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Patterns of Recombination in Coronaviruses
Ricardo Soares1,2,3,4, Cristina P Vieira1,2, Jorge Vieira1,2
1Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
International Journal of Molecular Sciences
|June 26, 2025
Summary
Recombination in coronaviruses drives adaptation and evolution. This study reveals consistent patterns across species, influenced by gene position and selection, highlighting its role in generating viral variability.
Area of Science:
- Virology
- Molecular Biology
- Evolutionary Biology
Background:
- Coronaviruses (CoV) exhibit recombination, a key evolutionary mechanism.
- Recombination contributes to adaptation in CoV species, including those causing human epidemics and pandemics.
- Understanding recombination is crucial for predicting viral evolution and spread.
Purpose of the Study:
- To investigate the impact of recombination inference methods and sample sizes on coronaviridae recombination analysis.
- To characterize recombination patterns within and between 21 coronaviridae species.
- To explore the relationship between gene position, selection, and recombination rates in coronaviruses.
Main Methods:
- Analysis of recombination patterns across 21 coronaviridae species.
- Utilizing various recombination inference methods and sample sizes.
- Phylogenetic approaches to support recombination inferences.
- Correlation analysis between gene position, recombination rates, and selection.
Main Results:
- Recombination patterns show minimal variation across coronaviridae species.
- A positive correlation exists between gene position and recombination rates, indicating genomic variation.
- Within- and between-species recombination patterns differ, with module-type recombination prevalent except for Membrane and Nucleocapsid genes.
- Module-type recombination is prevalent for the Spike gene within species.
- A positive correlation between recombination and selection was observed.
Conclusions:
- Recombination is a significant driver of genetic variability in coronaviruses.
- Selection actively shapes intratypic recombination patterns.
- Understanding these processes is vital for managing coronavirus evolution and pathogenicity.
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