ArticleMolecular biology and evolution2014
Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- The spatial structure of dengue transmission in Kamphaeng Phet Thailand.PLoS neglected tropical diseases · 2026Article
- Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics.PLoS pathogens · 2023Review
- Epidemiological inference for emerging viruses using segregating sites.Nature communications · 2023Article
- Markov genealogy processes.Theoretical population biology · 2022Article
- Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.Virus evolution · 2022Review
- Phylodynamic analysis in the understanding of the current COVID-19 pandemic and its utility in vaccine and antiviral design and assessment.Human vaccines & immunotherapeutics · 2021Article
- Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad.PLoS neglected tropical diseases · 2021Article
- Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics.PLoS neglected tropical diseases · 2020Article
- Evolutionary Virology at 40.Genetics · 2018Review
- Bayesian phylodynamic inference with complex models.PLoS computational biology · 2018Article
- Understanding dengue virus evolution to support epidemic surveillance and counter-measure development.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa.Virus evolution · 2018Article
- Challenges in dengue research: A computational perspective.Evolutionary applications · 2018Review
- Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa.Frontiers in genetics · 2018Review
- Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil.Scientific reports · 2017Article
- Identifying spatio-temporal dynamics of Ebola in Sierra Leone using virus genomes.Journal of the Royal Society, Interface · 2017Article
- Phylodynamic Inference across Epidemic Scales.Molecular biology and evolution · 2017Article
- Emerging Concepts of Data Integration in Pathogen Phylodynamics.Systematic biology · 2017Review
- Synchrony of Dengue Incidence in Ho Chi Minh City and Bangkok.PLoS neglected tropical diseases · 2016Article
- Identifying predictors of time-inhomogeneous viral evolutionary processes.Virus evolution · 2016Article
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3 authors.
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Abstract
Coalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches-often referred to as phylodynamic methods-have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred from viral genealogies often differ widely from those observed from other sources of epidemiological data, such as hospitalization records. We demonstrate how a modeling framework that allows for the direct fitting of mechanistic epidemiological models to genealogies can be used to test different hypotheses about what ecological factors cause phylodynamic inferences to differ from observed dynamics. We use this framework to test different hypotheses about why dengue serotype 1 (DENV-1) population dynamics in southern Vietnam inferred using existing phylodynamic methods differ from hospitalization data. Specifically, we consider how factors such as seasonality, vector dynamics, and spatial structure can affect inferences drawn from genealogies. The coalescent models we derive to take into account vector dynamics and spatial structure reveal that these ecological complexities can substantially affect coalescent rates among lineages. We show that incorporating these additional ecological complexities into coalescent models can also greatly improve estimates of historical population dynamics and lead to new insights into the factors shaping viral genealogies.
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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.