Patterns of Recombination in Coronaviruses

By bringing together different variant combinations, recombination can contribute to adaptation in <i>Coronaviridae</i> species, some of which infect humans, and have given rise to epidemics and a pandemic. Therefore, in this work, the impact of the use of different recombination inference methods and sample sizes is addressed using data from 21 <i>Coronaviridae</i> species, and recombination inferences are further supported using a phylogenetic approach. Recombination patterns are shown not to vary greatly between species. A positive correlation is found between gene position and recombination rates, suggesting intrinsic variation in recombination rates along the genome. Within and between species recombination patterns are shown to differ, the module type being the most prevalent between species except for the <i>Membrane</i> and <i>Nucleocapsid</i> genes, whose products are known to interact and thus must co-evolve, explaining why the two genes are often recombined as one unit. It is also shown that within species, the module type is prevalent for the <i>Spike</i> gene only. Moreover, a positive correlation between recombination and selection is here reported. Therefore, intratypic recombination patterns are also shaped by selection. Recombination may thus be an important source of variability upon which selection can act.