The innate immune response provides a first line of defense against pathogens by 
targeting generic differential features that are present in foreign organisms 
but not in the host. These innate responses generate selection forces acting 
both in pathogens and hosts that further determine their co-evolution. Here we 
analyze the nucleic acid sequence fingerprints of these selection forces acting 
in parallel on both host innate immune genes and ssRNA viral genomes. We do this 
by identifying dinucleotide biases in the coding regions of innate immune 
response genes in plasmacytoid dendritic cells, and then use this signal to 
identify other significant host innate immune genes. The persistence of these 
biases in the orthologous groups of genes in humans and chickens is also 
examined. We then compare the significant motifs in highly expressed genes of 
the innate immune system to those in ssRNA viruses and study the evolution of 
these motifs in the H1N1 influenza genome. We argue that the significant 
under-represented motif pattern of CpG in an AU context--which is found in both 
the ssRNA viruses and innate genes, and has decreased throughout the history of 
H1N1 influenza replication in humans--is immunostimulatory and has been selected 
against during the co-evolution of viruses and host innate immune genes. This 
shows how differences in host immune biology can drive the evolution of viruses 
that jump into species with different immune priorities than the original host.