title: Genomic characterization of influenza A (H7N9) viruses isolated in Shenzhen, Southern China, during the second epidemic wave.
abstract: There were three epidemic waves of human infection with avian influenza A (H7N9) virus in 2013-2014. While many analyses of the genomic origin, evolution, and molecular characteristics of the influenza A (H7N9) virus have been performed using sequences from the first epidemic wave, genomic characterization of the virus from the second epidemic wave has been comparatively less reported. In this study, an in-depth analysis was performed with respect to the genomic characteristics of 11 H7N9 virus strains isolated from confirmed cases and four H7N9 virus strains isolated from environmental samples in Shenzhen during the second epidemic wave. Phylogenetic analysis demonstrated that six internal segments of the influenza A (H7N9) virus isolated from confirmed cases and environmental samples in Shenzhen were clustered into two different clades and that the origin of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen was different from that of viruses isolated during the first wave. In addition, H9N2 viruses, which were prevalent in southern China, played an important role in the reassortment of the influenza A (H7N9) virus isolated in Shenzhen. HA-R47K and -T122A, PB2-V139I, PB1-I397M, and NS1-T216P were the signature amino acids of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen. We found that the HA, NA, M, and PA genes of the A(H7N9) viruses underwent positive selection in the human population. Therefore, enhanced surveillance should be carried out to determine the origin and mode of transmission of the novel influenza A (H7N9) virus and to facilitate the formulation of effective policies for prevention and containment of a human infection epidemics.
authors.affiliation: Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Shisong
authors.initials: S
authors.lastname: Fang
authors.affiliation: Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: College of Medicine, Jinan University, 601 Huangpu Avenue West, Guangzhou, China.
authors.forename: Fangyuan
authors.initials: F
authors.lastname: Dong
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Jin
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Guang
authors.initials: G
authors.lastname: Liu
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Lu
authors.affiliation: Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Peng
authors.affiliation: Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Weihua
authors.initials: W
authors.lastname: Wu
authors.affiliation: Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Dongfeng
authors.initials: D
authors.lastname: Kong
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Xiujuan
authors.initials: X
authors.lastname: Tang
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Yanmin
authors.initials: Y
authors.lastname: Qin
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Shujiang
authors.initials: S
authors.lastname: Mei
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Xie
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Jianfan
authors.initials: J
authors.lastname: He
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
authors.forename: Hanwu
authors.initials: H
authors.lastname: Ma
authors.affiliation: Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China. renlizhangszcdc@aliyun.com.
authors.forename: Renli
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China. cjinquan@vip.sohu.com.
authors.forename: Jinquan
authors.initials: J
authors.lastname: Cheng
mesh_terms: D000818:Animals; D002645:Chickens; D002681:China / Q000453:epidemiology; D016679:Genome, Viral; D023281:Genomics; D006801:Humans; D064766:Influenza A Virus, H7N9 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology*; D010802:Phylogeny; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins