title: Novel antigenic shift in HA sequences of H1N1 viruses detected by big data analysis.
abstract: The influenza virus H1N1 has been prevalent all over the world for nearly a century. Many studies on its evolutionary history, substitution rate and antigenicity-associated sites have been done with small datasets. To have a complete view, we analysed 3171 full-length HA sequences from human H1N1 viruses sampled from 1918 to 2016, and discovered a new clade has formed with sequences isolated in Iran. Based on genetic distance calculations, we revealed an uneven evolutionary rate among sequences isolated in different years. We also found that the HA1 fragment of the new clade is like that of viruses that existed in the 1930s, while the HA2 fragment is closely associated with strains isolated after the 2009 pandemic. This new, "mixed" HA sequence indicates a cryptic antigenic shift event occurred, and it should draw more attention to the new clade identified from sequences from Iran.
authors.affiliation: Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Ruiying
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Chongfeng
authors.initials: C
authors.lastname: Xu
authors.affiliation: Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: zyduan@genetics.ac.cn.
authors.forename: Ziyuan
authors.initials: Z
authors.lastname: Duan
mesh_terms: D000956:Antigens, Viral / Q000235:genetics* / Q000276:immunology; D001208:Asia / Q000453:epidemiology; D005060:Europe / Q000453:epidemiology; D019143:Evolution, Molecular; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics* / Q000276:immunology; D049673:History, 20th Century; D049674:History, 21st Century; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics* / Q000276:immunology; D064149:Influenza Pandemic, 1918-1919 / Q000266:history*; D007251:Influenza, Human / Q000453:epidemiology* / Q000266:history* / Q000821:virology; D007492:Iran / Q000453:epidemiology; D010802:Phylogeny; D014481:United States / Q000453:epidemiology
chemical_list: D000956:Antigens, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus; C483468:hemagglutinin, human influenza A virus
keywords: Cryptic antigenic shift; Genetic distance; H1N1; HA1; HA2