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Estimating the basic reproductive number from viral sequence data

Stadler, Tanja
Kouyos, Roger
von Wyl, Viktor
Böni, Jürg
Bürgisser, Philippe
Klimkait, Thomas
Joos, Beda
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Published in Molecular Biology and Evolution. 2012, vol. 29, no. 1, p. 347-57
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.
Keywords Basic Reproduction NumberBayes TheoremHIV Infections/epidemiology/virologyHIV-1/geneticsHumansModels, BiologicalModels, StatisticalPhylogeny
PMID: 21890480
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Research group Groupe Laurent Kaiser (virologie clinique) (668)
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STADLER, Tanja et al. Estimating the basic reproductive number from viral sequence data. In: Molecular Biology and Evolution, 2012, vol. 29, n° 1, p. 347-57. doi: 10.1093/molbev/msr217 https://archive-ouverte.unige.ch/unige:74519

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Deposited on : 2015-08-06

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