Evolution of Picornaviridae: An examination of phylogenetic relationships and cophylogeny

Picornaviruses are responsible for some of the most common and debilitating illnesses affecting humans and animals worldwide. To extend our knowledge of the evolution of picornaviruses and their molecular epidemiology, phylogenetic relationships among 11 genera and the unassigned seal picornavirus type 1 were estimated from the conserved proteins 2C, 3Cpro, and 3Dpol. Each gene was analyzed separately and as a combined dataset. Different tree topologies were recovered from each gene. However, their sequences were determined to be combinable based on our finding of no recombination among genera and failing to reject the hypothesis of homogeneity among datasets using ILD tests. The combined data tree topology was identical to the 3Dpol gene tree; a topology largely consistent with previous phylogenetic hypotheses based on 3Dpol and the coding genome. Phylogenetic trees estimated from six phenotypic characters were not congruent with those recovered from molecular datasets; further supporting the hypothesis that viral phenotypes are highly plastic. Finally, we tested the hypothesis of host–virus cophylogeny. Both global and individual tests of the relationships between host and virus trees failed to detect a significant association. These results emphasize the importance of horizontal transmission among host species for picornavirus diversification rather than vertical transmission accompanying speciation.