title: Whole-genome analysis of porcine epidemic diarrhea virus (PEDV) from eastern China.
abstract: The complete genome sequence of a porcine epidemic diarrhea virus variant, strain SHQP/YM/2013, from China was determined and compared with those of other porcine epidemic diarrhea viruses. The full-length genome was 28,038 nucleotides (nt) in length without the poly (A) tail, and it was similar to that of other reported PEDV strains, with the characteristic gene order 5'-replicase (1a/1b) -S-ORF3-E-M-N-3'. Nucleotide sequence analysis based on individual virus genes indicated a close relationship between the S gene of SHQP/YM/2013 and those of the four Korean field strains from 2008-2009. Its ORF3 gene, however, fell into three groups. Recent prevalent Chinese PEDV field isolates were divided between group 1 and group 3, which suggests that the recent prevalent Chinese PEDV field isolates represent a new genotype that differs from the genotype that includes the vaccine strains. Based on phylogenetic analysis of the M gene, ORF3 gene and S gene, our study demonstrated that prevalent PEDV isolates in China may have originated from Korean strains. This report describes the complete genome sequence of SHQP/YM/2013, and the data will promote a better understanding of the molecular epidemiology and genetic diversity of PEDV field isolates in eastern China.
authors.affiliation: Shanghai Animal Disease Control Center, Shanghai, 201103, People's Republic of China, dequan_yang@126.com.
authors.forename: De-Quan
authors.initials: DQ
authors.lastname: Yang
authors.forename: Fei-Fei
authors.initials: FF
authors.lastname: Ge
authors.forename: Hou-Bin
authors.initials: HB
authors.lastname: Ju
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Jian
authors.initials: J
authors.lastname: Liu
authors.forename: Kun
authors.initials: K
authors.lastname: Ning
authors.forename: Pei-Hong
authors.initials: PH
authors.lastname: Liu
authors.forename: Jin-Ping
authors.initials: JP
authors.lastname: Zhou
authors.forename: Quan-Yun
authors.initials: QY
authors.lastname: Sun
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002681:China; D018352:Coronavirus Infections / Q000821:virology; D005243:Feces / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D053485:Porcine epidemic diarrhea virus / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D013552:Swine / Q000821:virology; D013553:Swine Diseases / Q000821:virology; D015678:Viral Structural Proteins / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D015678:Viral Structural Proteins