Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses.

Recombination is a driving force for the emergence, evolution and virulence/epidemics of viruses, comprising the Enterovirus genus of the Picornaviridae family, important for human and animal health. By analyzing 2949 complete genomes/coding sequences, we provide a thorough and up-to-date overview of the genome-wide patterns and hotspots of intertypic recombination between the genogroups of this genus. Two prominent recombination hotspots are identified/verified, at the 5'UTR-capsid region junction, and at the beginning of the P2 region. In general, P2 was enriched in recombination events. Key phylogenetic groups implicated in recombination events are E71 and CVA6 in Enterovirus A species, E30 and E6 in Enterovirus B species, polioviruses 1 and 2 in Enterovirus C species. In addition, many events involve recombination partners that have not been sequenced yet, thus strongly suggesting a large environmental reservoir of genetic variation with a high potential for the emergence of new modified pathogens by recombination.