ArticleMolecular biology and evolution2019
Estimating Epidemic Incidence and Prevalence from Genomic Data.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Comparing methods to estimate time-varying reproduction numbers using genomic and epidemiological data.Infectious Disease Modelling · 2026Article
- Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process.bioRxiv : the preprint server for biology · 2026Article
- Viral emergence and pandemic preparedness in a One Health framework.Nature reviews. Microbiology · 2026Review
- Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.medRxiv : the preprint server for health sciences · 2025Article
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data.Molecular biology and evolution · 2025Article
- Estimating epidemic dynamics with genomic and time series data.Journal of the Royal Society, Interface · 2025Article
- Genomic Epidemiology for Estimating Pathogen Burden in a Population.Emerging infectious diseases · 2025Article
- Mechanistic yellow fever modelling under climate change in Brazil and beyond: Information gaps and future steps.Wellcome open research · 2025Article
- EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.PLoS computational biology · 2024Article
- Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Fitness, growth and transmissibility of SARS-CoV-2 genetic variants.Nature reviews. Genetics · 2023Review
- 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
- Bayesian phylodynamics reveals the transmission dynamics of avian influenza A(H7N9) virus at the human-live bird market interface in China.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Fitting stochastic epidemic models to gene genealogies using linear noise approximation.The annals of applied statistics · 2023Article
- The Occurrence Birth-Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology.Systematic biology · 2022Article
- Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.Nature reviews. Genetics · 2022Review
- Statistical Challenges in Tracking the Evolution of SARS-CoV-2.Statistical science : a review journal of the Institute of Mathematical Statistics · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death, or behavior change). Birth-death and coalescent processes have been introduced to model the stochastic dynamics of epidemic spread under common epidemiological models such as the SIS and SIR models and are successfully used to infer phylogenetic trees together with transmission (birth) and removal (death) rates. These methods either integrate analytically over past incidence and prevalence to infer rate parameters, and thus cannot explicitly infer past incidence or prevalence, or allow such inference only in the coalescent limit of large population size. Here, we introduce a particle filtering framework to explicitly infer prevalence and incidence trajectories along with phylogenies and epidemiological model parameters from genomic sequences and case count data in a manner consistent with the underlying birth-death model. After demonstrating the accuracy of this method on simulated data, we use it to assess the prevalence through time of the early 2014 Ebola outbreak in Sierra Leone.
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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.