1 Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences (Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology|Center of Bioinformatics, Key Lab of System Biology|Lab of Synthetic Biology, Institute of Plant Physiology &|Ecology|Institute Pasteur), Shanghai 200031, China; 
2 School of Life Sciences, Fudan University, Shanghai 200433, China; 
3 Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China; 
4 Cancer Institute, Second Military Medical University, Shanghai 200433, China; 
5 School of Life Sciences and Technology, South China University of Technology, Guangzhou 510641, China; 
6 National Engineering Research Center for Antibody Drugs, Shanghai 201203, China; 
7 Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China; 
8 Shanghai Municipal Center for Disease Control &|Prevention, Shanghai 200336, China; 
9 Shanghai Center for Bioinformation Technology, Shanghai 200235, China; 
10 School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; 
11 National Institute for Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China; 
12 Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; 
13 Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; 
14 National Engineering Research Center for Biochip Technology, Shanghai Biochip Co. Ltd, Shanghai 201203, China

A mutation network for the hemagglutinin gene (HA) of the novel type A (H1N1) influenza virus was constructed. Sequence homology analysis indicated that one HA sequence type from the viruses mainly isolated from Mexico was likely the original type in this epidemic. Based on the 658A and 1408T mutations in HA, the viruses evolving into this epidemic were divided into three categories, the Mexico, the transitional and the New York type. The three groups of viruses presented distinctive clustering features in their geographic distributions.