title: Comparison of the RNA polymerase genes of marine birnavirus strains and other birnaviruses.
abstract: The cDNA nucleotide sequence of the genome segment B encoding the VP1 protein, the putative RNA-dependent RNA polymerase (RdRp), was determined for 5 marine birnavirus (MABV) strains from different host or geographic origins and 1 infectious pancreatic necrosis virus (IPNV) strain AM-98. Segment B of the IPNV AM-98 strain and 4 MABV strains, Y-6, YT-01A, H1 and NC1, contained a 2535 bp ORF, which encoded a protein of 845 amino acid residues with a predicted MW of 94.4 kDa. Only the MABV AY-98 RdRp had 1 amino acid shorter RdRp. Pairwise comparisons were made among our data and 4 other known IPNV sequences. The nucleotide sequences of the 5 MABV strains were very similar each other, with identities of 98.3-99.7%. The highest divergence of the nucleotide level was between MABV strains and IPNV SP strain (serotype A2), with 20.4-20.8% divergences in the coding region, which gave 10.1-11.3% divergence in the amino acid level. The aquabirnavirus RdRp was noticeably conserved in amino acid sequences. Though the identities of the nucleotide sequences of encoding region were 85.1-85.9% between MABV strains and IPNV serotype A1 strains, they shared as high as 95.1-95.9% identities in amino acid level. A phylogenetic tree was constructed based on the amino acid sequences of the RdRp gene from different birnaviruses including avibirnavirus and entomobirnavirus. Ten aquabirnavirus strains were clustered into 3 Genogroups. The Genogroup I consisted of four IPNV A1 serotype strains. All MABV strains were clustered into Genogroup II. Only IPNV SP strain was clustered into an independent Genogroup III.
authors.affiliation: Centre for Marine Environmental Studies, Ehime University, Ehime, Japan.
authors.forename: C X
authors.initials: CX
authors.lastname: Zhang
authors.forename: S
authors.initials: S
authors.lastname: Suzuki
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018059:Birnaviridae / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D005399:Fishes / Q000821:virology*; D005432:Flounder / Q000821:virology; D005814:Genes, Viral; D018061:Infectious pancreatic necrosis virus / Q000201:enzymology / Q000235:genetics; D007564:Japan; D007723:Korea; D008969:Molecular Sequence Data; D008970:Molecular Weight; D017683:Oncorhynchus / Q000821:virology; D016366:Open Reading Frames; D036441:Osmeriformes / Q000821:virology; D010473:Perciformes / Q000821:virology; D010802:Phylogeny; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012324:RNA-Dependent RNA Polymerase