Evolution analysis for HA gene of human influenza A H3N2 virus (1990 – 2013)

Human influenza A virus is an important pathogen which threatens the health of human in a long time. The mutation study of HA gene is the most important. Here we investigate the evolution characteristics of HA gene of H3N2 influenza virus from 1990 to 2013. Numerical mapping and PCA clustering analysis are applied to the gene evolution analysis. The clustering diagram by MATLAB represents the mapping of HA gene in 2D space. The first two principal components account for 78.48% by PCA analysis. And the points are clustered into three parts, 1990~1999, 2000~2005 and 2006~2013. However, there is no obvious interval among them. Then we show the graphical representation of HA gene sequences according to the emerging time of isolates and different continents. Results show that during 1990 to 2013 human influenza A H3N2 virus has been evoluting gradually. There was not large genetic recombination. Even so, it is necessary to continuously monitor the human influenza A (H3N2) viruses.