Identification of novel conserved functional motifs across most Influenza A viral strains

Across all species and strains 87 highly conserved regions (conservation percentage > = 90%) and 19 functional motifs (conservation percentage = 100%) were found in PB2, PB1, PA, NP, M, and NS segments. The conservation percentage of these segments ranged between 94 - 98% in human strains (the most conserved), 85 - 93% in swine strains (the most variable), and 91 - 94% in avian strains. The most conserved segment was different in each host (PB1 for human strains, NS for avian strains, and M for swine strains). Target accessibility prediction yielded 324 accessible regions, with a single stranded probability > 0.5, of which 78 coincided with conserved regions. Some of the interesting annotations in these regions included sites for protein-protein interactions, the RNA binding groove, and the proton ion channel.The influenza virus has evolved to adapt to its host through variations in the GC content and conservation percentage of the conserved regions. Nineteen universal conserved functional motifs were discovered, of which some were accessible regions with interesting biological functions. These regions will serve as a foundation for universal drug targets as well as universal vaccine design.The influenza A virus is a major threat to world health and economy. The polymerase of this RNA virus lacks proof reading activity [1], which gives rise to considerable viral variability culminating in the 3 different types A, B and C, in addition to many subtypes based on variations in the hemagglutinin (HA) and the neuraminidase (NA) surface proteins [2]. The influenza genome consists of 8 RNA segments and encodes 10 proteins including the internal structural proteins, nucleocapsid protein (NP), and the two matrix proteins (M1 & M2) [3,4].The surface proteins neuraminidase (NA) and hemagglutinin (HA) have been studied extensively and the antigenic variations in the these surface glycoproteins are used to subtype influenza A. Additionally, three of the influenza polypeptides are