title: Complete sequence of RNA1 and subgenomic RNA3 of Atlantic halibut nodavirus (AHNV).
abstract: The Nodaviridae are divided into the alphanodavirus genus, which infects insects, and the betanodavirus genus, which infects fishes. Betanodaviruses are the causative agent of viral encephalopathy and retinopathy (VER) in a number of cultivated marine fish species. The Nodaviridae are small non-enveloped RNA viruses that contain a genome consisting of 2 single-stranded positivesense RNA segments: RNA1 (3.1 kb), which encodes the viral part of the RNA-dependent RNA polymerase (RdRp); and RNA2 (1.4 kb), which encodes the capsid protein. In addition to RNA1 and RNA2, a subgenomic transcript of RNA1, RNA3, is present in infected cells. We have cloned and sequenced RNA1 from the Atlantic halibut Hippoglossus hippoglossus nodavirus (AHNV), and for the first time, the sequence of a betanodaviral subgenomic RNA3 has been determined. AHNV RNA1 was 3100 nucleotides in length and contained a main open reading frame encoding a polypeptide of 981 amino acids. Conservative motifs for RdRp were found in the deduced amino acid sequence. RNA3 was 371 nucleotides in length, and contained an open reading frame encoding a peptide of 75 amino acids corresponding to a hypothetical B2 protein, although sequence alignments with the alphanodavirus B2 proteins showed only marginal similarities. AHNV RNA replication in the fish cell-line SSN-1 (derived from striped snakehead) was analysed by Northern blot analysis, which indicated that RNA3 was synthesised in large amounts (compared to RNA1) at an early point in time post-infection.
authors.affiliation: Institute of Marine Research, Department of Aquaculture, PO Box 1870, Nordnes, 5817 Bergen, Norway. ingunn.sommerset@intervet.com
authors.forename: Ingunn
authors.initials: I
authors.lastname: Sommerset
authors.forename: Audun H
authors.initials: AH
authors.lastname: Nerland
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics; D005393:Fish Diseases / Q000821:virology*; D005432:Flounder; D008969:Molecular Sequence Data; D030381:Nodaviridae / Q000235:genetics*; D012327:RNA Virus Infections / Q000662:veterinary*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D012324:RNA-Dependent RNA Polymerase