Abstract
Endemic and emerging viruses are essential to study in order to understand their prevalence and disease association within Northern Ireland’s livestock and wildlife as, they may be considered an important risk factor to food security, food safety and public health. In recent decades, the prevalence of viral zoonotic pathogens transmitted from animals to humans is currently creating an increasing socio-economic impact. Accordingly, routine pathogen molecular epidemiology surveillance is the key to the identification and mitigation of new and endemic viruses but is often lacking with undiagnosed diseases not being thoroughly investigated. This thesis focuses on four research areas that fall within the scope of molecular detection and investigation of emerging and endemic viruses in Northern Ireland’s livestock and wildlife including; the study of novel porcine parvoviruses (PPV) coinfection status with porcine circovirus 2 (PCV2) and statistical disease association, hepatitis E virus (HEV) prevalence, enteric virome of clinically diseased animals and the prevalence and genotyping of rotavirus (RV) by utilising real-time PCR, Sanger sequencing, Illumina second generation sequencing and bioinformatic analysis. 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.Thesis embargoed until 31st December 2024
Date of Award | Dec 2022 |
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Original language | English |
Awarding Institution |
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Sponsors | Agri-Food and Biosciences Institute |
Supervisor | Mark Mooney (Supervisor) & Ken Lemon (Supervisor) |
Keywords
- Virome
- viral metagenomics
- NGS
- zoonosis
- bioinformatics
- phylogenetics
- hepatitis e virus
- rotavirus
- porcine parvovirus
- epidemiology
- qPCR
- virology