title: Genetic characteristics of 2009 pandemic H1N1 influenza a viruses isolated from Mainland China.
abstract: A total of 100 H1N1 flu real-time-PCR positive throat swabs collected from fever patients in Zhejiang, Hubei and Guangdong between June and November 2009, were provided by local CDC laboratories. After MDCK cell culture, 57 Influenza A Pandemic (H1N1) viruses were isolated and submitted for whole genome sequencing. A total of 39 HA sequences, 52 NA sequences, 36 PB2 sequences, 31 PB1 sequences, 40 PA sequences, 48 NP sequences, 51 MP sequences and 36 NS sequences were obtained, including 20 whole genome sequences. Sequence comparison revealed they shared a high degree of homology (96%-99%) with known epidemic strains (A/California/04/2009(H1N1). Phylogenetic analysis showed that although the sequences were highly conserved, they clustered into a small number of groups with only a few distinct strains. Site analysis revealed three substitutions at loop 220 (221-228) of the HA receptor binding site in the 39 HA sequences: A/Hubei/86/2009 PKVRDQEG → PKVRDQEA, A/Zhejiang/08/2009 PKVRDQEG → PKVRDQER, A/Hubei/75/2009 PKVRDQEG → PKVRDQGG, the A/Hubei/75/2009 was isolated from an acute case, while the other two were from patients with mild symptoms. Other key sites such as 119, 274, 292 and 294 amino acids of NA protein, 627 of PB2 protein were conserved. Meanwhile, all the M2 protein sequences possessed the Ser32Asn mutation, suggesting that these viruses were resistant to adamantanes. Comparison of these sequences with other H1N1 viruses collected from the NCBI database provides insight into H1N1 transmission and circulation patterns.
authors.affiliation: State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
authors.forename: Jiu-Ru
authors.initials: JR
authors.lastname: Zhao
authors.forename: Yong-Dong
authors.initials: YD
authors.lastname: Li
authors.forename: Li-Min
authors.initials: LM
authors.lastname: Pan
authors.forename: Na
authors.initials: N
authors.lastname: Zhu
authors.forename: Hong-Xia
authors.initials: HX
authors.lastname: Ni
authors.forename: Guo-Zhang
authors.initials: GZ
authors.lastname: Xu
authors.forename: Yong-Zhong
authors.initials: YZ
authors.lastname: Jiang
authors.forename: Xi-Xiang
authors.initials: XX
authors.lastname: Huo
authors.forename: Jun-Qiang
authors.initials: JQ
authors.lastname: Xu
authors.forename: Han
authors.initials: H
authors.lastname: Xia
authors.forename: Na
authors.initials: N
authors.lastname: Han
authors.forename: Shuang
authors.initials: S
authors.lastname: Tang
authors.forename: Zhong
authors.initials: Z
authors.lastname: Zhang
authors.forename: Zheng
authors.initials: Z
authors.lastname: Kou
authors.forename: Simon
authors.initials: S
authors.lastname: Rayner
authors.forename: Tian-Xian
authors.initials: TX
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D002681:China / Q000453:epidemiology; D014644:Genetic Variation; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins