Nodavirus RNA Recombination

The genomes of nodaviruses contain two positive-sense RNAs that encode the RNA polymerase and capsid proteins, respectively. In this system, recombination occurs when the polymerase switches templates during negative strand RNA synthesis, usually at a site where the nascent strand can form 4–5 bp with the acceptor template. Two other factors influence the choice of recombination site: (1) template secondary structure, which is predicted to hold the recombination sites in close proximity; and (2) similarity of the cross-over site to an origin of replication, which suggests that the polymerase interacts directly with the acceptor template.