A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences

Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C

To demonstrate the utility of our method's effectiveness for overlapping gene screening, we individually analyzed all reference linear RNA genomes available on GenBank. This provided evidence for 29 undocumented overlapping ORFs of which we expect only 3 to be false positives, although all should be verified experimentally. One notable ORF identified here is the exceptionally long (708 codons) antisense ORF in Nhumirim virus, a single-stranded positive-sense RNA virus from the family Flaviviridae, which suggests that this virus may employ a novel method of transcription and clearly merits further investigation. We also identified several undiscovered ORFs in the phosphoprotein P within the Paramyxoviridae family, a region known to frequently contain overlapping genes in other reading frames due to RNA editing. Within Bovine respirovirus virus 3, the ORF codon sequence discovered here aligned with many V proteins of other members of the Paramyxoviridae. As the V protein in these viruses also overlaps with the phosphoprotein P protein, this suggests that the V protein also exists in Bovine respirovirus virus 3. In other Paramyxoviridae, notably Tioman virus, we also identified antisense ORFs in the phosphoprotein.