title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation.
abstract: Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28-714 (10-238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease.
authors.affiliation: Laboratory of Veterinary Pathology, Department of Veterinary, Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Nguyen Van
authors.initials: NV
authors.lastname: Diep
authors.affiliation: Laboratory of Veterinary Pathology, Department of Veterinary, Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Junzo
authors.initials: J
authors.lastname: Norimine
authors.affiliation: Laboratory of Veterinary Pathology, Department of Veterinary, Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Masuo
authors.initials: M
authors.lastname: Sueyoshi
authors.affiliation: Department of Veterinary Pathology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam.
authors.forename: Nguyen Thi
authors.initials: NT
authors.lastname: Lan
authors.affiliation: Laboratory of Veterinary Pathology, Department of Veterinary, Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Ryoji
authors.initials: R
authors.lastname: Yamaguchi
mesh_terms: D000818:Animals; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D004196:Disease Outbreaks; D014644:Genetic Variation; D005838:Genotype; D007564:Japan / Q000453:epidemiology; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000145:classification / Q000235:genetics*; D017384:Sequence Deletion / Q000235:genetics*; D064370:Spike Glycoprotein, Coronavirus / Q000235:genetics*; D034421:Sus scrofa; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*
chemical_list: D064370:Spike Glycoprotein, Coronavirus