Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology
Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, D-17493 Greifswald—Insel Riems, Germany
Friedrich-Loeffler-Institut, Institute of Epidemiology, D-17493 Greifswald—Insel Riems, Germany
Clinic for Swine, Ludwig-Maximilians-University Munich, D-85764 Oberschleissheim, Germany
Österreichische Agentur für Gesundheit und Ernährungssicherheit GmbH, A-2340 Mödling, Austria
Vaxxinova GmbH, Standort Leipzig, D-04103 Leipzig, Germany
Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, D-70736 Fellbach, Germany,
Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-University Munich, D-80539 Munich, Germany
Author to whom correspondence should be addressed.
Academic Editor: Andrew Mehle
Viruses 2017, 9(7), 177; https://doi.org/10.3390/v9070177
Received: 24 May 2017 / Revised: 29 June 2017 / Accepted: 30 June 2017 / Published: 6 July 2017
(This article belongs to the Section Animal Viruses)
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.