Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks

Abstract

BackgroundSince 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.ResultsPhylogenetic 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.ConclusionsThese 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.Electronic supplementary materialThe online version of this article (10.1186/s12917-018-1409-0) contains supplementary material, which is available to authorized users.

Updated phylogenetic analysis of the spike gene and identification of a novel recombinant porcine epidemic diarrhoea virus strain in Taiwan

“…Before 2010, PEDV was endemic in these countries and caused mild diarrhoea predominantly in postweaning pigs (Song & Park, ). However, the emerging new variants of group 2 (G2) PEDV since 2010 in China and PEDV in late 2013 in North America and Asia caused up to 100% mortality in piglets less than 7 days old and severe economic losses (Alonso et al, ; Lin et al, ; Pasick et al, ; Steinrigl et al, ; Stevenson et al, ; Van Diep et al, ). The outbreaks of the new G2 PEDV variants suggest that the classical G1 PEDV‐based vaccines elicited limited protection against the new G2b PEDVs (Opriessnig et al, ) and highlight the importance of continuously monitoring genetic alterations of the virus for controlling outbreaks of the disease.…”

“…The G2 group includes PEDV G2a, such as the KNU‐1302/Korea/2013 strain, and G2b strains, such as the USA/Illinois262/2014 strain, have caused outbreaks in North America and Asia (Lee, ; Vlasova et al, ). Mutations in the S gene of G2 PEDVs that led to viral escape from existing antibodies elicited by CV777‐based vaccine or a historic G1a or G1b PEDV strain infection have been speculated to be responsible for the G2 PEDV outbreaks in Asia (Chiou et al, ; Lee & Lee, ; Van Diep et al, ; Zhang et al, ; Zhao et al, ).…”

Single-domain antibodies as promising experimental tools in imaging and isolation of porcine epidemic diarrhea virus

“…PEDV, a member of the genus Coronavirus, family Coronaviridae, is the causative agent of porcine epidemic diarrhea (International Committee on Taxonomy of Viruses. and King 2012), the most economically important disease affecting the global swine industry today (Van Diep et al 2018). PEDV encodes four major structural proteins, membrane (M) (27-32 kDa), envelope (E) (7 kDa), spike (S) (180-220 kDa), and nucleocapsid (N) (55-58 kDa) (Utiger et al 1995;Yeo et al 2003).…”

EuNPs-mAb fluorescent probe based immunochromatographic strip for rapid and sensitive detection of porcine epidemic diarrhea virus

“…As early as the 1970s, PEDV was reported in European and Asian pig industries. Since then, PEDV has spread to the United States, Canada, Mexico, China, South Korea and other countries, and has induced a worldwide disease [4,5]. PEDV has the highest incidence of all the pandemic viruses in China, accounting for about 46% of pandemic viruses [6,7].…”