title: Characterization of Chinese Porcine Epidemic Diarrhea Virus with Novel Insertions and Deletions in Genome.
abstract: Outbreaks of porcine epidemic diarrhoea virus (PEDV) have caused great economic losses to the global pig industry. PEDV strains with variants in the spike (S) gene have been reported in several countries. To better understand the molecular epidemiology and genetic diversity of PEDV field isolates, in this study, we characterised the complete genome sequence of a novel PEDV variant JSCZ1601 from a outbreak in China in 2016. The PEDV isolate was 28,033 nucleotides (nt) in length without the polyadenylated sequences. Phylogenetic analysis based on the full-length genome sequence of JSCZ1601 grouped it with the pandemic variants determined post-2010 into group 2 (G2). However, the S gene of JSCZ1601 formed a new subgroup separated from the subgroups containing the other G2 strains. Comparative analysis of the amino acids encoded by the S genes revealed the N-terminal of the deduced JSCZ1601 S protein had a novel two-amino-acid deletion (N58 and S59) compared with all identified genogroups. Further, compared with the reference strains, a 'G' insertion was detected in the 5' terminal of the 5'UTR of the JSCZ1601. The animal experiment revealed that this strain was high pathogenic to neonatal pigs. Taken together, a PEDV strain with the new molecular characterizations and phylogenies was found in mainland China. It is necessary to strengthen the monitoring of PEDV variations.
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Baochao
authors.initials: B
authors.lastname: Fan
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.|College of animal science and technology, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Dian
authors.initials: D
authors.lastname: Jiao
authors.affiliation: Animal, Plant and Food Inspection Center, Jiangsu Entry-Exit Inspection and Quarantine Bureau, Nanjing 210000, China.
authors.forename: Xiaona
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Fengjiao
authors.initials: F
authors.lastname: Pang
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Xiao
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Zhengyu
authors.initials: Z
authors.lastname: Yu
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Aihua
authors.initials: A
authors.lastname: Mao
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Rongli
authors.initials: R
authors.lastname: Guo
authors.affiliation: College of Animal medicine, Agricultural University of Hebei, Baoding 071001, China.
authors.forename: Wanzhe
authors.initials: W
authors.lastname: Yuan
authors.affiliation: Henan University of Animal Husbandry and Economy, Zhengzhou 450000, China.
authors.forename: Pandeng
authors.initials: P
authors.lastname: Zhao
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Kongwang
authors.initials: K
authors.lastname: He
authors.affiliation: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Li
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D018352:Coronavirus Infections / Q000453:epidemiology / Q000235:genetics / Q000662:veterinary; D004196:Disease Outbreaks; D016679:Genome, Viral; D054643:INDEL Mutation; D053485:Porcine epidemic diarrhea virus / Q000235:genetics* / Q000302:isolation & purification; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000235:genetics / Q000821:virology