Abstract
The family Dicistroviridae (order Picornavirales) includes species that infect insects and other arthropods. These viruses have a linear positive-sense ssRNA genome of ~8-10 kb, which contains two long ORFs. The 5' ORF encodes the nonstructural polyprotein while the 3' ORF encodes the structural polyprotein. The dicistroviruses are noteworthy for the intergenic Internal Ribosome Entry Site (IGR-IRES) that mediates efficient translation initation on the 3' ORF without the requirement for initiator Met-tRNA. Acute bee paralysis virus, Israel acute paralysis virus of bees and Kashmir bee virus form a distinct subgroup within the Dicistroviridae family. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF in these viruses. The ORF overlaps the 5' end of the structural polyprotein coding sequence in the +1 reading frame. We also identify a potential 14-18 bp RNA stem-loop structure 5'-adjacent to the IGR-IRES. We discuss potential translation initiation mechanisms for the novel ORF in the context of the IGR-IRES and 5'-adjacent stem-loop.
Highlights
The family Dicistroviridae includes a number of insect- and arthropod-infecting species such as Cricket paralysis virus, Black queen cell virus, Plautia stali intestine virus and Taura syndrome virus
The species Acute bee paralysis virus (ABPV), Israel acute paralysis virus of bees (IAPV) and Kashmir bee virus (KBV) - which have been associated with Colony Collapse Disorder of honeybees - form a tight subclade within the family (Figure 1; [1,2,3,4,5])
We have been using a number of complementary approaches to systematically identify new overlapping genes in virus genomes [13,14,15,16,17]. When we applied these methods to the dicistroviruses, we found strong evidence for a new coding sequence - hereafter ORFX - in the bee paralysis viruses (i.e. ABPV, IAPV and KBV), overlapping the 5'-terminal region of CDS2 in the +1 reading frame (Figure 2)
Summary
The family Dicistroviridae includes a number of insect- and arthropod-infecting species such as Cricket paralysis virus, Black queen cell virus, Plautia stali intestine virus and Taura syndrome virus. When we applied these methods to the dicistroviruses, we found strong evidence for a new coding sequence - hereafter ORFX - in the bee paralysis viruses (i.e. ABPV, IAPV and KBV), overlapping the 5'-terminal region of CDS2 in the +1 reading frame (Figure 2).
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