Estimating the generation time of within-host HIV population

Yunxin Fu

I will present a simple method for estimating the mutation rate and generation time of fast evolving populations, such as HIV, taking advantage of DNA polymorphisms in longitudinal samples. The estimator is unbiased under a number of population models, including population structure and variable population size over time. From a longitudinal sample of DNA sequences of the env gene of human immunodeficiency virus type 1 (HIV-1) from a single patient, we estimated using this method that mutation rate per site per year is 9.89x10-3 and the length of onegeneration is 0.9 to 1 day.

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