Sequence mutation is the most common mechanism for the evolution of RNA viruses. However, major changes of viral genotype often involve exchanges of RNA segments between viruses, as exemplified by influenza virus evolution. For viruses with non-segmented RNA genomes, genetic exchange was previously thought to be rare. In recent years, however, sequence analyses of viral RNA revealed that many RNA viruses have apparently evolved from other viruses by exchange or rearrangement of genome sequences. Furthermore, experimental systems have been established for several viruses, in which recombination could be demonstrated between two viral RNAs. Thus, genetic recombination appears to be more important in RNA virus evolution than was previously realized.

Mechanistically, RNA recombination is similar to the generation of defective-interfering (DI) RNA, as both involve polymerase jumping during RNA synthesis. Many RNA viruses generate DI RNA and, thus, can potentially undergo genetic recombination. However, recombination has not been commonly observed. Therefore, there may be genetic restriction on RNA recombination or selective disadvantage for recombinant viruses.

RNA recombination in experimental systems with animal viruses

Evidence for RNA recombination was first obtained in classical genetic studies involving polioviruses (family Picornaviridae). When cells were co-infected with virus resistant to the antibodies in horse or cattle serum and virus resistant to guanidine, viruses resistant to both antibody and guanidine could be isolated at a higher frequency than by spontaneous mutation, suggesting that recombination may have occurred (Hirst, 1962; Ledinko, 1963). Similar observations were made on foot-andmouth disease virus (FMDV) (Pringle, 1965).