ArticleRevue scientifique et technique (International Office of Epizootics)2016
Using genomics data to reconstruct transmission trees during disease outbreaks.
Article in Revue scientifique et technique (International Office of Epizootics), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.Nature communications · 2025Article
- Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.bioRxiv : the preprint server for biology · 2024Article
- Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation.Molecular biology and evolution · 2024Article
- Article
- Colonization and transmission ofMicrobial genomics · 2023Article
- Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission.PLoS computational biology · 2022Article
- Population-based sequencing ofeLife · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- A curated dataset of peste des petits ruminants virus sequences for molecular epidemiological analyses.PloS one · 2022Article
- Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.Virus evolution · 2022Article
- Apathogenic proxies for transmission dynamics of a fatal virus.Frontiers in veterinary science · 2022Article
- Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times.Statistical applications in genetics and molecular biology · 2020Article
- Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-ProducingJournal of clinical microbiology · 2019Article
- Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.PLoS computational biology · 2019Article
- Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions.Molecular biology and evolution · 2019Article
- Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases.Frontiers in public health · 2019Review
- Tracking virus outbreaks in the twenty-first century.Nature microbiology · 2019Review
- TB Transmission: Closing the Gaps.EBioMedicine · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Genetic sequence data from pathogens present a novel means to investigate the spread of infectious disease between infected hosts or infected premises, complementing traditional contact-tracing approaches, and much recent work has gone into developing methods for this purpose. The objective is to recover the epidemic transmission tree, which identifies who infected whom. This paper reviews the various approaches that have been taken. The first step is to define a measure of difference between sequences, which must be done while taking into account such factors as recombination and convergent evolution. Three broad categories of method exist, of increasing complexity: those that assume no withinhost genetic diversity or mutation, those that assume no within-host diversity but allow mutation, and those that allow both. Until recently, the assumption was usually made that every host in the epidemic could be identified, but this is now being relaxed, and some methods are intended for sparsely sampled data, concentrating on the identification of pairs of sequences that are likely to be the result of direct transmission rather than inferring the complete transmission tree. Many of the procedures described here are available to researchers as free software.
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