Detection of structural constraints and conformational transitions in the influenza virus RNA genome using structure predictions and mutual information calculations

Influenza A virus is characterised by remarkable genome diversity in multiple virus strains. New strains are continuously evolved, occasionally leading to dangerous outbreaks and pandemics. Local RNA secondary structures were predicted in several regions of the influenza A virus genome. The conserved structures may be functional in either genomic negative-sense RNA (e.g. involved in vRNA packaging) or positivesense mRNA, regulating gene expression. As thousands of genomic sequences are available, it is important to estimate the extent of structure conservation and statistically significant structural constraints. Such constraints are detected using calculations of mutual information and entropy values for the paired nucleotide positions in the conserved structures. Furthermore, these calculations demonstrate the presence of evolutionarily conserved alternative conformations such as pseudoknot/hairpin equilibria or alternative hairpins. Remarkably, conformational transitions in some of the influenza virus lineages that determined major virus outbreaks can also be predicted. The analysis of influenza virus RNA structure evolution shows that it has an epochal character resembling the evolution of its antigenic properties.