Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene

The genus Waikavirus belongs to the order Picornavirales , whose members all use a polyprotein expression strategy. With the exception of Theiler’s virus, overlapping genes are essentially unknown in the order. Recently, we reported experimental verification for a new short overlapping coding sequence (CDS) in the Potyviridae —a family in which overlapping genes were previously unknown. Using the same bioinformatics software (MLOGD), we have identified an ~89-codon conserved open reading frame (ORF) with a strong coding signature in members of the genus Waikavirus . The ORF overlaps the polyprotein ORF but is in the +1 reading frame. Here, we describe the bioinformatic analysis.