Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology
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...
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| Format: | Article |
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MDPI AG
2017-07-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/9/7/177 |
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| author | Dennis Hanke Anne Pohlmann Carola Sauter-Louis Dirk Höper Julia Stadler Mathias Ritzmann Adi Steinrigl Bernd-Andreas Schwarz Valerij Akimkin Robert Fux Sandra Blome Martin Beer |
| author_facet | Dennis Hanke Anne Pohlmann Carola Sauter-Louis Dirk Höper Julia Stadler Mathias Ritzmann Adi Steinrigl Bernd-Andreas Schwarz Valerij Akimkin Robert Fux Sandra Blome Martin Beer |
| author_sort | Dennis Hanke |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T13:37:05Z |
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| id | doaj.art-2c1a4297c0f14a03af1f27e0ccfeaffe |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-21T13:37:05Z |
| publishDate | 2017-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-2c1a4297c0f14a03af1f27e0ccfeaffe2022-12-21T19:02:08ZengMDPI AGViruses1999-49152017-07-019717710.3390/v9070177v9070177Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular EpidemiologyDennis Hanke0Anne Pohlmann1Carola Sauter-Louis2Dirk Höper3Julia Stadler4Mathias Ritzmann5Adi Steinrigl6Bernd-Andreas Schwarz7Valerij Akimkin8Robert Fux9Sandra Blome10Martin Beer11Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, D-17493 Greifswald—Insel Riems, GermanyFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, D-17493 Greifswald—Insel Riems, GermanyFriedrich-Loeffler-Institut, Institute of Epidemiology, D-17493 Greifswald—Insel Riems, GermanyFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, D-17493 Greifswald—Insel Riems, GermanyClinic for Swine, Ludwig-Maximilians-University Munich, D-85764 Oberschleissheim, GermanyClinic for Swine, Ludwig-Maximilians-University Munich, D-85764 Oberschleissheim, GermanyÖsterreichische Agentur für Gesundheit und Ernährungssicherheit GmbH, A-2340 Mödling, AustriaVaxxinova GmbH, Standort Leipzig, D-04103 Leipzig, GermanyChemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, D-70736 Fellbach, Germany, <email>Valerij.Akimkin@cvuas.bwl.de</email>Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-University Munich, D-80539 Munich, GermanyFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, D-17493 Greifswald—Insel Riems, GermanyFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, D-17493 Greifswald—Insel Riems, GermanyPorcine 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.https://www.mdpi.com/1999-4915/9/7/177porcine epidemic diarrheaporcine epidemic diarrhea virusphylogenetic analysesmetagenome |
| spellingShingle | Dennis Hanke Anne Pohlmann Carola Sauter-Louis Dirk Höper Julia Stadler Mathias Ritzmann Adi Steinrigl Bernd-Andreas Schwarz Valerij Akimkin Robert Fux Sandra Blome Martin Beer Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology Viruses porcine epidemic diarrhea porcine epidemic diarrhea virus phylogenetic analyses metagenome |
| title | Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology |
| title_full | Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology |
| title_fullStr | Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology |
| title_full_unstemmed | Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology |
| title_short | Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology |
| title_sort | porcine epidemic diarrhea in europe in detail analyses of disease dynamics and molecular epidemiology |
| topic | porcine epidemic diarrhea porcine epidemic diarrhea virus phylogenetic analyses metagenome |
| url | https://www.mdpi.com/1999-4915/9/7/177 |
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