The Eukaryotic virome of neonatal piglets suffering from new neonatal porcine diarrhoea syndrome

A new neonatal porcine diarrhoea syndrome (NNPDS) unresponsive to traditional prophylaxis and treatment has been reported from a number of European countries during the last years. However, the aetiology of this condition remains uncertain. This study aimed at describing the intestinal virome of piglets with neonatal porcine diarrhoea of uncertain aetiology by the use of viral metagenomics in an effort to discern a possible viral involvement.

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 subjected to sequence-independent amplification before sequencing. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. Samples were sequenced using the Ion Torrent technology on the Ion Proton platform. The resulting sequence data was subjected to taxonomic classification using KRAKEN with a customized database enriched with viral sequences.

Sequencing data averaged 220Mbases at a mean read length of 185 bases. Mammalian viruses were detected in five out of ten pooled diarrhoeic samples and 14 out of 19 individual samples from the healthy controls. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, Reoviridae) compared to five in the pooled diarrhoeic samples (Adenoviridae, Anelloviridae, Picornaviridae, Reoviridae).

The data did not support an association between the diarrhoea and previously known mammalian viruses. There were however several eukaryotic viruses present in the samples of both healthy and sick animals. Since most samples were collected within 24-48 hours of birth this also indicates immediate postpartum infection or possibly transplacental infection. The findings provide important information on the developing virome of neonates as well as a starting point for further investigations of neonatal porcine diarrhoea of uncertain aetiology.

Disclosure of Interest: None Declared.