ArticleProceedings. Biological sciences2012
Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data.
Article in Proceedings. Biological sciences, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 1 of them a synthesis that pooled it.
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Who cites it
84 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Modelling the transmission of healthcare associated infections: a systematic review.BMC infectious diseases · 2013Pooled it
- Design and methods of a social network isolation study for reducing respiratory infection transmission: The eX-FLU cluster randomized trial.Epidemics · 2016Trial
- Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.Molecular biology and evolution · 2025Article
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019.Emerging infectious diseases · 2023Article
- Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea.Virus evolution · 2023Article
- Molecular source attribution.PLoS computational biology · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints.Microbial genomics · 2022Article
- Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics.Frontiers in microbiology · 2022Article
- Article
- Sample size calculation for phylogenetic case linkage.PLoS computational biology · 2021Article
- Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa.PLoS pathogens · 2021Article
- Nosocomial transmission and outbreaks of coronavirus disease 2019: the need to protect both patients and healthcare workers.Antimicrobial resistance and infection control · 2021Review
- Social structure defines spatial transmission of African swine fever in wild boar.Journal of the Royal Society, Interface · 2021Article
- Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations.Scientific reports · 2020Article
- Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times.Statistical applications in genetics and molecular biology · 2020Article
- Sampling and summarizing transmission trees with multi-strain infections.Bioinformatics (Oxford, England) · 2020Article
- Estimating the relative probability of direct transmission between infectious disease patients.International journal of epidemiology · 2020Article
- Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data.Statistics in medicine · 2020Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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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