Influenza differentiation and evolution

Paper in proceeding, 2010

The aim of the study is to do a very wide analysis of HA, NA and M influenza gene segments to find short nucleotide regions, which differentiate between strains (i.e. H1, H2, ⋯ etc.), hosts, geographic regions, time when sequence was found and combination of time and region using a simple methodology. Finding regions differentiating between strains has as its goal the construction of a Luminex microarray which will allow quick and efficient strain recognition. Discovery for the other splitting factors could shed light on structures significant for host specificity and on the history of influenza evolution. A large number of places in the HA, NA and M gene segments were found that can differentiate between hosts, regions, time and combination of time and region. Also very good differentiation between different Hx strains can be seen. We link one of our findings to a proposed stochastic model of creation of viral phylogenetic trees.