Identification of Orchid fleck virus by Reverse Transcriptase-Polymerase Chain Reaction and Analysis of Isolate Relationships

Using reverse transcription-polymerase chain reaction (RT-PCR) tests with a primer complementary to a region of its nucleoprotein gene together with a polydT/ SP6 primer, Orchid ¯eck virus (OFV) was detected in 34 samples of infected orchids of several di€erent genera from world-wide sources. The resulting DNA fragments were approximately 800 bp in length and their sequences were determined directly. Analysis of sequences of the major open reading frame (ORF) within the DNA fragments obtained showed the presence of two virus strains. The ®rst group was of two isolates, the original Japanese isolate from which the primers were derived and one from Germany, and the second group con- tained 33 isolates from four continents. The sequences of di€erent groups di€ered from one another by at least 15.6% (nucleotide) and 1.8% (amino-acid), but the within-group di€erences were much less (<1.7% di€er- ence). A search of the international nucleotide database with the OFV sequences showed them to be related, but distantly, to nucleoprotein regions of the genomes of four plant-infecting rhabdoviruses.