Short report
Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene
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Corresponding authors: Andrew E Firth A.Firth@ucc.ie - John F Atkins j.atkins@ucc.ie
1 BioSciences Institute, University College Cork, Cork, Ireland
2 Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
Virology Journal 2009, 6:222 doi:10.1186/1743-422X-6-222
Published: 17 December 2009Abstract
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.