title: Evolution and variation of the H3 gene of influenza A virus and interaction among hosts.
abstract: OBJECTIVE
  Continual mutations to the hemagglutinin (HA) gene of influenza A virus generate novel antigenic strains that cause annual epidemics. The aim of this study was to evaluate evolution tendency of the H3 gene in a long period of time.
  
  
  METHODS
  1842 H3 HA1 nucleotide strains of different hosts were collected for analysis. A two-step clustering method was used to divide strains into groups, and then a phylogenetic tree was constructed based on cluster results. Evolution rate in lineages were future estimated.
  
  
  RESULTS
  Tree structure showed three lineages: horse/canine, human/swine and avian. As a single trunk, the human/swine lineage was mainly composed of human strains, and more big branches appeared in recent years. Tree topology showed no evidence that swine affected the main evolution tendency of human H3 strains. The evolution rate of H3 strains varied between lineages. We observed that the rate in the human lineage decreased from 3.2 substitutions/year before 1980 to 1.8 after 1997.
  
  
  CONCLUSIONS
  We concluded that the variation of human H3 gene was associated with swine strains but independent of others, including bird strains. The evolution rate of human H3 strains seems to have decreased in recent years, while the reasons for the rate change need to be further explored.
authors.affiliation: Department of Health Statistics and Social Medicine, School of Public Health, Fudan University, Shanghai, PR China. wtzhang@shmu.edu.cn <wtzhang@shmu.edu.cn>
authors.forename: Wentong
authors.initials: W
authors.lastname: Zhang
authors.forename: Qingwu
authors.initials: Q
authors.lastname: Jiang
authors.forename: Yue
authors.initials: Y
authors.lastname: Chen
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D016000:Cluster Analysis; D019143:Evolution, Molecular; D014644:Genetic Variation; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D006801:Humans; D009980:Influenza A virus / Q000145:classification / Q000235:genetics*; D008390:Markov Chains; D009154:Mutation; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus