The role of “commensal” viruses in health and disease Thesis by Charlotte Rickli

Viruses have always been regarded as equivalent to disease and death. However, the development of next generation sequencing (NGS) that allows unspecific detection of viruses, has revealed the presence of many “new”, seemingly non-pathogenic viruses. Kobu-, boca-, astroviruses and the like seem to be ubiquitous in faeces of many mammal species but are not associated to overt clinical signs which points to a well-established and balanced virus-host interaction. This leads to the question, what role these viruses play within the enteric microbiome and what their importance is regarding the health status of the host.
In piglets, infectious diarrhoea is an important economic factor. The knowledge about the role of commensal viruses for health and disease might help to improve animal health. Therefore, we want to find out which enteric viruses might be “commensal” (e.g. associated with health) in piglets and are negatively correlated with known enteric viral or bacterial pathogens.
We have analysed faecal samples of 100 piglets; half from healthy control animals and half with diarrhoea. The bacterial spectrum present in these animals is determined by 16S metagenomic next generation sequencing (NGS), while the virome is analysed by NGS shotgun sequencing following our in-house developed ViroScreen (PDF, 376 KB) protocol. First results indicate a strong correlation of several virus genera or species such as Porprismaco- and pig faeces-associated small circular viruses with health rather than diarrhoea. These viruses are also negatively correlated to known pathogenic viruses such as the diarrhea-causing Rotaviruses and certain bacterial clades. For these promising candidates specific real-time (RT-)PCRs are being developed to quantify the viral genomes present in diarrheic and healthy pigs.