ArticleProceedings of the National Academy of Sciences of the United States of America2024
Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- PhyloCNN: Improving Tree Representation and Neural Network Architecture for Deep Learning from Trees in Phylodynamics and Diversification Studies.Systematic biology · 2026Article
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- The emergence of Clade IIb and Ib mpox viruses: a state-of-the-art review.Annals of medicine and surgery (2012) · 2026Review
- Review
- Estimating epidemic dynamics with genomic and time series data.Journal of the Royal Society, Interface · 2025Article
- Accounting for contact tracing in epidemiological birth-death models.PLoS computational biology · 2025Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach.Molecular biology and evolution · 2024Article
- Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.Nature reviews. Genetics · 2022Review
- Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.Nature communications · 2022Article
- Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.Nature communications · 2022Article
- A computationally tractable birth-death model that combines phylogenetic and epidemiological data.PLoS computational biology · 2022Article
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4 authors.
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Abstract
We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations (10 countries and one cruise ship), based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, the reproductive numbers for 10 (out of 15) of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.8. These estimates provide a view which is complementary to that provided by those based on traditional line listing data. The genomic-based view is arguably less susceptible to biases resulting from differences in testing protocols, testing intensity, and import of cases into the community of interest. In the analyses reported here, the genomic data primarily provide information regarding which samples belong to a particular outbreak. We observe that once these outbreaks are identified, the sampling dates carry the majority of the information regarding the reproductive number. Finally, we provide genome-based estimates of the cumulative number of infections for each outbreak. For 7 out of 11 of the populations studied, the number of confirmed cases is much bigger than the cumulative number of infections estimated from the sequence data, a possible explanation being the presence of unsequenced outbreaks in these populations.
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