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Elena E Giorgi, Alan S Perelson, Tanmoy Bhattacharya

Age-structured Stochastic Model of Intrapatient HIV Evolution Page 1 Short Abstract — We study a stochastic linear birth and death process where the birth and death rates depend on age. The novelty of this work is in keeping track of the distribution of generation numbers, ie, the number of HIV replication cycles that have occurred since the initial infecting genome entered the host. We derive the master equation of the process and compare to a Monte Carlo simulation. The summary statistics obtained here provide a more robust alternative to coalescent theory for estimating times to the last common ancestor for an exponentially growing population. I. BACKGROUND HE occurrence of a genetic bottleneck in HIV sexual or mother to infant transmissions has been well documented [1-4]. This results in a majority of new infections being homogeneous, ie, initiated by a single genetic strain [5]. Furthermore, the viral …