Complete Genome Sequence of a Porcine Epidemic Diarrhea S Gene Indel Strain Isolated in France in December 2014

Abstract

We report the first and only case of a porcine epidemic diarrhea (PED) outbreak occurring in December 2014 in northern France, and we show using the full-length genome sequence of the French PED virus (PEDV) isolate that it was a PEDV indel strain close to German PEDV strains recently isolated.

First Detection and Clinical Presentation of Porcine Epidemic Diarrhea Virus (Pedv) in Serbia

“…The only well documented is a typical PED epidemic in Europe which occurred during the winter of 2005-2006 in Northern Italy [16]. Recently, the PED-confi rmed outbreaks have been reported in several Central European countries: Portugal [7], Germany [15], Austria [17], France [18], Belgium [19], Ukraine [20], Italy [21] and Slovenia [22]. The full genome sequencing of recent PEDV strains from Germany, Belgium and France [17][18][19] shows that they are all highly similar and closely related to S-INDEL strains from USA [9,13].…”

Porcine epidemic diarrhea virus: current insights

“…23,41,55,[58][59][60][61][62]74,81,84,99,100 Those OH851-like variants, which belong to genotype Ib and are distributed in the People's Republic of China, the United States, South Korea, Japan, and Europe, have generally been associated with mildto-moderate clinical outbreaks. 15,20,21,56,57,81 However, severe cases associated with OH851-like strains were reported in Germany, where mortality in suckling piglets reached almost 70% in one of two sow farms, and in Portugal (mortality rate was not given). 16,22 A comparison experiment on the pathogenesis of three US prototype strains and one OH851-like variant reported recently by Chen et al 100 demonstrated that the OH851-like variant had significantly diminished clinical signs, virus shedding in feces, gross or histopathological lesions in small intestines, and immunohistochemistry (IHC) scores in ileum compared to three US prototype isolates.…”

“…57,85 Possible recombination events might contribute to a rapid evolution of US strains. 57 Recently, OH851-like strains have been detected in South Korea 56 and Japan 81 in Asia, and Germany, 15,16 Italy, 17 the Netherlands, 18 Belgium, 19 France, 20 Portugal, 22 Slovenia, 21 and Austria 21 in Europe. A novel variant TC-PC22A (GenBank accession number KM392224), which has a large deletion (197-aa) in the N-terminal portion of the S protein, was recently isolated in the United States.…”

“…15 Thereafter, 20 Italy, 17 Austria, 21 Belgium, 19 the Netherlands, 18 Portugal, 22 and Slovenia. 21 Different from the aforementioned European countries, in 2014, severe PED outbreaks occurred in Ukraine, and the isolates clustered phylogenetically with genotype IIa US strains.…”

“…Genotype Ia contains classical strains, including the prototype strain CV777 and historical vaccine strains, and genotype Ib includes some variants such as OH851-like isolates from the People's Republic of China, the United States, South Korea, Europe, and Austria. 16,[19][20][21]56,57 Genotype II contains historical isolates in South Korea, and currently prevalent global field isolates. Genotype IIa was a recently prevalent genotype in the People's Republic of China, 58,59 Taiwan, [60][61][62] South Korea, 55,63 and the United States.…”