of the HIV-1 pandemic strains.
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.
Korber
B
B
Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Muldoon
M
M
Theiler
J
J
Gao
F
F
Gupta
R
R
Lapedes
A
A
Hahn
B H
BH
Wolinsky
S
S
Bhattacharya
T
T
D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D000349:Africa / Q000453:epidemiology; D000818:Animals; D016001:Confidence Intervals; D016384:Consensus Sequence; D004196:Disease Outbreaks; D005060:Europe / Q000453:epidemiology; D019143:Evolution, Molecular; D015752:Genes, env; D019302:HIV Envelope Protein gp160 / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006205:Haiti / Q000453:epidemiology; D006801:Humans; D016013:Likelihood Functions; D002679:Pan troglodytes; D010802:Phylogeny; D016097:Simian Acquired Immunodeficiency Syndrome / Q000635:transmission / Q000821:virology; D015302:Simian Immunodeficiency Virus / Q000235:genetics; D013997:Time Factors; D014481:United States / Q000453:epidemiology; D015047:Zoonoses
D019302:HIV Envelope Protein gp160