title: Estimating the basic reproductive number from viral sequence data.
abstract: 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.
authors: Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland. tanja.stadler@env.ethz.ch
authors: Tanja
authors: T
authors: Stadler
authors: Roger
authors: R
authors: Kouyos
authors: Viktor
authors: V
authors: von Wyl
authors: Sabine
authors: S
authors: Yerly
authors: Jürg
authors: J
authors: Böni
authors: Philippe
authors: P
authors: Bürgisser
authors: Thomas
authors: T
authors: Klimkait
authors: Beda
authors: B
authors: Joos
authors: Philip
authors: P
authors: Rieder
authors: Dong
authors: D
authors: Xie
authors: Huldrych F
authors: HF
authors: Günthard
authors: Alexei J
authors: AJ
authors: Drummond
authors: Sebastian
authors: S
authors: Bonhoeffer
mesh_terms: D050936:Basic Reproduction Number; D001499:Bayes Theorem; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008954:Models, Biological; D015233:Models, Statistical; D010802:Phylogeny