Chimeric Sindbis-Ross River viruses to study interactions between alphavirus nonstructural and structural regions

Sindbis virus and Ross River virus are alphaviruses whose nonstructural proteins share 64% identity and whose structural proteins share 48% identity. Starting from full-length cDNA clones of both viruses, we have generated two reciprocal Sindbis-Ross River chimeric viruses in which the structural and nonstructural regions have been exchanged. These chimeric viruses replicate readily in several cell lines. Both chimeras grow more poorly than do the parental viruses, with the chimera containing Sindbis virus nonstructural proteins and Ross River virus structural proteins growing considerably better in both mosquito and Vero cell lines than the reciprocal chimera does. The reduction in replicative capacity in comparison with the parental viruses appears to result at least in part from a reduction in RNA synthesis, which suggests that the structural proteins or sequence elements within the structural region interact with the nonstructural proteins or sequence elements within the nonstructural region, that these interactions are required for efficient RNA replication, and that these interactions are suboptimal in the chimeras. The chimeras are able to infect mice, but their growth is attenuated. Western equine encephalitis virus, a virus widely distributed throughout the Americas, has been previously shown to have arisen by natural recombination between two distinct alphaviruses, but other naturally occurring recombinant alphaviruses have not been found. The present results suggest that most nonstructural/structural chimeras that might arise by natural recombination will be viable but that interactions between different regions of the genome, some of which were previously known but some of which remain unknown, limit the ability of such recombinants to become established.