RNA secondary structures in RNA viral genomes play important roles in a range of functions, including packaging, protection from cellular nucleases, and regulating viral replication. Furthermore, RNA structures have been shown to be immunostimulatory. In the case of Influenza A virus (IAV), during infection aberrant RNAs are produced. One of these are mini-viral RNAs (mvRNAs) which are very potent RIG-I stimulators. However, our understanding of the mechanisms that underlie the role of RNA structures in the above processes and how RNA structures evolve is still limited. In my thesis I first investigate whether mvRNAs are produced in human patients. Clinical samples were obtained from three influenza seasons and presence of mvRNAs were analysed via RT-PCR. Due to both technical and sample issues, no conclusion was reached. I next examined how RNA structures, including those capable of inducing mvRNA synthesis and increasing their immunostimulatory potential, are changing during pandemic IAV H3N2 evolution. Using in silico analyses, I observed a decline in RNA structure stability in the polymerase segments over time. Control analyses showed that this change was independent to amino acid mutation and reduced in human-adapted viruses, but present in emerging H1N1 IAV. Using transfections, I subsequently identified that amino acid changes in the IAV RNA polymerase make the enzyme more sensitive to RNA structures, suggesting that the loss in RNA structure stability and change in enzyme activity are linked. To determine if the loss of RNA structure was present in other emerging viruses, I analysed sequences of SARS-CoV-2 and found a similar decline in thermodynamic stability over time. Having identified a pattern of RNA structure loss in both IAV and SARS-CoV-2 I repeated the analysis on Ebola Zaire and Lassa virus to determine if similar patterns are observed in zoonotic viruses. I found this not to be the case. Based on these observations, I propose a novel model for emerging and pandemic RNA virus adaptation and hypothesise that immune pressure may select for viruses with improved replication efficiency, leading to RNA structure loss and a reduction in detection by immune receptors over time.