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.

Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique

“…The virus discovery rate in different species, such as mosquitoes, have increased through the availability of deep-sequencing technologies combined with viral metagenomic approaches. Apart from novel virus discovery, viral metagenomics have become a powerful method for genetically characterizing the complete viral populations of different sample [ 2 , 3 , 8 , 9 ]. The aim of the current study was to use viral metagenomics, combined with deep-sequencing, to identify mosquito-borne viruses circulating in the Zambezia province in Mozambique.…”

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies

“…Options to allow the user to extract reads of interest will be added in the near future. MetLab has already successfully been used internally for several studies, including “The intestinal eukaryotic virome in healthy and diarrhoeic neonatal piglets” [ 63 ].…”

The porcine virome and xenotransplantation

“…Although investigations of the porcine intestinal virome are so far limited [7][8][9], samples from the distal jejunum of 19 healthy pigs in a Swedish conventional herd yielded eight different viral families ( Table 1). The most common were picornaviruses, followed by circoviruses [10]. Viral infections were already observed 24 to 48 h after birth, indicating infection immediately post-partum, or alternatively, transplacental infection.…”

“…It is interesting to note that porcine viruses with a known or suspected zoonotic potential such as the herpesviruses PCMV and PLHV were not detected when viromes were analysed in faeces and blood [7][8][9][10] whereas PCV (mainly PCV2) was commonly found [7][8][9][10]. Presumably, the frequency of the herpesviruses is so low that their DNA cannot be detected by next generation sequencing.…”