Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry

► Phylogenetic and evolutionary analysis of Egyptian H5N1 viruses was undertaken. ► Evolution of H5N1 in countries applying or not vaccination was compared. ► Distinct Egyptian H5N1 subclades have co-circulated in poultry since late 2007. ► Evolutionary rates were different among countries applying or not vaccination.