The NV genes of fish rhabdoviruses: development of RNase protection assays for rapid assessment of genetic variation.

: The genomic RNA of the fish rhabdovirus infectious hematopoietic necrosis virus (IHNV) contains a small NV gene which is not present in any other rhabdoviruses characterized to date. We have constructed a plasmid which carries a full length cDNA copy of the IHNV NV gene between 2 RNA polymerase promoters such that plus-sense and minus-sense RNA transcripts of the IHNV NV gene can be synthesized. These were used to develop an RNase protection assay which was capable of detecting as little as 1-5 ng of NV mRNA or genomic RNA. RNA from tissue culture cells infected with 3 different strains of IHNV showed distinct, diagnostic cleavage patterns reflecting sequence variation in their NV genes.