Key result
Recent Japanese field PEDVs were genetically distinct from classical Japanese strains and classified into North American, S INDEL, and Asian non-S INDEL genotypes, with various mutations in epitope regions compared to vaccine strains.
Observational (n=45)
Recent PEDV outbreaks in Japan are caused by strains genetically distinct from classical strains and vaccine strains, showing close relation to US strains and possessing mutations in key epitope regions that may affect vaccine efficacy.
May indicate reduced PEDV vaccine efficacy in Japan; leaves open need for updated strain surveillance.
BACKGROUND: Since late 2013, porcine epidemic diarrhea virus (PEDV) has reemerged in Japan and caused severe economic losses to the swine industry. Although PEDV vaccines have been used widely, the disease has swept rapidly across the county, and is commonly observed in PED-vaccinated farms, and has recurred in domestic herds. To better understand PEDVs responsible for the reemerging outbreaks in Japan, full-length spike (S), membrane (M), and nucleocapsid (N) genes of 45 PEDVs collected in Japan during 2013-2016, were sequenced and analyzed. RESULTS: Phylogenetic analysis based on S gene sequences revealed that all the recent field PEDVs were genetically distinct from the classical Japanese strains, and were classified into three genotypes: North American (NA), S INDEL, and Asian non-S INDEL. Our data suggested a possibility that multiple parental PEDV strains were introduced into Japan from abroad at the same time or similar times. The newly identified Japanese strains showed the closest relationship to the US strains. Two sublineages of Japanese strains circulating in Japan were similar to two sublineages identified in the US, suggesting common ancestors for these strains. In comparison with two vaccine strains used in Japan, the field strains had various changes in epitope regions, glycosylation sites, and phosphorylation sites. These substitutions, particularly observed in epitope regions of the S (521, 553, 568, and 570), M (5), and N (123, 252, and 255) proteins, may have affected antigenicity and vaccine efficacy, resulting in an unsuccessful PEDV control. Sequence comparisons between PEDVs collected from primary and secondary outbreaks in three herds revealed that the disease has developed to an endemic stage in which PEDV could persist for nearly two years in the herds or local regions, causing subsequent epidemics. CONCLUSIONS: These results elucidate the genetic characteristics, origin, and molecular epidemiology of PEDVs circulating in Japan, as well as the PEDV strains causing recurrent outbreaks. This study provides a better insight into the PEDVs responsible for recent outbreaks in Japan, and could potentially help to develop measures for controlling and preventing the disease.
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Diep et al. (2018) conducted an observational in Porcine epidemic diarrhea virus (PEDV) (n=45). Recent field PEDV strains vs. Classical Japanese strains and vaccine strains was evaluated on Phylogenetic classification and genetic mutations of PEDV strains. Recent Japanese field PEDVs were genetically distinct from classical Japanese strains and classified into North American, S INDEL, and Asian non-S INDEL genotypes, with various mutations in epitope regions compared to vaccine strains.
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