Date of Award

2014

Document Type

Doctoral Thesis

Degree Name

Doctor of Philosophy

Department

Biological Sciences

First Advisor

Dr. Helen O'Shea

Abstract

Viral gastroenteritis is a common disease of both humans and animals. This thesis focuses on the use of classical virology, coupled with phylogenetics to study gastroenteritis viruses [Bocavirus (BoV), Coronavirus (CoV), and Rotavirus A (RVA)], isolated from selected samples from humans and animals. RVA was associated with outbreaks in elderly care facilities in Northern Ireland, isolates were genotyped and we reported the first detection of G2 lineage lie RVA in Ireland, with other common human RVA genotypes G1P[8], G2P[4] and G9P[8]. Evolutionary dynamics of human RVA VP7 genotypes was examined using codon models of evolution, results show heterogeneous selective pressure between genotypes, with evidence of lineage-specific patterns of positive selection. Equine RVA was investigated; common genotypes G3P[12] and G14P[12] were detected, analysis of NSP4 genotypes revealed the first human to equine reassortment event. Bovine CoV was detected in Southern Ireland and subsequently characterized. Phylogenetic analysis shows that European BCoV appears to be distinct from other global isolates. Further analysis using codon models of evolution indicates site specific adaptation of all BCoV isolates. Archived faecal specimens from a commercial pig farm were investigated for PBoV and other GE viruses such as RVA, PAdV and PCV. This study is the first report of lineage 1 G5 RVA, PCV, PAdV and group 1 and 2 PBoV in Ireland, highlighting the diversity of viruses isolated from a single farm. Overall, the data from this thesis highlights the dynamic nature of gastroenteritis viruses in Ireland and the need for surveillance to assess vaccine design and efficacy, also risk to human and animal health.

Access Level

info:eu-repo/semantics/openAccess

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