Influenza A: Understanding changes in selective constraints occurring during host shifts. (360G-Wellcome-086713_Z_08_Z)

The proposed aims are to: 1) Develop methods of phylogenetic analysis that will allow us to identify changes in selective constraints that occur during host shifts in influenza. 2) Identify locations where such selective constraint shifts have occurred during shifts from avian to human hosts, and the nature of these changes. 3) Expansion of the model to include the selective constraints in swine influenza. 4) Establishment of measures of 'avianicity', 'humanicity', and 'swinicity', the propensity of a virus or genomic segment to undergo host shifts to humans or swine, respectively. 5) Identify whether the viral strains that underwent host shifts were random or exceptional, whether it was a question of mutations that made such a shift more likely, or rather random opportunism. 6) If time permits, develop other models that characterise the changing nature of the selective constraints in other circumstances.