ArticleBMC bioinformatics2016
Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it, 123 citations in OpenAlex.
- Influence of Host and Landscape-Associated Factors in the Infection and Transmission of Pathogens: The Case of Directly Transmitted Virus in Mammals.Veterinary medicine and science · 2025Pooled it
- Spatiotemporal diffusion of the 2024 Oropouche outbreak in Cuba.Nature medicine · 2026Article
- Genomic epidemiology and phylogeographic reconstruction of West Nile virus 2 in Italy from 2011 to 2023.One health (Amsterdam, Netherlands) · 2026Article
- Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology.Current biology : CB · 2026Article
- SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.Bioinformatics (Oxford, England) · 2026Article
- Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology.bioRxiv : the preprint server for biology · 2026Article
- Phylodynamic analyses reveal persistence and extensive intermixing of Usutu virus in the Netherlands.Virus evolution · 2026Article
- Continuous phylogeography reveals shifting environmental drivers of highly pathogenic avian influenza H5 spread in Italy, 2016-23.Virus evolution · 2026Article
- Molecular epidemiology and multi-scale drivers of piscine myocarditis virus dispersal in salmon aquaculture.Virus evolution · 2026Article
- Phylogenetic insights into the transmission dynamics of arthropod-borne viruses.Nature reviews. Genetics · 2026Review
- Historical and current spatiotemporal patterns of wild and vaccine-derived poliovirus spread.Nature microbiology · 2025Article
- Analysis of the prevalence, spread, and mutation patterns of SARS-CoV-2 variants: data from COVID-19 testing expansion strategy study in salvador, Northeast Brazil.Scientific reports · 2025Article
- Comparative performance of viral landscape phylogeography approaches.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genesis and Spread of Novel Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Genotype EA-2023-DG Reassortant, Western Europe.Emerging infectious diseases · 2025Article
- Tracing more than two decades of Japanese encephalitis virus circulation in mainland China.Journal of virology · 2025Article
- Article
- Detection of divergent Orthohantavirus tulaense provides insight into wide host range and viral evolutionary patterns.Npj viruses · 2024Article
- Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa.Emerging microbes & infections · 2024Article
- How fast are viruses spreading in the wild?PLoS biology · 2024Article
- Ecological Changes Exacerbating the Spread of Invasive Ticks has Driven the Dispersal of Severe Fever with Thrombocytopenia Syndrome Virus Throughout Southeast Asia.Molecular biology and evolution · 2024Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among infections that may not otherwise be evident. However, a remaining challenge is to develop an analytical framework that can test hypotheses about the effect of environmental variables on pathogen spatial spread. Recent phylogeographic approaches can reconstruct the history of virus dispersal from sampled viral genomes and infer the locations of ancestral infections. Such methods provide a unique source of spatio-temporal information, and are exploited here.
resultsWe present and apply a new statistical framework that combines genomic and geographic data to test the impact of environmental variables on the mode and tempo of pathogen dispersal during emerging epidemics. First, the spatial history of an emerging pathogen is estimated using standard phylogeographic methods. The inferred dispersal path for each phylogenetic lineage is then assigned a "weight" using environmental data (e.g. altitude, land cover). Next, tests measure the association between each environmental variable and lineage movement. A randomisation procedure is used to assess statistical confidence and we validate this approach using simulated data. We apply our new framework to a set of gene sequences from an epidemic of rabies virus in North American raccoons. We test the impact of six different environmental variables on this epidemic and demonstrate that elevation is associated with a slower rabies spread in a natural population.
conclusionThis study shows that it is possible to integrate genomic and environmental data in order to test hypotheses concerning the mode and tempo of virus dispersal during emerging epidemics.
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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.