The molecular population genetics of HIV-1 group O

Philippe Lemey, Oliver G. Pybus, Andrew Rambaut, Alexei J. Drummond, David L. Robertson, Pierre Roques, Michael Worobey, Anne Mieke Vandamme

Research output: Contribution to journalArticlepeer-review

98 Scopus citations

Abstract

HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.

Original languageEnglish (US)
Pages (from-to)1059-1068
Number of pages10
JournalGenetics
Volume167
Issue number3
DOIs
StatePublished - Jul 2004

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'The molecular population genetics of HIV-1 group O'. Together they form a unique fingerprint.

Cite this