title: The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets.
abstract: Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24-48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.
authors.affiliation: Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.|SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden.|The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.
authors.forename: Oskar E
authors.initials: OE
authors.lastname: Karlsson
authors.affiliation: Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: Jenny
authors.initials: J
authors.lastname: Larsson
authors.affiliation: SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden.
authors.forename: Juliette
authors.initials: J
authors.lastname: Hayer
authors.affiliation: Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.|The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.
authors.forename: Mikael
authors.initials: M
authors.lastname: Berg
authors.affiliation: Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Jacobson
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D016022:Case-Control Studies; D003967:Diarrhea / Q000662:veterinary* / Q000821:virology; D013552:Swine