ArticleEvolution, medicine, and public health2014
Phylogenetic tree shapes resolve disease transmission patterns.
Article in Evolution, medicine, and public health, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.Systematic biology · 2024Pooled it
- Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends.PLoS neglected tropical diseases · 2017Pooled it
- TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.bioRxiv : the preprint server for biology · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Article
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Phylogenetic Study of Local Patterns Influenza A(H3N2) Virus Transmission in a Semi-Isolated Population in a Remote Island in Japan Between 2011 and 2013.Influenza and other respiratory viruses · 2025Article
- Reading Yule in light of the history and present of macroevolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Tree balance in phylogenetic models.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Drug Resistance and Epidemiological Success of Modern Mycobacterium tuberculosis Lineages in Western India.The Journal of infectious diseases · 2025Article
- Integrating artificial intelligence with mechanistic epidemiological modeling: a scoping review of opportunities and challenges.Nature communications · 2025Article
- Exploring SNP filtering strategies: the influence of strict vs soft core.Microbial genomics · 2025Article
- Population genetics ofFrontiers in genetics · 2025Article
- A survey of chromosomal instability measures across mechanistic models.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Phylogenetic identification of influenza virus candidates for seasonal vaccines.Science advances · 2023Article
- A survey of CIN measures across mechanistic models.bioRxiv : the preprint server for biology · 2023Article
- ComparingEpidemiology and infection · 2023Article
- A Noncoding A-to-U Kozak Site Change Related to the High Transmissibility of Alpha, Delta, and Omicron VOCs.Molecular biology and evolution · 2023Article
- Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies.IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Superspreading in the emergence of COVID-19 variants.Trends in genetics : TIG · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
objectivesWhole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. METHODOLOGY: We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks.
resultsWe show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny's structure and find that computational classifiers based on these are capable of predicting an outbreak's transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. CONCLUSIONS AND IMPLICATIONS: There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.
Indexed as
Identifiers
What OpenQuestion holds
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.