Files and scripts for McCormick, et al. "The Role of Recombination in the Diversification of Enteroviruses"
Lauren McCormick1,2, Peter Simmonds3, Patrick T. Dolan1*, and Aris Katzourakis2* 1 Quantitative Virology and Evolution Unit, Laboratory of Viral Diseases, NIH-NIAID Division of Intramural Research, Bethesda, MD, USA 2 Department of Biology, University of Oxford, Oxford, UK 3 Institute of Biomedicine, University of Turku, Turku, Finland
Corresponding Authors Emails: patrick.dolan@nih.gov aris.katzourakis@biology.ox.ac.uk
Human enteroviruses are a collection of four RNA virus species within the Enterovirus genus that cause a range of clinical manifestations. Enteroviruses are genetically and antigenically diverse with each species containing several genetically-defined and antigenically-distinct types within it. Previously, it has been suggested that, due to pervasive recombination, enteroviruses may be best conceptualized as collections of capsids and nonstructural proteins that evolve independently. We employed complementary entropy, network, and phylogenetic approaches to quantify the genetic diversity and recombination frequencies of each species. We show that recombination differs substantially between species and identify a strong correlation between recombination and the difference in diversity between the capsid and nonstructural proteins of a given enterovirus species. Given this finding, we propose a model in which recombination does not simply decouple the evolution of genomic regions, but rather has a profound impact on the diversification patterns of human enteroviruses due to functional constraints on the set of compatible combinations.