Characterization of a Novel RNA Virus Discovered in the Autumnal Moth Epirrita autumnata in Sweden

de Miranda, Joachim R.; Hedman, Harald; Onorati, Piero; Stephan, Jörg; Karlberg, Olof; Bylund, Helena; Terenius, Olle

The Abisko virus sequence comprises a single-stranded RNA genome of about 10 kb, with a natural 3' poly-A tail a relatively large (782 nt) 3 untranslated region (3 UTR), a short 5 UTR, and three major ORFs, separated by an intergenic region (IGR) of about 229 nt and a 3 nt stretch following the end of the putative coat protein (Figure 1 ). ORF-1 contains clear domain signatures for a Methyl Transferase (MTR), a cysteine-protease (ProC3), a helicase, and an RNA-dependent RNA polymerase domains (RdRp). ORF-2 contains a coat protein (CP) while ORF-3 contains a 14 kDa protein with no clear homologues in the databases. The size and overall organization of the genome is most similar to that of the negeviruses, an insect-specific virus family [6, 7] . To confirm the integrity of the genome and its organization, a 1.5 kb fragment spanning ORF-1, the intergenic region, ORF-2 and ORF-3 was amplified and sequenced directly by Sanger sequencing, confirming all of the junctions and gaps. Usually with this type of genome organization, the second and third ORFs are either translated by an internal ribosome entry site (IRES) located in the intergenic region [24] or from a subgenomic RNA [25, 26] . No conserved sequence motifs for subgenomic promoters or IRES structures could be found in the Abisko genome. Indirect clues that Abisko virus may use a subgenomic RNA translation strategy are: (1) the highly elevated coverage for the 3 region of the genome; (2) the presence of a viral methyl transferase, responsible for producing CAP-like structures for stabilizing the 3 ends of viral (sub)genomic RNAs prior to translation through 'normal' ribosome AUG scanning; (3) most genera within the super-family to which Abisko virus and its close relatives belong tend to translate their 3 ORFs through subgenomic RNAs [25] (but see [27] ).