Molecular characterization of pig epidemic diarrhoea viruses isolated in Japan from 2013 to 2014

Suzuki, Tohru; Murakami, Satoshi; Takahashi, Osamu; Kodera, Aya; Masuda, Tsuneyuki; Itoh, Sakie; Miyazaki, Akira; Ohashi, Seiichi; Tsutsui, Toshiyuki

doi:10.1016/j.meegid.2015.10.017

Cited by 65 publications

(73 citation statements)

References 24 publications

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“…Within JKa-295, three variants with the 197-aa deletion shared 99.72–99.92% nucleotide sequence identity with each other but had 99.38–99.55% nucleotide sequence identity with JKa-295fSde204Co25, which possessed the 204-aa deletion (S1 Table). On the contrary, all strains found in JKa-295 and JMi-277 had the greatest nucleotide sequence identity (98.71–99.92%) with highly virulent strains isolated recently in the US, South Korea, and Japan [9, 13, 31] but exhibited relatively less nucleotide sequence identity (93.34–95.99%) with Japanese PEDV strains (NK, MK, KH, and 83P-5) reported prior to 2013 [39]. Furthermore, phylogenetic analysis based on the full-length S gene classified these Japanese strains into the North American (highly virulent) type as shown in Fig 2A.…”

Section: Resultsmentioning

confidence: 99%

“…This indicated that PEDV variants could be transmitted from farm to farm and/or that the proportion of the variants in samples collected at the primary outbreaks was insufficient to permit detection of the variants by PCR. Additionally, PED outbreaks in Japan since late 2013 were proposed to be caused by the invasion of recent overseas strains [15, 31]. Taken together, it is possible that in the recent pandemic, both the PEDV variants and the strains with an intact S gene were introduced together from other countries, after which they spread across Japan.…”

Section: Resultsmentioning

confidence: 99%

“…Thereafter, only sporadic PED cases were reported from 1997 to 2005. After an absence of seven years, PED reemerged, sweeping rapidly across the country since October 2013 [31]. Till August 2015, more than 490,000 pigs from approximately 1,000 infected farms have died of PED in Japan, according to the Ministry of Agriculture, Forestry, and Fisheries (http://www.maff.go.jp).…”

Section: Introductionmentioning

confidence: 99%

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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

et al. 2017

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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

et al. 2017

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“…64 In addition, from late 2013, PEDV outbreaks were reported in Japan, South Korea, and Taiwan. 55,60,80 The predominant genotypes of PEDV in these regions during 2013-2014 were all phylogenetically related to the highly pathogenic US-like lineage within the genotype IIa. 55,60,80 The source of PEDV incursion into swine populations in these regions has not yet been determined.…”

Section: Asiamentioning

confidence: 97%

“…55,60,80 The predominant genotypes of PEDV in these regions during 2013-2014 were all phylogenetically related to the highly pathogenic US-like lineage within the genotype IIa. 55,60,80 The source of PEDV incursion into swine populations in these regions has not yet been determined. Novel variant Ib isolates also have been detected in South Korea and Japan during 2013-2014, which were most closely related to the US variant OH851.…”

Section: Asiamentioning

confidence: 97%