'Primer alignment-and-extension': a novel mechanism of viral RNA recombination responsible for the rescue of inactivated poliovirus cDNA clones

In the course of experiments designed to assess the potential role of alter native open reading frames (ORF) present in the 5'-terminal untranslated re gion (5'-UTR) of poliovirus type 1 (Mahoney strain) genomic RNA, we came ac ross a double mutation that completely abrogated the infectivity of full-le ngth cDNA clones. The infectivity was rescued in trans by cotransfecting CO S-I cells with short RNA transcripts of the wild-type 5'-UTR of poliovirus type 2 Lansing, provided a free 3'-OH was available. Direct sequencing of t he viral RNA revealed that the infectious viruses recovered were recombinan ts Lansing/Mahoney, with variable points of 'crossing-over'. A novel mechan ism of RNA-RNA recombination, which we propose to call 'primer alignment-an d-extension !, is described that would explain the high rate of recombinati on of RNA viruses observed in natural conditions.