title: Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China.
abstract: BACKGROUND
  Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates.
  
  
  METHODS
  Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans.
  
  
  RESULTS
  The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)).
  
  
  CONCLUSIONS
  Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. amberfarooqui@hotmail.com.
authors.forename: Amber
authors.initials: A
authors.lastname: Farooqui
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. aleon@uhnresearch.ca.|Division of Experimental Therapeutics, University Health Network, Toronto, Ontario, Canada. aleon@uhnresearch.ca.
authors.forename: Alberto J
authors.initials: AJ
authors.lastname: Leon
authors.affiliation: Intensive Care Unit, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China. hlx1236@126.com.
authors.forename: Linxi
authors.initials: L
authors.lastname: Huang
authors.affiliation: Intensive Care Unit, Shantou Central Hospital, Shantou, Guangdong, China. 13502991856@163.com.
authors.forename: Suwu
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of Laboratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China. st_ymcai@126.com.
authors.forename: Yingmu
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Intensive Care Unit, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China. Lpz1701@qq.com.
authors.forename: Pengzhou
authors.initials: P
authors.lastname: Lin
authors.affiliation: Intensive Care Unit, Shantou Central Hospital, Shantou, Guangdong, China. chenweihong2006@163.com.
authors.forename: Weihong
authors.initials: W
authors.lastname: Chen
authors.affiliation: Intensive Care Unit, Shantou Central Hospital, Shantou, Guangdong, China. 1903003169@qq.com.
authors.forename: Xibin
authors.initials: X
authors.lastname: Fang
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. 872703935@qq.com.
authors.forename: Tiansheng
authors.initials: T
authors.lastname: Zeng
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. 786414772@qq.com.
authors.forename: Yisu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. 741033233@qq.com.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. 545776041@qq.com.
authors.forename: Ting
authors.initials: T
authors.lastname: Su
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. 342284415@qq.com.
authors.forename: Weibin
authors.initials: W
authors.lastname: Chen
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, Global Institute of Public Health, New York University, New York, USA. elodie.ghedin@nyu.edu.
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.affiliation: Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China. zhuhch@hku.hk.|State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China. zhuhch@hku.hk.
authors.forename: Huachen
authors.initials: H
authors.lastname: Zhu
authors.affiliation: Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China. yguan@hku.hk.|State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China. yguan@hku.hk.
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.affiliation: Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China. dkelvin@jidc.org.|Division of Experimental Therapeutics, University Health Network, Toronto, Ontario, Canada. dkelvin@jidc.org.
authors.forename: David J
authors.initials: DJ
authors.lastname: Kelvin
mesh_terms: D002681:China / Q000453:epidemiology; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D006801:Humans; D064766:Influenza A Virus, H7N9 Subtype / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis*
chemical_list: D012367:RNA, Viral