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.
Highlights
Neonatal porcine diarrhoea (NPD) is a common problem in pig farming worldwide and contributes to morbidity and mortality among piglets, in intensive farming systems [1,2]
Eukaryotic Virome in Healthy and Diarrhoeic Piglets publication reflects views only of the authors, and the European Commission cannot be held responsible for any use that may be made of the information contained therein; Swedish Farmers’ Foundation for Agricultural Research, grant H1050154, Neonatal diarrhoea in piglets- an emergent problem in modern pig production, awarded to MJ, http://www.lantbruksforskning.se/
An additional factor that could have contributed to the low number of viruses in neonatal piglets is the passive immunity received through colostrum. Another contradiction with previous studies is that we found a greater number of different virus families in healthy piglets compared to the pooled diarrhoeic samples
Summary
Neonatal porcine diarrhoea (NPD) is a common problem in pig farming worldwide and contributes to morbidity and mortality among piglets, in intensive farming systems [1,2]. Eukaryotic Virome in Healthy and Diarrhoeic Piglets publication reflects views only of the authors, and the European Commission cannot be held responsible for any use that may be made of the information contained therein Eu/dgs/home-affairs/index_en.htm); Swedish Farmers’ Foundation for Agricultural Research, grant H1050154, Neonatal diarrhoea in piglets- an emergent problem in modern pig production, awarded to MJ, http://www.lantbruksforskning.se/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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