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Using Human Immunodeficiency Virus Type 1 Sequences to Infer Historical Features of the Acquired Immune Deficiency Syndrome Epidemic and Human Immunodeficiency Virus Evolution

Karina Yusim, Martine Peeters, Oliver G. Pybus, Tanmoy Bhattacharya, Eric Delaporte, Claire Mulanga, Mark Muldoon, James Theiler and Bette Korber
Philosophical Transactions: Biological Sciences
Vol. 356, No. 1410, Origins of HIV and the AIDS Epidemic (Jun. 29, 2001), pp. 853+855-866
Published by: Royal Society
Stable URL: http://www.jstor.org/stable/3067038
Page Count: 13
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Using Human Immunodeficiency Virus Type 1 Sequences to Infer Historical Features of the Acquired Immune Deficiency Syndrome Epidemic and Human Immunodeficiency Virus Evolution
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Abstract

In earlier work, human immunodeficiency virus type 1 (HIV-1) sequences were analysed to estimate the timing of the ancestral sequence of the main group of HIV-1, the virus that is responsible for the acquired immune deficiency syndrome pandemic, yielding a best estimate of 1931 (95% confidence interval of 1915-1941). That work will be briefly reviewed, outlining how phylogenetic tools were extended to incorporate improved evolutionary models, how the molecular clock model was adapted to incorporate variable periods of latency, and how the approach was validated by correctly estimating the timing of two historically documented dates. The advantages, limitations, and assumptions of the approach will be summarized, with particular consideration of the implications of branch length uncertainty and recombination. We have recently undertaken new phylogenetic analysis of an extremely diverse set of human immunodeficiency virus envelope sequences from the Democratic Republic of the Congo (the DRC, formerly Zaire). This analysis both corroborates and extends the conclusions of our original study. Coalescent methods were used to infer the demographic history of the HIV-1 epidemic in the DRC, and the results suggest an increase in the exponential growth rate of the infected population through time.

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