title: Phylogenetic diversity and genotypic complexity of H1N1 subtype swine influenza viruses isolated in mainland China.
abstract: BACKGROUND
  After the occurrence of 2009 pandemic H1N1, close attention has been paid to the H1N1 subtype swine influenza viruses (H1N1 SIV) by scientific communities in many countries. A large-scale sequence analysis of the NCBI Influenza Virus Resource Database on H1N1 SIVs submitted primarily by scientists in China during 1992 to 2011 was performed. The aims of this study were to elucidate the genetic and evolutionary characteristics of H1N1 SIVs, to identify and unify the lineages and genetic characteristics of the H1N1 SIVs isolated in mainland China.
  
  
  RESULTS
  Most of the strains were isolated during the period of 2008 to 2010 from Guangdong and Shandong provinces, China. Based on the phylogenetic and genotypic analyses, all of the H1N1 SIV strains can be classified into 8 lineages and 10 genotypes. All strains were of the characteristics of low pathogenic influenza viruses. The viruses of different lineage are characterized with different amino acid residues at the receptor-binding sites. Viruses containing PB2 genes of the classical swine, early seasonal human and recent seasonal human lineage might be more infectious to human. Some genotypes were directly related with human influenza viruses, which include strains that harbored genes derived from human influenza viruses.
  
  
  CONCLUSIONS
  Phylogenetic diversity and complexity existed in H1N1 SIVs isolated in mainland China. These H1N1 SIV strains were closely related to other subtype influenza viruses, especially to human influenza viruses. Moreover, it was shown that, novel lineages and genotypes of H1N1 SIVs emerged recently in mainland China. These findings provided new and essential information for further understanding of the genetic and evolutionary characteristics and monitoring the H1N1 SIVs in mainland China.
authors.affiliation: College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Liu
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Ji
authors.forename: Shuang
authors.initials: S
authors.lastname: Chang
authors.forename: Chunyi
authors.initials: C
authors.lastname: Xue
authors.forename: Jingyun
authors.initials: J
authors.lastname: Ma
authors.forename: Yingzuo
authors.initials: Y
authors.lastname: Bi
authors.forename: Qingmei
authors.initials: Q
authors.lastname: Xie
mesh_terms: D000818:Animals; D002681:China; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D005838:Genotype; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D009976:Orthomyxoviridae Infections / Q000821:virology; D010802:Phylogeny; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D011991:Receptors, Virus / Q000235:genetics; D020539:Sequence Analysis, Protein; D013552:Swine / Q000821:virology; D013997:Time Factors; D014764:Viral Proteins / Q000235:genetics
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; C057027:PB2 protein, Influenzavirus A; D011991:Receptors, Virus; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase