ArticleVirus evolution2019
Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Enriching Public Pathogen Genomic Records With Patient Metadata: Quantitative Study and Exploratory Case Analysis.JMIR bioinformatics and biotechnology · 2026Article
- A Metadata-Driven Framework for Strengthening Pathogen Genomics Lessons from SARS-CoV-2.medRxiv : the preprint server for health sciences · 2025Article
- Phylodynamics for Human Immunodeficiency Virus Prevention: A Miami-Dade County Case Study.The Journal of infectious diseases · 2025Article
- From emergence to endemicity of highly pathogenic H5 avian influenza viruses in Taiwan.Nature communications · 2024Article
- Phylodynamics of HIV in the Mexico City Metropolitan Region.Journal of virology · 2022Article
- Accommodating sampling location uncertainty in continuous phylogeography.Virus evolution · 2022Review
- H5Nx Viruses Emerged during the Suppression of H5N1 Virus Populations in Poultry.Microbiology spectrum · 2021Article
- Dynamics and Dispersal of Local Human Immunodeficiency Virus Epidemics Within San Diego and Across the San Diego-Tijuana Border.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study.Viruses · 2021Review
- Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST.Current protocols · 2021Article
- GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography.Bioinformatics (Oxford, England) · 2020Article
- Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.Nature communications · 2020Article
- Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.bioRxiv : the preprint server for biology · 2020Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Discrete phylogeography using software such as BEAST considers the sampling location of each taxon as fixed; often to a single location without uncertainty. When studying viruses, this implies that there is no possibility that the location of the infected host for that taxa is somewhere else. Here, we relaxed this strong assumption and allowed for analytic integration of uncertainty for discrete virus phylogeography. We used automatic language processing methods to find and assign uncertainty to alternative potential locations. We considered two influenza case studies: H5N1 in Egypt; H1N1 pdm09 in North America. For each, we implemented scenarios in which 25 per cent of the taxa had different amounts of sampling uncertainty including 10, 30, and 50 per cent uncertainty and varied how it was distributed for each taxon. This includes scenarios that: (i) placed a specific amount of uncertainty on one location while uniformly distributing the remaining amount across all other candidate locations (correspondingly labeled
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