Determinants of Recombination in RNA viruses

Recombination is a driving force in the evolution of RNA viruses and the understanding of this phenomenon is critical to improving the genetic stability of live attenuated vaccines. To identify what sequence motifs are responsible for non-random patterns of mutation within similar viruses, a synthetic poliovirus 1 virus was generated with densely-spaced synonymous mutations to act as markers and a recombination map was created using a novel deep sequencing technique. This map identified multiple sequence motifs that were associated with increased or decreased local recombination, which were then engineered into a new virus to successfully modulate recombination. In contrast to frequent recombination events between strains, inter-family recombination is rare. Due to the small number of known inter-family recombinants, little is know about the determinants either for the generation of such recombinants or their viability. Deep sequencing-based viral discovery techniques were employed to discover 51 new virus species, four of which represent inter-family recombinants between the nodavirus-like superfamily and the tetraviridae. These recombination events coincided with switches between bipartite and monopartitie genome organization. No inter-family recombination events were observed in the order Picornavirales despite frequent observations of known and novel species, suggesting a predisposition towards such recombination in the Nodavirales and Tetraviridae. These studies demonstrate new techniques to study viral recombination at all taxonomic levels, describe new motifs associated with recombination and set the stage for viral engineering to control recombination