Complete nucleotide sequence of the hirame rhabdovirus, a pathogen of marine fish

Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed for the hirame rhabdovirus (HIRRV) CA-9703 strain from Korea, and the DNA was sequenced. The 3'-end of genomic RNA was cloned by poly(A)-tailing of the genomic RNA before reverse transcription, and the 5'-end of the genome was cloned by poly(G)- or poly(C)-tailing of the first strand, followed by PCR. The remainder of the genomic DNA was cloned by reverse transcription-polymerase chain reaction using primers that were based on the published rhabdovirus sequences. The complete genome of HIRRV CA-9703 strain comprises 11,034 nucleotides and encodes six genes in the order of: 3'-leader, N, P, M, G, NV, L, and 5'-trailer. These genes are separated by conserved sequences or gene junctions, with one-nucleotide gene spacers. The first 16 of the 19 nucleotides at the ends of the HIRRV genome are complementary, and the first four nucleotides at the 3'-ends of the HIRRV, infectious hematopoietic necrosis virus (IHNV), viral hemorrhagic septicemia virus (VHSV), and snakehead rhabdovirus (SHRV) genomes are identical. The HIRRV proteins share the highest amino acid sequence homology (ranging from 72% to 92%) with the proteins of IHNV, of all the known fish rhabdoviruses, and the highest sequence homology with respect to the L protein was shared among HIRRV, IHNV, VHSV, and SHRV. Although there were differences in the degrees of relatedness, phylogenetic trees that were derived from multiple sequence alignments of the rhabdovirus proteins showed similar patterns of relationship among these viruses, in which fish Novirhabdoviruses formed a separate clade from spring viremia of carp virus (SVCV), unassigned fish rhabdovirus that was closer to mammalian rhabdoviruses.