ArticleNature communications2020
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review.The Lancet. Microbe · 2025Pooled it
- HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.Research square · 2026Article
- Genomic epidemiology and phylogeographic reconstruction of West Nile virus 2 in Italy from 2011 to 2023.One health (Amsterdam, Netherlands) · 2026Article
- HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.medRxiv : the preprint server for health sciences · 2026Article
- Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology.Current biology : CB · 2026Article
- Emergence of D1.1 reassortant H5N1 avian influenza viruses in North America.bioRxiv : the preprint server for biology · 2026Article
- SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.Bioinformatics (Oxford, England) · 2026Article
- Genomic Epidemiology of West Nile Virus in Paris.JAMA network open · 2026Article
- Mapping the bird risk index for West Nile virus in Europe and its relationship with disease occurrence in humans.Epidemiology and infection · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology.bioRxiv : the preprint server for biology · 2026Article
- Continuous phylogeography reveals shifting environmental drivers of highly pathogenic avian influenza H5 spread in Italy, 2016-23.Virus evolution · 2026Article
- Phylodynamic analyses reveal persistence and extensive intermixing of Usutu virus in the Netherlands.Virus evolution · 2026Article
- Phylogenetic insights into the transmission dynamics of arthropod-borne viruses.Nature reviews. Genetics · 2026Review
- Genomic characterization of a severe West Nile Virus transmission season using a single reaction amplicon sequencing approach.PLoS neglected tropical diseases · 2026Article
- Historical and current spatiotemporal patterns of wild and vaccine-derived poliovirus spread.Nature microbiology · 2025Article
- Host-Microbe Interactions: Prospects of Machine Learning and Deep Learning Technologies in Animal Viral Disease Management.Veterinary sciences · 2025Review
- Active West Nile virus transmission in Brazil: an epidemiological study.Lancet regional health. Americas · 2025Article
- larch: mapping the parsimony-optimal landscape of trees for directed exploration.bioRxiv : the preprint server for biology · 2025Article
- Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review.The Lancet. Microbe · 2025Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.
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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.