title: Molecular characterization of pig epidemic diarrhoea viruses isolated in Japan from 2013 to 2014.
abstract: Since October 2013, approximately 1000 outbreaks of porcine epidemic diarrhoea (PED) have occurred, spanning almost all prefectures of Japan, after a period of seven years without a reported case. In order to consider occurrence factor of PED outbreaks, we determined the whole-genome sequences of 38 PED virus (PEDV) strains from diarrheal samples collected at swine farms in 18 prefectures between 2013 and 2014 using next-generation sequencing technology. Using these data, we investigated genetic variation among the recent Japanese PEDV strains and the genetic relationships between these strains and global PEDV strains isolated recently from multiple swine-industrial countries. Eleven out of 38 PEDV strains were isolated successfully on Vero cells with trypsin treatment and subjected to genome sequence analysis. In a comparative genome analysis, we detected two novel PEDV variants, TTR-2/JPN/2014 and MYG-1/JPN/2014, with large deletions in the spike and ORF3 genes, respectively. A phylogenetic analysis based on the spike gene showed that the 38 Japanese PEDV strains were classified into two PEDV types: the North American type with high virulence (n=34) and the INDEL type (n=4). In addition, the recent Japanese PEDV isolates had a close relationship to global PEDV strains isolated in recent years than to the classical PEDV strains detected in Japan the past decades ago. Moreover, the phylogenetic dendrogram of the complete genomes also indicated that the 38 Japanese PEDV strains, including the two novel PEDV variants discovered in this study, are closely related to the PEDV strains that were widespread in the United States and Korea in 2013-2014. These findings suggest that the re-emergence of PED outbreaks since the last reported case in 2006 was caused by the introduction of recent PEDV strains to Japan from overseas.
authors.affiliation: Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan. Electronic address: tohru_suzuki@affrc.go.jp.
authors.forename: Tohru
authors.initials: T
authors.lastname: Suzuki
authors.affiliation: Life Technologies Japan ltd., Thermo Fisher Scientific, 4-2-8 Shibaura, Minato-ku, Tokyo 108-0023, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Murakami
authors.affiliation: Life Technologies Japan ltd., Thermo Fisher Scientific, 4-2-8 Shibaura, Minato-ku, Tokyo 108-0023, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Takahashi
authors.affiliation: Sendai Livestock Hygiene Service Center, 3-11-22 Sendai, Miyagi 983-0832, Japan.
authors.forename: Aya
authors.initials: A
authors.lastname: Kodera
authors.affiliation: Kurayoshi Livestock Hygiene Service Center, 2-132 Kurayoshi, Tottori 682-0017, Japan.
authors.forename: Tsuneyuki
authors.initials: T
authors.lastname: Masuda
authors.affiliation: Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan.
authors.forename: Sakie
authors.initials: S
authors.lastname: Itoh
authors.affiliation: Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Miyazaki
authors.affiliation: Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan.
authors.forename: Seiichi
authors.initials: S
authors.lastname: Ohashi
authors.affiliation: Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Tsutsui
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002522:Chlorocebus aethiops; D018352:Coronavirus Infections / Q000453:epidemiology* / Q000821:virology*; D004196:Disease Outbreaks; D005814:Genes, Viral; D016679:Genome, Viral; D007564:Japan / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology*; D014709:Vero Cells
keywords: Full genome; Japan; Outbreak; Phylogenetic analysis; Porcine epidemic diarrhoea