Use of highly conserved motifs in plant virus RNA polymerases as the tags for specific detection of carmovirus-related RNA-dependent RNA polymerase genes.

Two highly degenerate primers for sequence-specific amplification and cloning of a 510-nucleotide-long segment of RNA-dependent RNA-polymerase (RdRp) genes were selected and synthesized on the basis of available plant carmovirus-like viral RdRp sequences. These primers were shown to be efficient in PCR screening of different RdRp genes including those of carmoviruses, dianthoviruses, and tombusviruses. In particular, they were used for amplification, cloning, and sequencing of an RdRp gene fragment of an isometric plant virus with unknown evolutionary relationships, pelargonium flower break virus (PFBV). Alignment of the respective nucleotide and amino acid sequences indicates a very close similarity between PFBV and carnation mottle virus, the type member of carmoviruses.