title: Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data.
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.
authors: National Institute of Public Health and the Environment, Bilthoven, The Netherlands. rolf.ypma@rivm.nl
authors: R J F
authors: RJ
authors: Ypma
authors: A M A
authors: AM
authors: Bataille
authors: A
authors: A
authors: Stegeman
authors: G
authors: G
authors: Koch
authors: J
authors: J
authors: Wallinga
authors: W M
authors: WM
authors: van Ballegooijen
mesh_terms: D000822:Animal Husbandry; D000818:Animals; D002645:Chickens; D016384:Consensus Sequence; D004372:Ducks; D058872:Epidemics / Q000662:veterinary*; D006388:Hemagglutinins / Q000235:genetics; D006801:Humans; D053126:Influenza A Virus, H7N7 Subtype / Q000235:genetics / Q000502:physiology*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000635:transmission*; D016013:Likelihood Functions; D008390:Markov Chains; D009010:Monte Carlo Method; D009426:Netherlands / Q000453:epidemiology; D009439:Neuraminidase / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000662:veterinary; D013997:Time Factors; D014422:Turkeys; D014764:Viral Proteins / Q000235:genetics
chemical_list: D006388:Hemagglutinins; C057027:PB2 protein, Influenzavirus A; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase; D009439:Neuraminidase