Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 429305
Title Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data
Author(s) Ypma, R.J.F.; Bataille, A.; Stegeman, A.; Koch, G.; Wallinga, J.; Ballegooijen, W.M.
Source Proceedings of the Royal Society. B: Biological Sciences 279 (2012)1728. - ISSN 0962-8452 - p. 444 - 450.
Department(s) CVI Virology
Publication type Refereed Article in a scientific journal
Publication year 2012
Keyword(s) influenza-a virus - mouth-disease - h7n7 - netherlands - outbreak - foot
Abstract Knowledge on the transmission tree of an epidemic can provide valuable insights into disease dynamics. The transmission tree can be reconstructed by analysing either detailed epidemiological data (e.g. contact tracing) or, if sufficient genetic diversity accumulates over the course of the epidemic, genetic data of the pathogen. We present a likelihood-based framework to integrate these two data types, estimating probabilities of infection by taking weighted averages over the set of possible transmission trees. We test the approach by applying it to temporal, geographical and genetic data on the 241 poultry farms infected in an epidemic of avian influenza A (H7N7) in The Netherlands in 2003. We show that the combined approach estimates the transmission tree with higher correctness and resolution than analyses based on genetic or epidemiological data alone. Furthermore, the estimated tree reveals the relative infectiousness of farms of different types and sizes.
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