We have developed a platform that combines genetics, biochemical and computational approaches to examine the role of recombination on the evolution of RNA virus. The integration of recombination defective variants, experimental and computational tools will allow liking recombination rates on the ability of a virus population to evolve and adapt to various selective pressures, including in infected animals. This may allow better mechanistic understanding of the recombination process, as well as the role of recombination in evolution and adaptation.
A key survival strategy of RNA viruses is their ability to populate a diverse sequence space that creates a 'cloud' of potentially beneficial mutations at the population level affording the viral quasispecies a greater probability of evolving and adapting to new environments and challenges during infection. One established mechanism relies on high mutation rates of viral RNA replication. It is becoming increasingly clear that an additional mechanism to expand and retain genetic diversity relies on RNA recombination that enables exchange of genetic material between RNA viruses. Furthermore, these recombination mechanisms may provide viruses with two advantages: (i) purge their genomes of accumulated deleterious changes and (ii) create or spread beneficial combinations of mutations in an efficient manner. Despite its importance, the mechanism of viral recombination is poorly understood. Genetic experiments have suggested that homologous RNA recombination occurs by dissociation of the RNA-dependent RNA polymerase and nascent RNA strand before replication completes, and the re-association of that nascent strand-polymerase complex with another template. However, this mechanism remains largely untested. We propose to combine genetics, biochemistry and ultra-deep sequencing approaches with classical virology experiments in cell culture and animal models to define the mechanism of viral recombination and determine its role in virus evolution and pathogenesis. A central hypothesis in this application is that RNA recombination plays a critical role in the generation of virus diversity and evolution and is critial for viral fitness and pathogenesis.