Abstract
Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease of swine caused by the eponymous virus (PEDV) which belongs to the genus Alphacoronavirus within the Coronaviridae virus family. Following the disastrous outbreaks in Asia and the United States, PEDV has been detected also in Europe. In order to better understand the overall situation, the molecular epidemiology, and factors that might influence the most variable disease impact; 40 samples from swine feces were collected from different PED outbreaks in Germany and other European countries and sequenced by shot-gun next-generation sequencing. A total of 38 new PEDV complete coding sequences were generated. When compared on a global scale, all investigated sequences from Central and South-Eastern Europe formed a rather homogeneous PEDV S INDEL cluster, suggesting a recent re-introduction. However, in-detail analyses revealed two new clusters and putative ancestor strains. Based on the available background data, correlations between clusters and location, farm type or clinical presentation could not be established. Additionally, the impact of secondary infections was explored using the metagenomic data sets. While several coinfections were observed, no correlation was found with disease courses. However, in addition to the PEDV genomes, ten complete viral coding sequences from nine different data sets were reconstructed each representing new virus strains. In detail, three pasivirus A strains, two astroviruses, a porcine sapelovirus, a kobuvirus, a porcine torovirus, a posavirus, and an enterobacteria phage were almost fully sequenced.
Highlights
Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease of swine that results in severe enteritis, diarrhea, vomiting, and dehydration
32 complete coding sequences were obtained from German PED cases, four Porcine epidemic diarrhea virus (PEDV) complete coding sequences were generated from Austrian samples, and two complete coding sequences were assembled analyzing samples from Romanian PED cases
All sequences from recent PED cases in Germany, Austria, and Romania formed a distinct cluster, which was closely related to S INDEL strains from the USA and Asia
Summary
Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease of swine that results in severe enteritis, diarrhea, vomiting, and dehydration. After its first recognition in the 1970s in Europe [3], the disease caused considerable economic losses, especially in Asia. In May 2013, a highly virulent PEDV variant emerged in the United States (US), with swine farms experiencing explosive epidemics affecting all age classes of animals, with up to 95% mortality in suckling pigs [5,6]. Apart from these highly virulent strains, apparently less-virulent so-called S INDEL (INDEL standing for insertions and deletions) strains were co-circulating in the US [7,8]
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