title: Estimating the date of origin of an HIV-1 circulating recombinant form.
abstract: HIV is capable of frequent genetic exchange through recombination. Despite the pandemic spread of HIV-1 recombinants, their times of origin are not well understood. We investigate the epidemic history of a HIV-1 circulating recombinant form (CRF) by estimating the time of the recombination event that lead to the emergence of CRF33_01B, a recently described recombinant descended from CRF01_AE and subtype B. The gag, pol and env genes were analyzed using a combined coalescent and relaxed molecular clock model, implemented in a Bayesian Markov chain Monte Carlo framework. Using linked genealogical trees we calculated the time interval between the common ancestor of CRF33_01B and the ancestors it shares with closely related parental lineages. The recombination event that generated CRF33_01B (t(rec)) occurred sometime between 1991 and 1993, suggesting that recombination is common in the early evolutionary history of HIV-1. The proof-of-concept approach provides a new tool for the investigation of HIV molecular epidemiology and evolution.
authors.affiliation: Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
authors.forename: Kok Keng
authors.initials: KK
authors.lastname: Tee
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.forename: Joe
authors.initials: J
authors.lastname: Parker
authors.forename: Kee Peng
authors.initials: KP
authors.lastname: Ng
authors.forename: Adeeba
authors.initials: A
authors.lastname: Kamarulzaman
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Takebe
mesh_terms: D019143:Evolution, Molecular; D005814:Genes, Viral / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics*; D015658:HIV Infections / Q000235:genetics / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008297:Male; D010802:Phylogeny; D011995:Recombination, Genetic; D017421:Sequence Analysis