title: Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China.
abstract: Two-way transmission of influenza viruses between humans and swine has been frequently observed, and the occurrence of the 2009 H1N1 pandemic influenza virus (pdm/09) demonstrated that swine-origin viruses could facilitate the genesis of a pandemic strain. Although multiple introductions to and reassortment in swine of the pdm/09 virus have been repeatedly reported in both Eurasia and the Americas, its long-term impact on the development of swine influenza viruses (SIVs) has not been systematically explored. Our comprehensive evolutionary studies of the complete genomes of 387 SIVs obtained from 2009 to 2012 by influenza virus surveillance in China revealed 17 reassortant genotypes with pdm/09-origin genes. Even though the entire 2009 pandemic virus and its surface genes cannot persist, its internal genes have become established and are now the predominant lineages in pigs in the region. The main persistent pdm/09-origin reassortant forms had at least five pdm/09-origin internal genes, and their surface genes were primarily of European avian-like (EA) or human H3N2-like SIV origin. These findings represent a marked change in the evolutionary patterns and ecosystem of SIVs in China. It is possible that the pdm/09-origin internal genes are in the process of replacing EA or triple-reassortant-like internal genes. These alterations in the SIV gene pool need to be continually monitored to assess changes in the potential for SIV transmission to humans.
  
  
  OBJECTIVE
  Shortly after the emergence of the 2009 pandemic H1N1 (pdm/09) influenza virus, it was transmitted from humans to pigs and this continues to occur around the world. Many reassortants between pdm/09-origin viruses and enzootic swine influenza viruses (SIVs) have been detected. However, the long-term impact of pdm/09-origin viruses on the SIV gene pool, which could lead to the generation of influenza viruses with the potential to infect humans, has not been systematically examined. From extensive surveillance of SIVs over a 38-month period in southern China, it was found that although neither complete pdm/09 viruses nor their surface genes could persist in pigs, their internal genes did persist. Over the survey period, these internal genes became predominant, potentially replacing those of the enzootic SIV lineages. The altered diversity of the SIV gene pool needs to be closely monitored for changes in the potential for SIV transmission to humans.
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Huyi
authors.initials: H
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Tommy Tsan-Yuk
authors.initials: TT
authors.lastname: Lam
authors.affiliation: Department of Microbiology, Guangxi Medical University, Nanning, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China.
authors.forename: Xinchun
authors.initials: X
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Lian
authors.initials: L
authors.lastname: Duan
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Maying
authors.initials: M
authors.lastname: Tse
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Chung-Hei
authors.initials: CH
authors.lastname: Chan
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Tak-Ying
authors.initials: TY
authors.lastname: Leung
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Chun-Hung
authors.initials: CH
authors.lastname: Yip
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Chung-Lam
authors.initials: CL
authors.lastname: Cheung
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China.
authors.forename: Boping
authors.initials: B
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: David K
authors.initials: DK
authors.lastname: Smith
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Leo Lit-Man
authors.initials: LL
authors.lastname: Poon
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China.
authors.forename: Malik
authors.initials: M
authors.lastname: Peiris
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China yguan@hku.hk zhuhch@hku.hk.
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases (Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong (HKU), Hong Kong SAR, China Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China yguan@hku.hk zhuhch@hku.hk.
authors.forename: Huachen
authors.initials: H
authors.lastname: Zhu
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D011995:Recombination, Genetic; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins