Estimating the date of origin of an HIV-1 circulating recombinant form |
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Authors: | Kok Keng Tee Oliver G Pybus Joe Parker Adeeba Kamarulzaman |
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Institution: | a Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan b Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia c Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK d Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia |
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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 (trec) 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. |
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Keywords: | HIV Recombination Coalescence Reticulate evolution Genesis |
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