Estimating the basic reproductive number from viral sequence data

Stadler, T. and Kouyos, R. and von Wyl, V. and Yerly, S. and Boni, J. and Burgisser, P. and Klimkait, T. and Joos, B. and Rieder, P. and Xie, D. and Gunthard, H. F. and Drummond, A. J. and Bonhoeffer, S. and Swiss HIV Cohort Study, . (2012) Estimating the basic reproductive number from viral sequence data. Molecular biology and evolution, Vol. 29, no 1. pp. 347-357.

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Official URL: http://edoc.unibas.ch/dok/A6338388

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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.
Faculties and Departments:03 Faculty of Medicine > Departement Biomedizin > Division of Medical Microbiology > Molecular Virology (Klimkait)
UniBasel Contributors:Klimkait, Thomas
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:Oxford University Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:08 May 2015 08:45
Deposited On:08 May 2015 08:45

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