ArticleNature communications2020
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.
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 119 papers, 2 of them syntheses that pooled it.
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119 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Effects of COVID-19 Non-Pharmacological Interventions on Dengue Infection: A Systematic Review and Meta-Analysis.Frontiers in cellular and infection microbiology · 2022Pooled it
- Pooled it
- Genomic epidemiology of dengue virus serotype 3 lineage 3III_B.3.2 in Brazil: insights into its spread and dengue severity amid co-circulation of multiple dengue serotypes.Lancet regional health. Americas · 2026Article
- Global source-sink dynamics of dengue viruses and epidemic establishment in areas on the fringe of endemic transmission.National science review · 2026Article
- Genomic surveillance of a deeply sampled local population reveals age-specific drivers of RSV transmission.medRxiv : the preprint server for health sciences · 2026Article
- Global approaches to infectious disease surveillance and modeling.Nature medicine · 2026Review
- Distinct genomic trajectory among invasive Salmonella Typhimurium ST313 infections.Nature communications · 2026Article
- Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa.Virus evolution · 2026Article
- Genomic characterization of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b into wild seabirds from coastal Ecuador.Frontiers in microbiology · 2026Article
- Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.medRxiv : the preprint server for health sciences · 2025Article
- Genomics in Epidemiology and Disease Surveillance: An Exploratory Analysis.Life (Basel, Switzerland) · 2025Review
- Navigating Sampling Bias in Discrete Phylogeographic Analysis: Assessing the Performance of an Adjusted Bayes Factor.Molecular biology and evolution · 2025Article
- TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.bioRxiv : the preprint server for biology · 2025Article
- BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference.Nature methods · 2025Article
- Multiple introductions of equine influenza virus into the United Kingdom resulted in widespread outbreaks and lineage replacement.PLoS pathogens · 2025Article
- Estimating epidemic dynamics with genomic and time series data.Journal of the Royal Society, Interface · 2025Article
- Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count statistic.Communications medicine · 2025Article
- Unveiling the Dynamics of SARS-CoV-2 Gamma and Delta Waves in Paraná, Brazil - Delta Displacing a Persistent Gamma Through Alternative Routes of Dispersal.Journal of medical virology · 2025Article
- Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus.Science advances · 2025Article
- Retrospective detection of severe fever with thrombocytopenia syndrome virus (SFTSV) revises timeline of emergence in Thailand.Virus evolution · 2025Article
59 more citing papers are in PubMed but not listed here.
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13 authors.
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Abstract
Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.
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