NONHOMOLOGOUS RNA RECOMBINATION DURING NEGATIVE-STRAND SYNTHESIS OF FLOCK HOUSE VIRUS-RNA

During sequential replicative passages of viral RNA from the nodavirus flock house virus, spontaneous deletion of RNA sequences occurred fre quently. Families of deleted RNA molecules were derived from both segm ents of the bipartite viral genome and found to contain single, double , or triple deletions. These deletions were attributed to template swi tching by the flock house virus RNA replicase, resulting in recombinat ion between distant sequences and excision of the intervening nucleoti des. From sequence analysis of the recombination junctions, we conclud ed that the process of template switching was influenced by both the p rimary sequence and the secondary structure of the RNA and that it occ urred predominantly during synthesis of RNA negative strands.