title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China.
abstract: A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and complete M gene were amplified from PEDV-positive strains by RT-PCR, cloned, sequenced and compared with each other, as well as with the reference strains in GenBank. Sequence homology results of the partial S gene and complete M gene showed that all south China field PEDV strains had nucleotide (deduced amino acid) sequence identities of 86.7-98.7 % (83.2-99.3 %) and 96.1-100 % (95.0-100%), respectively, with the foreign reference strains reported in GenBank. Phylogenetic analysis of the partial S gene showed that all the south China PEDV strains and two Thailand strains (08UB01 and 08RB07) belong to the same group and differ genetically from European strains and early domestic strains. Phylogenetic analysis of the complete M gene showed that all south China PEDV strains have a close relationship with most of the strains in Korea and Thailand, but differ genetically from the vaccine strain (CV777).
authors.affiliation: South China Agricultural University, Tianhe District, Wushan Road, Guangzhou, 510642 Guangdong, People's Republic of China.
authors.forename: Zhi-Li
authors.initials: ZL
authors.lastname: Li
authors.forename: Ling
authors.initials: L
authors.lastname: Zhu
authors.forename: Jing-Yun
authors.initials: JY
authors.lastname: Ma
authors.forename: Qing-Feng
authors.initials: QF
authors.lastname: Zhou
authors.forename: Yan-Hua
authors.initials: YH
authors.lastname: Song
authors.forename: Bao-Li
authors.initials: BL
authors.lastname: Sun
authors.forename: Rui-Ai
authors.initials: RA
authors.lastname: Chen
authors.forename: Qing-Mei
authors.initials: QM
authors.lastname: Xie
authors.forename: Ying-Zuo
authors.initials: YZ
authors.lastname: Bee
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D000086862:Coronavirus M Proteins; D008562:Membrane Glycoproteins / Q000235:genetics; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D064370:Spike Glycoprotein, Coronavirus; D013552:Swine / Q000821:virology*; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology; D014759:Viral Envelope Proteins / Q000235:genetics; D014763:Viral Matrix Proteins / Q000235:genetics
chemical_list: D000086862:Coronavirus M Proteins; C000706236:M protein, Porcine epidemic diarrhea virus; C000706238:M protein, Transmissible gastroenteritis virus; D008562:Membrane Glycoproteins; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; D014763:Viral Matrix Proteins