Picornaviruses as a Model for Studying the Nature of RNA Recombination

Abstract

The possibility of recombination should obviously depend on the fate and status of the viral RNA in the infected cell. Two fundamentally different but not mutually exclusive mechanisms of RNA recombination were proposed at an early step of investigation of this phenomenon. The preciseness of recombination may also be interpreted in favor of the replicative model. Perhaps the most formidable problem of replicative RNA recombination is finding the proper anchoring site on the secondary template. The crossovers during RNA recombination can be distributed over the whole viral genome, indicating that no specific sequences or structures are required. Numerous examples of natural interserotype picornavirus recombinants have been described in this chapter. The chapter focuses on an aspect especially important from the evolutionary perspective, namely, the possible role of RNA recombination in viral speciation. Remarkably, IRESs of some picornaviruses exhibit marked structural similarities to respective cis-elements of viruses belonging to other families of RNA viruses, e.g., Flaviviridae. In addition to picornaviruses, it is very common in nidoviruses, in particular, coronaviruses and toroviruses. It should be noted that mechanisms of RNA recombination other than the aforementioned classical template switch and apparently host protein-dependent nonreplicative mode have been proposed to occur in some systems. Another promising approach consists of using small interfering RNA to identify host genes involved in RNA recombination, a technique not yet attempted for picornaviruses.