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Human Rhinoviruses (HRVs) utilize Internal Ribosome Entry Sites (IRES) to drive viral protein synthesis. IRESs are specialized RNA elements present within the 5’ UTR of mRNAs that recruit ribosomes independently of the 5’ m7G cap structure. hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1), a multifunctional RNA binding protein, is required for the IRES-dependent translation of many specific RNAs within the cell cytoplasm. The phosphorylation of hnRNP A1 is required for its cytoplasmic accumulation. I have identified and validated the role of HK2 in hnRNP A1 cellular localization by immunofluorescence microscopy, by analysis of HRV infection and by siRNA-based screening. These studies show that decreased HK2 protein levels lead to decreased cytoplasmic accumulation of hnRNPA1 during osmotic shock and HRV infection, to a decrease in HRV-infected cells and to decreased caspase activation in osmotically stressed and HRV-infected cells. Thus, HK2 may regulate hnRNP A1 cytoplasmic localization following HRV infection.

Picornaviruses are responsible for some of the most common and debilitating diseases affecting humans and animals worldwide. The objectives of this dissertation research were (1) estimate phylogenetic relationships among 11 picornavirus genera and within three species: foot-and-mouth disease virus (FMDV: Aphthovirus) which afflicts cloven-hoofed animals and human rhinovirus A and B (HRV: Enterovirus) which cause the common cold; (2) better understand the impact recombination has on genomic organization and evolution; (3) characterize where positive and purifying selection has occurred in proteins and how selection has influenced phenotype. The dissertation includes four studies. The first chapter provides an overview of the evolutionary significance of recombination, its detection and estimation, and its effect on phylogenetic analysis in four biological systems: bacteria, viruses, mitochondria, and the human genome. Chapter two investigates the inter- and intra-serotypic relationships within FMDV by examining 12 genes. Gene sequences were analyzed to assess recombination breakpoint locations, genetic diversity, and natural selection in FMDV. Recombination breakpoints were located throughout the genome. Paraphyletic relationships among serotypes were not as prevalent as previously reported, suggesting that convergent evolution was prevalent. Purifying selection was the dominant evolutionary force influencing both genotype and phenotype. Chapter three examines inter- and intra-specific relationships of HRV using 11 genes. Similar hypotheses were tested as in chapter two. No recombination was detected and phylogenetic relationships among enteroviruses, HRV-A, and HRV-B remain unresolved. The evolution of HRV-A major serotypes appeared to be under extensive purifying selection, HRV-A minor serotypes under predominantly positive selection, and a nearly equal influence from both kinds of selection was evident for HRV-B serotypes. Chapter four examines phylogenetic relationships among genera using three conserved genes. The hypothesis of cospeciation between picornaviruses and their hosts was also tested. The deepest split in the family separated Hepatovirus, ‘Tremovirus’, Parechovirus, and seal picornavirus type 1 from the remainder of the family. Enterovirus and ‘Sapelovirus’ were sister taxa. Cardiovirus, ‘Senecavirus’, Aphthovirus, Erbovirus, Teschovirus, and Kobuvirus were derived from a common ancestor with Kobuvirus occupying a basal position relative to the other genera in this clade. My analyses suggest that picornaviruses have not cospeciated with their known hosts.

<p><strong>Background</strong>: Human rhinovirus/enterovirus (HRV/ENT) infections are commonly identified in children with acute respiratory infections (ARIs), but data on their clinical severity remains limited. We compared the clinical severity of HRV/ENT to respiratory syncytial virus (RSV), influenza A/B (FLU) and other common respiratory virus in children.</p> <p><strong>Methods</strong>: Retrospective study of children with ARIs and confirmed single positive viral infections on mid-turbinate swabs by molecular assays. Outcome measures included hospital admission and, for inpatients, a composite end-point consisting of intensive care admission, hospitalization greater than 5 days, oxygen requirements or death.</p> <p><strong>Results</strong>: A total of 116 HRV/ENT, 102 RSV, 99 FLU and 64 other common respiratory viruses were identified. Children with single HRV/ENT infections presented with significantly higher rates of underlying immunosuppressive conditions compared to those with RSV (37.9% vs 13.6%; p</p> <p><strong>Conclusions</strong>: Children with HRV/ENT had a more severe clinical course than those with RSV and FLUA/B infections and often had significant comorbidities. These findings emphasize the importance of considering HRV/ENT infection in children presenting with severe acute respiratory tract infections.</p> / Master of Science (MSc)