title: Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China.
abstract: Since late 2010, porcine epidemic diarrhea virus (PEDV) has rapidly disseminated all over the China and caused considerable morbidity and high mortality (up to 100%) in neonatal piglets. 79.66% (141 of 177) pig farms in 29 provinces (excluding Tibet and Hainan, China) and 72.27% (417 of 577) samples were positive for PEDV confirmed by reverse transcription-polymerase chain reaction (RT-PCR). The full-length S genes of representative field strains were sequenced. 33 field strains share 93.5%-99.9% homologies with each other at the nucleotide sequence level and 92.3%-99.8% homologies with each other at the amino acids sequence level. Most field strains have nucleotide deletion and insertion regions, and show lower homologies (93.5%-94.2%) with Chinese classical strain CH/S, however higher homologies (97.1%-99.3%) with recent strain CHGD-1. The phylogenetic analysis showed there are classical strains and variants prevailing in pig herd in China. PEDV has a high detection rate in pig herds in China. Sequence analysis indicated the S genes of recent field strains have heterogeneity and the variants are predominant.
authors.affiliation: Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China. fl@hvri.ac.cn.
authors.forename: Jianfei
authors.initials: J
authors.lastname: Chen
authors.forename: Xiaozhen
authors.initials: X
authors.lastname: Liu
authors.forename: Da
authors.initials: D
authors.lastname: Shi
authors.forename: Hongyan
authors.initials: H
authors.lastname: Shi
authors.forename: Xin
authors.initials: X
authors.lastname: Zhang
authors.forename: Changlong
authors.initials: C
authors.lastname: Li
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Chi
authors.forename: Li
authors.initials: L
authors.lastname: Feng
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002681:China; D016000:Cluster Analysis; D018352:Coronavirus Infections / Q000662:veterinary* / Q000821:virology; D014644:Genetic Variation; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D064370:Spike Glycoprotein, Coronavirus / Q000235:genetics*; D013552:Swine; D013553:Swine Diseases / Q000821:virology*
chemical_list: D012367:RNA, Viral; D064370:Spike Glycoprotein, Coronavirus