Timing the ancestor of the HIV-1 pandemic strains

Science. 2000 Jun 9;288(5472):1789-96. doi: 10.1126/science.288.5472.1789.


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

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

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


  • HIV Envelope Protein gp160