Abstract
The genus Okavirus (order Nidovirales) includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.
Highlights
The genus Okavirus belongs to the family Roniviridae in the order Nidovirales
As with other members of the order Nidovirales, these viruses have a linear positive-sense ssRNA genome encoding a large replicase polyprotein that is expressed from the genomic RNA (ORF1a and, via ribosomal frameshifting, an ORF1aORF1b fusion product), and a number of other proteins including the structural proteins - which are translated from a nested set of 3'-coterminal sub-genomic RNAs [14]
We have been using a number of complementary approaches to systematically identify new overlapping genes in virus genomes [11,12,13,14,15]
Summary
The genus Okavirus belongs to the family Roniviridae in the order Nidovirales. Members include Gill-associated virus (GAV) and Yellow head virus (YHV), both of which infect Penaeus monodon shrimp. When we applied these methods to the okaviruses, we found strong evidence for a new coding sequence - hereafter ORFX - overlapping the 5'-terminal 88 codons of ORF3
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