Figure 1
From: Isolation of avian influenza H5N1 virus from vaccinated commercial layer flock in Egypt
Phylogenetic trees of H5 (A) and N1 (B) genes of A/chicken /Egypt/0987-NLQP/2009 virus with other H5N1 viruses currently circulating in poultry and human in Egypt. The evolutionary history of the HA and NA was inferred using the Neighbor-Joining method with 1000 bootstrap replicates and the evolutionary distances were computed using the Maximum Composite Likelihood method implemented in MEGA5. The bootstrap values are shown next to the branches. Trees were edited for publication using Inkscape software. Virus obtained from this study is highlighted in yellow while other related viruses are written in bold. The virus clustered with H5N1 viruses isolated from poultry in backyards, live bird market and confirmed human infections. Two major H5N1 genetic clusters are currently co-circulating in Egypt: newly designated 2.2.1.1 clade (depicted in red) representing variant viruses isolated exclusively from vaccinated poultry in commercial farms and group C of 2.2.1 clade (blue) denoted 2.2.1/C group that mainly isolated from human and backyard birds according to the recent classification of WHO/OIE/FAO Evolution Working Group. The 2.2.1 index virus introduced into 2006 (black) was no longer isolated and was denoted as 2.2.1 clade.