In order to get a first impression on the diversity and abundance of viruses present, we have analysed faeces, spleen and lung of 6 Swiss piglets using next generation sequencing (NGS). All animals were post-mortem examined in 2014 and 2015 at the Institute of Veterinary Pathology at the Vetsuisse faculty of the University of Zürich in the context of the PathoPig project. Four animals showed clinical signs of diarrhoea and were between 10-14 days old. Two additional animals were 7 weeks old. Samples were homogenised using TissueLyser (Qiagen), then centrifuged, and filtered (0.45um) to remove larger particles and cell debris. Free (mainly host-derived) RNA and DNA was digested using nucleases, followed by concurrent RNA and DNA isolation. RNA was reverse-transcribed into DNA and the total DNA amplified using sequence-independent single primer amplification (SISPA). Sequencing libraries were generated from the purified amplicons and sequenced at the functional genomic centre Zürich (FGCZ) on an Illumina NextSeq Sequencer. The NGS sequence reads were screened to the virus reference sequence database (RefSeq) of NCBI GenBank. In summary, we found 14 different types of viruses such as Astro-, Sapelo-, Boca-, Parvo-, Posa-, Entero- and Torque Teno virus. The most frequent virus in the 7-week old animals was PCV-2, in the 10-14 day old piglets porcine kobuvirus (PoKV) was detected in high numbers. The presence of PCV-2, Rotavirus and PoKV was also confirmed by specific PCR. Several of the detected viruses were described for the first time in Switzerland. Particularly the role PoKV as a potential cause auf disease in suckling piglets requires further investigations.
Cover Illustratiom: Piglets playing with a chew rope used for bulk saliva sampling
Picture at the bottom: Diversity of viruses detected in 6 piglets