Innate immunity as driving force of nucleotide bias in the influenza virus genome

The innate immune system can recognize non-self DNA and RNA. Viruses escape from this innate immunity by mutation, evolving to mimic host genome characteristics. In the vertebrate genome, a ?nucleotide bias? is present involving underrepresentation of cytosine-guanine (CpG) motifs. The same nucleotide bias is present in the RNA genome of influenza viruses, particularly in the double-stranded parts, and their CpG content decreases over time. We aim to elucidate whether this CpG nucleotide bias in influenza virus RNA is due to recognition of CpG motifs by the innate immune system. We will test the effects of CpG-rich and CpG-poor RNA on innate immune reactions by transfection of synthetic RNA into cells, infection of cells with artificial variants of influenza virus and mutational analyses of influenza viruses. Sequencing viruses after multiple passages in immunocompetent cells will reveal whether selection against CpG sequences occurs. To unravel the mechanism, we will use cells expressing or lacking specific receptors that may recognize CpG motifs, interfere with the location of RNA recognition and generate mRNA expression profiles. Together, this will shed light on the interplay between the genome of influenza viruses and human innate immunity. This knowledge may be used for immunotherapy and vaccine development.