Molecular diagnostic approaches to the detection, discovery and genotyping of emerging and endemic viruses circulating in Northern Ireland livestock and wildlife

The recently identified novel PPVs 2-4’s clinical significance is poorly understood. Pig endemic diseases for example porcine respiratory disease complex and porcine circovirus associated disease are caused initially by primary viral infections, however disease association by coinfections with novel parvoviruses and porcine circovirus 2 remains to be determined. The analysis of archival samples from clinically diseased pigs’ indicates that PPV2 is an emerging pathogenic agent, and is statistically associated with porcine respiratory disease complex in pigs.

The emerging HEV is ubiquitous in pig herds worldwide, and HEV genotypes 3 and 4 are zoonotic viruses transmitted mainly as a foodborne disease leading to subclinical to acute infections in humans. A HEV molecular epidemiology study on the prevalence of HEV through an abattoir study and the dynamics of the HEV infection in a longitudinal study were completed. The enteric microbiome is a complex community of bacteria, viruses, fungi and protozoa.

This a new area of research where limited studies exists on the enteric virome of livestock and wildlife. Studies of the virome will aid in the understanding of; viral taxonomic identification, viral prevalence, virus genetic and phenotypic diversity, coinfections and virus-bacteriome and host interactions modelling. Next generation viral metagenomics is a new tool for monitoring and detecting new emerging viruses and will help to fill the knowledge gap of the mammalian virome composition.

Rotavirus group A (RVA) is the major cause of acute diarrhoea and severe dehydration in children and young mammalian host species. Infection of neonate and young animals may lead to death, resulting in economic losses for the farmer. A rotavirus molecular epidemiological surveillance study was conducted mainly on clinically diseased Northern Ireland animals by Sanger sequencing for RVA detection, NGS whole genome amplification and phylogenetic analysis.

The study revealed a high level of rotavirus group A phylogenetic diversity and demonstrates the importance of accumulating knowledge of disease and molecular epidemiological surveillance coupled with viral metagenomics for understanding the viruses circulating in Northern Ireland livestock and wildlife.