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: C X Zhang, S Suzuki
• Journal: Archives of virology (Arch Virol) Vol. 148 Issue 4 Pg. 745-58 (Apr 2003) ISSN: 0304-8608 [Print] Austria
• PMID: 12664297 (Publication Type: Comparative Study, Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• RNA-Dependent RNA Polymerase

Topics

• Amino Acid Sequence
• Animals
• Birnaviridae (classification, enzymology, genetics)
• Fishes (virology)
• Flounder (virology)
• Genes, Viral
• Infectious pancreatic necrosis virus (enzymology, genetics)
• Japan
• Korea
• Molecular Sequence Data
• Molecular Weight
• Oncorhynchus (virology)
• Open Reading Frames
• Osmeriformes (virology)
• Perciformes (virology)
• Phylogeny
• RNA-Dependent RNA Polymerase (chemistry, genetics)
• Sequence Alignment
• Sequence Homology, Amino Acid
• Sequence Homology, Nucleic Acid