title: Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015.
abstract: In an effort to trace the evolution of porcine epidemic diarrhea virus (PEDV), S1 and ORF3 genes of viruses identified in 41 pig farms from seven regions (North, Northeast, Northwest, Central, East, South West, and South, respectively) of China in 2015 were sequenced and analyzed. Sequence analysis revealed that the 41 ORF3 genes and 29 S1 genes identified in our study exhibited nucleotide homologies of 98.2%-100% and 96.6%-100%, respectively; these two genes exhibited low nucleotide sequence similarities with classical CV777 strain and early Chinese strain LZC. Phylogenetic analysis indicated that the identified PEDV strains belonged to global non S-INDEL strains, and exhibited genetic diversity; S1 gene of the HLJ2015/DP1-1 strain harbored an unique deletion of 12 nucleotides (A1130CAACTCCACTG1141); while the Chinese PEDV S-INDEL reference strains included two types of the "CV777" S-INDEL as well as the "US" S-INDEL, and all co-circulated with Chinese non S-INDEL strains. Of 29 identified S1 genes, the SS2 epitope (Y748SNIGVCK755) was highly conserved, while the SS6 epitope (L764QDGQVKI771) and pAPN receptor-binding region (aa 490-615) exhibited amino substitutions. Nine possible recombination events were identified between the 29 identifed S1 genes and the 3 S1 reference genes from early Chinese PEDV strains. The complete S genes of selected Chinese PEDV field strains (2011-2015) showed 5.18%-6.07% nucleotide divergence, which is far higher than the divergence observed in early Chinese PEDV strains (3.1%) (P<0.05). Our data provide evidence that PEDV non S-INDEL strains with genetic diversities and potential recombination circulate in seven regions of China in 2015; Chinese PEDV S-INDEL strains exhibit genetic diversity and co-circulate with non S-INDEL strains.
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Enyu
authors: E
authors: Wang
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Donghua
authors: D
authors: Guo
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Chunqiu
authors: C
authors: Li
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Shan
authors: S
authors: Wei
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Zhihui
authors: Z
authors: Wang
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Qiujin
authors: Q
authors: Liu
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Bei
authors: B
authors: Zhang
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Fanzhi
authors: F
authors: Kong
authors: Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Nangang District, Harbin, P.R. China.
authors: Li
authors: L
authors: Feng
authors: College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Sartu District, Daqing, P.R. China.
authors: Dongbo
authors: D
authors: Sun
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary / Q000821:virology; D005814:Genes, Viral; D017720:Molecular Epidemiology; D016366:Open Reading Frames; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000235:genetics* / Q000302:isolation & purification; D011995:Recombination, Genetic; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology