ArticleVirus evolution2019
Inferring putative transmission clusters with Phydelity.
Article in Virus evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- Identification of ESBL-Producing Enterobacterales From Vegetable Plants: Preliminary Findings From a Small Cross-Sectional Study in a Rural Area of Madagascar.Environmental microbiology reports · 2025Article
- Competition between transmission lineages mediated by human mobility shapes seasonal influenza epidemics in the US.Nature communications · 2025Article
- Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.medRxiv : the preprint server for health sciences · 2024Article
- Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus.Virologica Sinica · 2024Article
- One Health compartment analysis of ESBL-producing Escherichia coli reveals multiple transmission events in a rural area of Madagascar.The Journal of antimicrobial chemotherapy · 2023Article
- From components to communities: bringing network science to clustering for molecular epidemiology.Virus evolution · 2023Article
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.PLoS computational biology · 2022Article
- Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization.Microorganisms · 2022Article
- SARS-CoV-2: Two Years in the Pandemic: What Have We Observed from Genome Sequencing Results in Lithuania?Microorganisms · 2022Article
- Relationship and distribution of Salmonella enterica serovar I 4,[5],12:i:- strain sequences in the NCBI Pathogen Detection database.BMC genomics · 2022Article
- Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach.Frontiers in microbiology · 2022Article
- Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.Virus evolution · 2022Article
- Spatiotemporal Phylodynamics of Hepatitis C Among People Who Inject Drugs in India.Hepatology (Baltimore, Md.) · 2021Article
- Serologic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Infection Among Hospital Health Care Workers.JAMA network open · 2021Article
- Identification of Hidden Population Structure in Time-Scaled Phylogenies.Systematic biology · 2020Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current phylogenetic clustering approaches for identifying pathogen transmission clusters are limited by their dependency on arbitrarily defined genetic distance thresholds for within-cluster divergence. Incomplete knowledge of a pathogen's underlying dynamics often reduces the choice of distance threshold to an exploratory, ad hoc exercise that is difficult to standardise across studies. Phydelity is a new tool for the identification of transmission clusters in pathogen phylogenies. It identifies groups of sequences that are more closely related than the ensemble distribution of the phylogeny under a statistically principled and phylogeny-informed framework, without the introduction of arbitrary distance thresholds. Relative to other distance threshold- and model-based methods, Phydelity outputs clusters with higher purity and lower probability of misclassification in simulated phylogenies. Applying Phydelity to empirical datasets of hepatitis B and C virus infections showed that Phydelity identified clusters with better correspondence to individuals that are more likely to be linked by transmission events relative to other widely used non-parametric phylogenetic clustering methods without the need for parameter calibration. Phydelity is generalisable to any pathogen and can be used to identify putative direct transmission events. Phydelity is freely available at https://github.com/alvinxhan/Phydelity.
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