Article: article from journal or magazin.
Estimating the basic reproductive number from viral sequence data.
Molecular Biology and Evolution
Swiss HIV Cohort Study
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth-death model (BDM) rather than the commonly used coalescent as the model for the epidemiological transmission of the pathogen. Using the BDM has the advantage that transmission and death rates are estimated independently and therefore enables for the first time the estimation of the basic reproductive number of the pathogen using only sequence data, without further assumptions like the average duration of infection. We apply the method to genetic data of the HIV-1 epidemic in Switzerland.
Basic Reproduction Number, Bayes Theorem, HIV Infections/epidemiology, HIV Infections/virology, HIV-1/genetics, Humans, Models, Biological, Models, Statistical, Phylogeny
Web of science
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