Isolation and identification of inter-species Enterovirus recombinant genomes

Positive-strand RNA virus evolution is partly attributed to the process of recombination. Although common between closely genetically related viruses, such as within species of the Enterovirus genus of the Picornaviridae family, inter-species recombination is rarely observed in nature. Recent studies have shown recombination is a ubiquitous process resulting in a wide range of recombinant genomes and progeny viruses. While not all recombinant genomes yield infectious virus progeny, their existence and continued evolution during replication has critical implications for evolution of the virus population. In this study we utilised an in vitro recombination assay to demonstrate inter-species recombination events between viruses from four enterovirus species’, A-D. We show that inter-species recombinant genomes are generated in vitro with polymerase template-switching events occurring within the virus polyprotein coding region. However, these genomes did not yield infectious progeny virus. Analysis and attempted recovery of a constructed recombinant cDNA revealed a restriction in positive- but not negative -strand RNA synthesis, indicating a significant block in replication. This study demonstrates the propensity for inter-species recombination at the genome level but suggests that significant sequence plasticity would be required in order to overcome blocks in the virus life cycle and allow for the production of infectious virus.