Estimating the basic reproductive number from viral sequence data

Stadler, Tanja and Kouyos, Roger and von Wyl, Viktor and Yerly, Sabine and Böni, Jürg and Bürgisser, Philippe and Klimkait, Thomas and Joos, Beda and Rieder, Philip and Xie, Dong and Günthard, Huldrych F. and Drummond, Alexei J. and Bonhoeffer, Sebastian and Swiss HIV Cohort Study, . (2012) Estimating the basic reproductive number from viral sequence data. Molecular biology and evolution, 29 (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
Publisher:Oxford University Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:17 Aug 2020 13:59
Deposited On:08 May 2015 08:45

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