title: Detection and phylogenetic analysis of porcine epidemic diarrhea virus in central China based on the ORF3 gene and the S1 gene.
abstract: Porcine epidemic diarrhea (PED) has increased in severity in China since 2010. To investigate further the infectivity, genetic diversity and molecular epidemiology of its causative agent, the porcine epidemic diarrhea virus (PEDV), we assessed 129 clinical samples, which were the intestinal tissue of piglets with severe diarrhea, from 17 cities in central China. Both the spike (S) glycoprotein (S1, 1-789 amino acids (aa)) and the full-length ORF3 gene of 21 representative field strains from 21 farms in 11 cities were sequenced and analysed.
  
  
  
  PEDV was detected by reverse transcription-polymerase chain reaction (RT-PCR), and S1 and ORF3 sequences were processed by the Clustal W method via DNAMAN 8 software, and phylogenetic trees were constructed by the neighbor-joining method using MEGA 6 software.
  
  
  
  The prevalence of PEDV was 92.25% and was detected in 119 of 129 samples, with 94.03% (63 of 67) of pig farms harbouring the disease. According to the phylogenetic analysis of the S1 genes, our isolates all fell into group G2 (variants) and showed a close relationship to isolates from Chinese (HN1303, CH/ZMDZY/11 and AJ1102), Korean (AD01), American (MN, IA1, IA2 and 13-019349) sources, and these isolates differed genetically from other Chinese (LZC, CH/HNZZ/2011 and SD-M) and Korean (SM98) strains as well Japanese (83-P5 and MK) strains. In addition, our isolates differed from attenuated vaccine strains, CV777 (used in China) and DR13 (used in Korea). According to our derived amino acid sequence analysis, we detected one novel variant PEDV, viz: CH/HNLY, with 4-aa insertion/deletion (RSSS/T) at position 375 and 1-aa (D) deletion at position 430 compared to the CV777 attenuated strain. These mutations were located on the receptor binding domain. Our ORF3 gene analyses showed that the prevalent PEDV isolates were variants, and the isolated strains differed genetically from the vaccine strains.
  
  
  
  These findings illustrated the existence of genetic diversity among geographically distinct PEDV strains, and our study has provided an impetus to conduct further research on the PEDV receptor binding protein and on the new and efficacious vaccines design.
authors.affiliation: College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
authors.forename: Yunfang
authors.initials: Y
authors.lastname: Su
authors.affiliation: Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Science, Zhengzhou, 450002, China. yunchaoliu2012@163.com.
authors.forename: Yunchao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Science, Zhengzhou, 450002, China.
authors.forename: Yumei
authors.initials: Y
authors.lastname: Chen
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Baolei
authors.initials: B
authors.lastname: Zhao
authors.affiliation: College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
authors.forename: Pengchao
authors.initials: P
authors.lastname: Ji
authors.affiliation: Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Science, Zhengzhou, 450002, China.
authors.forename: Guangxu
authors.initials: G
authors.lastname: Xing
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Jiang
authors.affiliation: Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Science, Zhengzhou, 450002, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Yapeng
authors.initials: Y
authors.lastname: Song
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Guoqiang
authors.initials: G
authors.lastname: Wang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Dongliang
authors.initials: D
authors.lastname: Li
authors.affiliation: Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Science, Zhengzhou, 450002, China.
authors.forename: Ruiguang
authors.initials: R
authors.lastname: Deng
authors.affiliation: Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Science, Zhengzhou, 450002, China. zhanggaiping2003@163.com.|College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. zhanggaiping2003@163.com.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China. zhanggaiping2003@163.com.
authors.forename: Gaiping
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D002947:Cities / Q000453:epidemiology; D016000:Cluster Analysis; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D014644:Genetic Variation; D017720:Molecular Epidemiology; D058974:Phylogeography; D053485:Porcine epidemic diarrhea virus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D015995:Prevalence; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: ORF3 gene; PEDV; Phylogenetic analysis; S1 gene; Variants