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A Bayesian approach to infer recombination patterns in coronaviruses.
Nicola F Müller1, Kathryn E Kistler2,3, Trevor Bedford2,3,4
1Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. nicola.felix.mueller@gmail.com.
Nature Communications
|July 20, 2022
Summary
Recombination is common in coronaviruses, challenging traditional phylogenetic methods. This study introduces a new network approach to track evolving and recombining viruses like SARS-CoV-2.
Area of Science:
- Virology
- Computational Biology
- Evolutionary Biology
Background:
- Phylogenetic and phylodynamic methods are crucial for tracking pathogen spread and evolution, as seen during the SARS-CoV-2 pandemic.
- These methods assume a simple branching tree model for pathogen history, which is violated by recombination.
- Recombination complicates the study of evolving pathogens, including coronaviruses.
Purpose of the Study:
- To develop a novel computational method for inferring recombination networks from genetic sequence data.
- To investigate the prevalence and impact of recombination in the evolutionary history of SARS-like coronaviruses.
- To explore the relationship between recombination rates and adaptation in human seasonal coronaviruses.
Main Methods:
- Introduced a Markov chain Monte Carlo (MCMC) approach for inferring recombination networks.
- Utilized a template switching model to represent recombination events.
- Applied the method to genetic sequence data of SARS-like and human seasonal coronaviruses.
Main Results:
- Demonstrated that recombination is highly prevalent in the evolutionary history of SARS-like coronaviruses.
- Showed significant variation in recombination rates across the genomes of human seasonal coronaviruses (229E, OC43, NL63).
- Found a correlation between recombination rates and rates of adaptation in human seasonal coronaviruses.
Conclusions:
- Recombination is a major factor in coronavirus evolution, necessitating advanced analytical methods.
- Recombination may confer fitness advantages to human seasonal coronaviruses.
- The developed method provides a foundation for future phylogenetic tracking of rapidly evolving and recombining viruses, including SARS-CoV-2.
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