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Molecular Characterization of Naturally Occurring RNA1 Recombinants of the Comovirus Bean pod mottle virus

The Bean pod mottle virus, a member of the genus Comovirus, has a bipartite genome consisting of RNA1 and RNA2. We previously reported the occurrence in nature of two distinct subgroups of BPMV strains (subgroups I and II), as well as reassortants between the two subgroups. Here, we report on the isolation and molecular characterization of RNA1 recombinants from soybean plants infected with the partial diploid reassortant strain IL-Cb1, which induces very severe symptoms on soybean. cDNA cloning and sequencing of RNA1 from strain IL-Cb1 revealed the presence of chimeric and mosaic recombinant RNA1s. The full-length mosaic and chimeric recombinant RNA1s were infectious and induced mild symptoms on soybean. Although the recombinant RNA1 accumulated to high levels in the absence of wild-type RNA1, its accumulation level was low in mixed infections with wild-type RNA1. Recombinant RNA1 molecules with similar structures to the naturally occurring recombinant RNA1s were generated in soybean after four passages following inoculation with RNA1 transcripts derived from cDNAs of two distinct strains. This suggests that recombination events are frequent and that a recombination hot spot exists. Sequence analysis of the recombination region showed that it has AU-rich sequences characteristic of recombination hot spots.