Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution

In earlier work, human immunodeficiency virus type 1 (HIV-1) sequences were analysed to estimate the timing of the ancestral sequence of the main grou p of HIV-1, the virus that is responsible for the acquired immune deficienc y syndrome pandemic, yielding a best estimate of 1931 (95% confidence inter val of 1915-1941). That work will be briefly reviewed, outlining how phylog enetic tools were extended to incorporate improved evolutionary models, how the molecular clock model was adapted to incorporate variable periods of l atency, and how the approach was validated by correctly estimating the timi ng of two historically documented dates. The advantages, limitations, and a ssumptions of the approach will be summarized, with particular consideratio n of the implications of branch length uncertainty and recombination. We ha ve recently undertaken new phylogenetic analysis of an extremely diverse se t of human immunodeficiency virus envelope sequences from the Democratic Re public of the Congo (the DRC, formerly Zaire). This analysis both corrobora tes and extends the conclusions of our original study. Coalescent methods w ere 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.