ArticlePLoS computational biology2016
SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
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- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
- Ethics of Identifying Individuals Involved in HIV Transmission Events by Phylogenetics in Molecular Surveillance.Bioethics · 2025Article
- MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.PLoS computational biology · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Epidemiology and economics of foot-and-mouth disease: current understanding and knowledge gaps.Veterinary research · 2025Review
- ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.PLoS computational biology · 2025Article
- Independent introductions and nosocomial transmission ofMicrobiology spectrum · 2025Article
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics ofJAC-antimicrobial resistance · 2024Article
- The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years.Genome medicine · 2024Article
- Nosocomial surveillance of multidrug-resistantMicrobiology spectrum · 2024Article
- HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.Microbial genomics · 2024Article
- Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.Molecular biology and evolution · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- Methods to Estimate the Between-Population Level Effective Reproductive Number for Infectious Disease Epidemics: Foot-And-Mouth Disease (FMD) in Vietnam.Transboundary and emerging diseases · 2024Article
- Inferring viral transmission time from phylogenies for known transmission pairs.bioRxiv : the preprint server for biology · 2023Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events. Our computationally efficient implementation of this model enables the inference of host-to-host transmission while accommodating within-host evolution and non-sampled hosts. SCOTTI is distributed as an open source package for the phylogenetic software BEAST2. We show that SCOTTI can generally infer transmission events even in the presence of considerable within-host variation, can account for the uncertainty associated with the possible presence of non-sampled hosts, and can efficiently use data from multiple samples of the same host, although there is some reduction in accuracy when samples are collected very close to the infection time. We illustrate the features of our approach by investigating transmission from genetic and epidemiological data in a Foot and Mouth Disease Virus (FMDV) veterinary outbreak in England and a Klebsiella pneumoniae outbreak in a Nepali neonatal unit. Transmission histories inferred with SCOTTI will be important in devising effective measures to prevent and halt transmission.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.