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

Department of Cellular and Developmental Biology, University of Rome `La Sapienza', Viale di Porta Tiburtina 28, 00185-Rome, Italy¹
Istituto Superiore di Sanità, 00161-Rome, Italy²

Author for correspondence: Raul Pérez Bercoff.Fax +39 06 446 2306. e-mail bercoff{at}caspur.it

In the course of experiments designed to assess the potential role of alternative open reading frames (ORF) present in the 5'-terminal untranslated region (5'-UTR) of poliovirus type 1 (Mahoney strain) genomic RNA, we came across a double mutation that completely abrogated the infectivity of full-length cDNA clones. The infectivity was rescued in trans by cotransfecting COS-1 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 the viral RNA revealed that the infectious viruses recovered were recombinants Lansing/Mahoney, with variable points of `crossing-over'. A novel mechanism of RNA–RNA recombination, which we propose to call `primer alignment-and-extension', is described that would explain the high rate of recombination of RNA viruses observed in natural conditions.

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