Abstract
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 progeny virus, their existence and continued evolution during replication have critical implications for the 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-strand 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 viruses.
Highlights
Recombination is a common process amongst positive-strand RNA viruses and is a strong driver of virus evolution through the exchange of genomic sequences that can be directly advantageous or result in the removal of deleterious mutations [1,2,3]
There is evidence to suggest that inter-species recombination between members of the Enterovirus genera can occur [11,12], and has occurred [13], such examples are restricted to the exchange of the 5’ untranslated regions (UTR), a functionally constrained region that exhibits significant sequence plasticity [14,15]
The extreme rarity of inter-species recombinants isolated in nature suggests that recombination outside of the 5 UTR is severely restricted between viruses of different species
Summary
Recombination is a common process amongst positive-strand RNA viruses and is a strong driver of virus evolution through the exchange of genomic sequences that can be directly advantageous or result in the removal of deleterious mutations [1,2,3]. All enteroviruses have a single-stranded, positive-sense RNA genome, of approximately 7.5 Kb, encoding a single polyprotein flanked by 5 and 3 untranslated regions (UTR). There is evidence to suggest that inter-species recombination between members of the Enterovirus genera can occur [11,12], and has occurred [13], such examples are restricted to the exchange of the 5’ UTR, a functionally constrained region that exhibits significant sequence plasticity [14,15]
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