Putative bundling signals incompatible between influenza C and D viruses

Genomes of influenza C (ICV) and D (IDV) viruses consist of seven segments of single-stranded negative-sense RNAs called viral RNAs (vRNAs). Reportedly, eight segments are contained in the virions of ICV and IDV, in which at least one copy each of seven genomic segments is thought to be selectively packaged. Although the mechanism of selective packaging is not fully understood, it is thought that a set of vRNAs are bundled through intersegmental interactions of bundling signals, which are likely to be pairs of complementary genomic sequences between vRNAs. Here bundling signals incompatible between ICV and IDV were searched for by the analysis of genomic sequences for four ICV and 21 IDV strains. One pair each of genomic loci between the P3 and HEF vRNAs and within the HEF vRNA were found to be complementary within IDV but noncomplementary between ICV and IDV. Many of these genomic loci appeared to be associated with hairpin and internal loops in vRNAs, suggesting that they may be free from nucleoprotein (NP) in viral ribonucleoproteins (vRNPs) and involved in intersegmental interactions as bundling signals. The virion of IDV may contain one copy each of seven genomic segments together with one extra copy of the HEF segment.