ArticleNature communications2022
A Bayesian approach to infer recombination patterns in coronaviruses.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 55 citations in OpenAlex.
- Evaluation of Molecular Phylogenetic Trees by an Information-Theoretic Metric.Journal of molecular evolution · 2026Article
- Synthetic Integration of an FCS into Coronaviruses-Hype or an Unresolved Biorisk? An Integrative Analysis of DNA Repair, Cancer Research, Drug Development, and Escape Mutant Traits.Life (Basel, Switzerland) · 2026Article
- Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.PLoS pathogens · 2025Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
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- 'Vivaldi': an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2.Microbial genomics · 2025Article
- The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.Cell · 2025Article
- Current Evolutionary Dynamics of Porcine Epidemic Diarrhea Virus (PEDV) in the U.S. a Decade After Introduction.Viruses · 2025Article
- SARS-CoV-2: The Interplay Between Evolution and Host Immunity.Annual review of immunology · 2025Review
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Phylogeographic Characterizations of Recent (2015-2023) Senecavirus A Isolates from Canada.Viruses · 2025Article
- Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses.Npj viruses · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Whole-genome demography of COVID-19 virus during its pandemic period and on "panvalent" vaccine design.Scientific reports · 2024Article
- Seasonal human coronaviruses OC43, 229E, and NL63 induce cell surface modulation of entry receptors and display host cell-specific viral replication kinetics.Microbiology spectrum · 2024Article
- Data-driven recombination detection in viral genomes.Nature communications · 2024Article
- SARS-CoV-2 biology and host interactions.Nature reviews. Microbiology · 2024Review
- Genetic characterization and pathogenicity in a mouse model of newly isolated bat-originated mammalian orthoreovirus in South Korea.Microbiology spectrum · 2024Article
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3 authors at 3 institutions in 2 countries.
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Abstract
As shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. This makes it problematic to apply phylogenetic methods to study recombining pathogens, including, for example, coronaviruses. Here, we introduce a Markov chain Monte Carlo approach that allows inference of recombination networks from genetic sequence data under a template switching model of recombination. Using this method, we first show that recombination is extremely common in the evolutionary history of SARS-like coronaviruses. We then show how recombination rates across the genome of the human seasonal coronaviruses 229E, OC43 and NL63 vary with rates of adaptation. This suggests that recombination could be beneficial to fitness of human seasonal coronaviruses. Additionally, this work sets the stage for Bayesian phylogenetic tracking of the spread and evolution of SARS-CoV-2 in the future, even as recombinant viruses become prevalent.
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