Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp.
The complete nucleotide sequence of the genomic RNA of a marine fungoid protist-infecting virus (Schizochytrium single-stranded RNA virus; SssRNAV) has been determined. The viral RNA is single-stranded with a positive sense and is 9,018 nt in length [excluding the 3' poly(A) tail]. It contains two long open reading frames (ORFs), which are separated by an intergenic region of 92 nt. The 5' ORF (ORF1) is preceded by an untranslated leader sequence of 554 nt. The 3' large ORF (ORF2) and an additional ORF (ORF3) overlap ORF2 by 431 nt and are followed by an untranslated region of 70 nt [excluding the 3' poly(A) tail]. The deduced amino acid sequences of ORF1 and ORF2 products show similarity to non-structural and structural proteins of dicistroviruses, respectively. However, Northern blot analysis suggests that SssRNAV synthesizes subgenomic RNAs to translate ORF2 and ORF3, showing that the translation mechanism of downstream ORFs is distinct from that of dicistroviruses. Furthermore, although considerable similarities were detected by using a blast genome database search, phylogenetic analysis based on both the nucleotide and amino acid sequences of the putative RNA-dependent RNA polymerase (RdRp) and the RNA helicase suggests that SssRNAV is phylogenetically distinct from other virus families. Therefore, it is concluded that SssRNAV is not a member of any currently defined virus family and belongs to a novel, unrecognized virus group.
Takao
Yoshitake
Y
Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501, Japan.
Mise
Kazuyuki
K
Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Nagasaki
Keizo
K
Harmful Algal Bloom Division, National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hiroshima, Japan.
Okuno
Tetsuro
T
Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Honda
Daiske
D
Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501, Japan.
D000595:Amino Acid Sequence; D000818:Animals; D036022:Capsid Proteins / Q000235:genetics; D056890:Eukaryota / Q000821:virology*; D016679:Genome, Viral; D008386:Marine Biology; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D020365:RNA Helicases / Q000235:genetics; D012328:RNA Viruses / Q000145:classification / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity; D014764:Viral Proteins / Q000235:genetics
D036022:Capsid Proteins; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase; D020365:RNA Helicases