ArticleProceedings. Biological sciences2008
Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus.
Article in Proceedings. Biological sciences, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed.
- Generalizing an outbreak cluster detection method for two groups: an application to rabies.Royal Society open science · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Epidemiology and economics of foot-and-mouth disease: current understanding and knowledge gaps.Veterinary research · 2025Review
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.Research square · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.medRxiv : the preprint server for health sciences · 2025Article
- Multiple incursions of foot-and-mouth disease virus serotype O into the Republic of Korea between 2010 and 2019.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2024Article
- Inferring Viral Transmission Pathways from Within-Host Variation.medRxiv : the preprint server for health sciences · 2023Article
- Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea.Virus evolution · 2023Article
- Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus.Veterinary research · 2022Article
- Molecular source attribution.PLoS computational biology · 2022Article
- The potential of genomics for infectious disease forecasting.Nature microbiology · 2022Review
- SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.Cell systems · 2022Article
- An open-access database of infectious disease transmission trees to explore superspreader epidemiology.PLoS biology · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics.Frontiers in microbiology · 2022Article
- Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK.Frontiers in microbiology · 2022Article
- Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission.Scientific reports · 2021Article
- Finding disease outbreak locations from human mobility data.EPJ data science · 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
40 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Estimating detailed transmission trees that reflect the relationships between infected individuals or populations during a disease outbreak often provides valuable insights into both the nature of disease transmission and the overall dynamics of the underlying epidemiological process. These trees may be based on epidemiological data that relate to the timing of infection and infectiousness, or genetic data that show the genetic relatedness of pathogens isolated from infected individuals. Genetic data are becoming increasingly important in the estimation of transmission trees of viral pathogens due to their inherently high mutation rate. Here, we propose a maximum-likelihood approach that allows epidemiological and genetic data to be combined within the same analysis to infer probable transmission trees. We apply this approach to data from 20 farms infected during the 2001 UK foot-and-mouth disease outbreak, using complete viral genome sequences from each infected farm and information on when farms were first estimated to have developed clinical disease and when livestock on these farms were culled. Incorporating known infection links due to animal movement prior to imposition of the national movement ban results in the reduction of the number of trees from 41472 that are consistent with the genetic data to 1728, of which just 4 represent more than 95% of the total likelihood calculated using a model that accounts for the epidemiological data. These trees differ in several ways from those constructed prior to the availability of genetic data.
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