The Picornavirus family of positive sense RNA viruses includes some significant human and animal pathogens including Poliovirus (PV), Foot-and-Mouth disease virus (FMDV) and Human Rhinovirus (HRV). The genome is translated within the host cell into a polyprotein that is proteolytically cleaved into the structural and nonstructural proteins. The highly conserved, non-structural protein 2C has numerous roles during the virus life cycle and is essential for virus replication. Although the protein has been well studied in the case of PV, its interactions with the host cell during picornavirus infection is poorly understood. Theiler’s Encephalomyelitis virus (TMEV) is a picornavirus that infects mice, and is being used in our laboratory as a model in which to study the 2C protein. In this study, polyclonal antibodies against the TMEV 2C protein were generated and used to localise the protein in infected cells by indirect immunofluorescence. To produce antigen for immunisation purposes, the TMEV-2C protein sequence was analysed to identify hydrophilic and antigenic regions. An internal region of the 2C representing amino acid residues 31-210 was selected, expressed in bacteria and purified by nickel NTA affinity chromatography. Time course analysis of 2C (31-210) showed that the peptide was maximally expressed at 5 hours post induction. The peptide was solubilised using a mild detergent and 1.5 mg of purified antigen was used for immunisation of rabbits. Western blot analysis confirmed that the antibodies could detect both bacteriallyexpressed antigen, and virally-expressed 2C. Examination of virus-infected baby hamster kidney cells by immunofluorescence and confocal microscopy using the antiserum (anti-TMEV 2C antibodies) showed that the protein had a diffuse distribution upon early infection and at later stages it was located in a large perinuclear structure representing the viral replication complex. Furthermore, 2C localised to the Golgi apparatus as revealed by dual-label immunofluorescence using anti-TMEV 2C antibodies and wheat germ agglutinin (WGA). Furthermore, it was shown that TMEV infection results in changes in cell morphology and a redistribution of the cytoskeletal protein, β-actin. The successful production of antibodies that recognise TMEV 2C opens the way for further studies to investigate interactions between 2C and hostencoded factors.

published_or_final_version / Microbiology / Master / Master of Philosophy

Thesis (Ph.D.) - University of St Andrews, August 2008.

Picornavirus proteins VP1 to VP3 are exposed on the surface of the virus particle whereas VP4 is internal and modified at its amino terminus by the addition of myristic acid (Chow et al., 1987; Paul et al., 1987). Myristic acid occupies a position in the core of mature poliovirus particles; it has been suggested that it may be important for particle integrity or in the localization of the capsid protein precursor on the hydrophobic membranes during virion assembly (Chow et al., 1987). To determine the function of the amino-terminal myristylation of VP4 in picornaviruses, and to establish whether competition for the acylation site is a possible approach to antiviral chemotherapy, the effect of fatty acids on virus replication has been examined. Some fatty acids are able to enter picornavirus-infected cells and compete for the myristylation site on VP4. Unexpectedly, it was found that short chain fatty acids also inhibit an early event in the replication of bovine enterovirus (BEV) at concentrations which have no detectable effect on cellular macromolecular synthesis and cloning. These findings indicate that fatty acids inhibit cell-mediated uncoating. Short chain fatty acids inhibit the replication of bovine enterovirus but are almost ineffective against poliovirus type 1, coxsackievirus B5, encephalomyocarditis virus and human rhinovirus lB. Lauric acid binds to bovine enterovirus, thereby stabilizing the virus particle to heat degradation. Fatty acid-bound virions attach to susceptible cells but fail to undergo cell-mediated uncoating. The inhibitory effect is reversible with chloroform and may result from a hydrophobic interaction between the fatty acid and a specific site on the virus particie.

Please read the abstract in the section 00front of this document / Dissertation (MSc (Medical Virology))--University of Pretoria, 2005. / Medical Virology / unrestricted

It is well recognized that regulatory T cells (Tregs) are immunosuppressive, by which they prevent systemic autoimmunity throughout life. Beyond this stereotypical function, however, a growing body of evidence demonstrates that Tregs in distinct tissues, including the visceral adipose tissue, dystrophic muscle, the flu-infected lung, and wounded skin can acquire unique functions directed by their local environment. Tregs in these tissues can employ a wide variety of mechanisms to accumulate and acquire tissue-specific function, including conversion from conventional T cells, canonical T cell receptor (TCR)-dependent expansion and non-canonical, TCR-independent, cytokine-dependent expansion. Intriguingly, the niche-specific function of tissue Tregs can be independent of, and mutually exclusive of, their immunosuppressive capacity. Together, this recent literature reveals that Tregs can accumulate in discrete tissue sites through non-canonical mechanisms, and in response to niche-specific cues can acquire distinct functions, which distinguish them from their peripheral, lymphoid Treg counterparts. Other tissue Treg populations remain to be identified and characterized. Moreover, it is unknown whether other tissue Tregs rely on non-canonical mechanisms of accumulation, and exhibit functions distinct from the typical Treg immunosuppressive role. Tregs are known to accumulate in the CNS during infection, injury and inflammation. The CNS is an organ with distinctive architecture that maintains a regulated interaction with the peripheral immune system due to its critical function and poor regenerative capacity. While it is known that Tregs broadly protect against excessive tissue pathology in the diseased CNS, the origin, localization, function, mechanism of accumulation, and gene signature of CNS-infiltrating Tregs have not been studied, likely due to the challenge of isolating these rare cells and distinguishing them from circulating cells left over after perfusion. Here, we establish a safe model of CNS infection using encephalomyocarditis virus and employ a series of methods to locate, monitor and isolate CNS-infiltrating Tregs free from contamination from the circulation. We show that a distinct population of thymus-derived Tregs accumulates within the cerebrospinal fluid (CSF) of the EMCV-infected CNS, independently of lymph node priming. Tregs function in this unique niche to limit excessive tissue pathology. While CNS Tregs maintain expression of core Treg signature genes, including FoxP3, their global transcriptome is more similar to that of conventional T cells (Tcons) harvested from the infected CNS than to that of peripheral Tregs. Bioinformatics analysis reveals that genes shared by CNS Tcons and CNS Tregs are also shared by Tregs and Tcons from injured muscle and from the visceral adipose tissue of aged mice, indicating that tissue inflammation and injury, rather than viral infection per se, contribute to CNS Treg accumulation, function and phenotype. Additionally, we observe that CNS Treg accumulation during infection is associated with a simultaneous increase in meningeal/choroid plexus dendritic cells (m/chDCs), which are professional antigen presenting cells that localize to the gates of the CNS. Splenic cDC and peripheral lymphoid Treg homeostasis are linked, and both populations can be artificially increased by treatment with the DC-poietin and adjuvant, Ftlt3L. Therefore, we hypothesized that CNS Tregs and m/chDCs may also be linked and could also be manipulated by Flt3L treatment. Indeed, treatment with Flt3L in conjunction with EMCV infection results in enhanced CNS Treg and m/chDC accumulation, independent of Flt3 receptor expression on Tregs. In an effort to determine if dendritic cells mediate CNS Treg increase during infection, we turned to a DC-ablative mouse model in which all CD11c-expressing cells express the catalytic subunit of diphtheria toxin and are depleted. Surprisingly, while splenic cDCs are completely abrogated in these mice, a portion of m/chDCs persists, unaffected. Moreover, CNS Tregs accumulate normally in these mice during infection. This data suggests an unappreciated heterogeneity in m/chDCs, and indicates that those that remain unaffected in these mice may mediate CNS Treg accumulation during infection. While characterizing m/chDC heterogeneity, we found that m/chDCs comprise three distinct subsets with unknown potential. Whereas m/chDCs were previously considered to be a homogeneous, CD45hiB220-CD11c+MHCII+ population, we have found them to contain three subsets, distinguishable by IRF8 and FcR-γ expression. This finding paves the way for further study of the origin, localization, and division of labor between these three m/chDC subsets. In summary, our studies clarify the distinct compartmentalization, lymph node-independent accumulation, and inflammation-associated gene signature of CNS Tregs. Most importantly, these findings have implications for neuro-immune cross-talk, particularly at the interface of the CSF and brain parenchyma. That is, neural progenitors extend their apical domains into the CSF of the ventricles, and therefore may be subject to regulation by CSF-borne Tregs. Further, while many studies have focused on the differences between tissue Treg subsets, we find a core set of genes expressed by CNS Tregs, injured muscle Tregs and VAT Tregs. This data suggests that common mechanisms may be used for therapeutic manipulation of these cells.

published_or_final_version / Microbiology / Master / Master of Medical Sciences

Gastroenteritis in the form of diarrhea and vomiting is common in human and is mostly caused by viral infection. As the significant proportion of gastrointestinal infections are still not diagnosed, novel viruses are suggested to be the causative agents of unknown gastroenteritis. Novel and emerging picornaviruses, including human parechovirus (HPeV), Aichi virus (AiV) and salivirus (SalV) are suggested to play an important role in acute gastroenteritis. Since little was known about the molecular and clinical epidemiology of these viruses, the present study aims to investigate the presence of HPeV, AiV and SalV in fecal samples of children with acute gastroenteritis in Hong Kong. Retrospective and prospective studies were performed using fecal samples from pediatric patients hospitalized for acute gastroenteritis from November 2004 to August 2005, August 2006 to October 2006 and September 2012 to August 2013. Among 1708 fecal samples subjected to RT-PCR using primers targeted to 5’NCR of picornaviruses, viruses were detected in 57 samples, with 47 patients (2.8%) positive for HPeVs, three patients (0.18%) positive for AiV and one patient (0.1%) positive for SalV. Phylogenetic analysis of the partial VP1 capsid gene of the 33 HPeV strains revealed the presence of genotypes of HPeV- 1, 3, 4, 5, 7, 10, among which HPeV1 was the predominant genotype circulating in our population. The peak activity of HPeV infection was in autumn. Of the three children with AiV detected in fecal samples, phylogenetic analysis of the partial VP1 and 3CD regions indicated the three AiV strains from fecal samples belonged to the AiV genotype A. Co-detection of different pathogens was noted in 6 samples (10.5%) of 57 stool samples positive for picornaviruses. Among the five samples with HPeV, co-detection with HBoV, AiV, SalV and Aeromonas were observed. In one sample with AiV, picobirnavirus was identified. In conclusion, HPeV, AiV and SalV were found to be present in fecal samples of Hong Kong children with gastroenteritis, with HPeV being the most common virus detected. Routine screening for these viruses in young children with gastroenteritis may better define their epidemiology and help prevent their transmission. / published_or_final_version / Microbiology / Master / Master of Medical Sciences

Background: Respiratory tract infection is one of the major diseases to cause morbidity and mortality worldwide. Undiagnosed respiratory infection remains unclear. Picornavirus is most common to cause respiratory infection after the influenza virus and RSV. There were numerous notorious pathogens in the Picornaviridae family, for instance, human parechovirus and Saffold virus. These emerging and novel viruses are reported sporadically in respiratory infection and amongst children in particular. This study is aimed to assess the potential role of HPeV and SAFV in respiratory infection in Hong Kong. Methods: Between May 2013 and April 2014, nasopharyngeal aspirates (NPA) were collected from hospitalized patients who have respiratory infection. The collected samples were tested negative for respiratory syncytial virus, adenovirus, influenza A and B viruses, parainfluenza viruses types 1, 2 and 3 by direct immunofluorescence. RT-PCR was used to target the HPeV and SAFV corresponding region of 5'UTR and analyze by the BioEdit sequence Alignment Editor and Basic Local Alignment Search Tool. Results: 597 female and 603 male were included in 1200 NPA samples. 20% of these samples were under the age of 5. However, there were no HPeV and SAFV detected in all 1200 NPA samples. Conclusion: To reveal the possible association between viruses and respiratory infection, the sampling size and district area should be expanded. The single detection method may not be able to detect all the viruses in the current study. / published_or_final_version / Microbiology / Master / Master of Medical Sciences

The picornavirus family includes significant human and animal viruses such as poliovirus (PV), human rhinovirus (HRV) and foot-and-mouth-disease virus (FMDV). Current disease treatment and control strategies are limited by an incomplete understanding of the interactions between the non-structural, replicative picornavirus proteins and host cell components. To investigate these interactions, Theiler's murine encephalomyelitis virus (TMEV) 2B, 2C, 2BC and 3A proteins were transiently expressed in BHK-21 cells and detected by indirect immunostaining and laser-scanning or epifluorescence microscopy. The signal of the 2B protein overlapped with that of the ER marker protein, ERp60, as well as that of the peripheral Golgi marker protein, β-COP. The 2C protein overlapped with ERp60 in a faint reticular stain, and localised to large punctate structures that partially overlapped with β-COP at higher levels of expression. The 2BC protein located to large perinuclear structures that overlapped exclusively with β-COP. The TMEV 3A protein signal overlapped with both ERp60 and β-COP stains, in addition in cells expressing the 3A protein the ER appeared swollen and bulbous while the Golgi was dispersed in some cells. 2C and 2BC proteins with C-terminal deletions localised in the same manner as the wild type proteins indicating that the localisation signals that determine subcellular localisation of the proteins are within the N-terminal 60 amino acids of the 2C protein. The significance of the high degree of conservation of the N-terminal domain of the 2C protein throughout the Picornaviridae was investigated through the introduction of amino acid substitution mutations at highly conserved residues in the N-terminal domain of 2C into the viral cDNA. Upon transfection of the viral RNA into BHK-21 cells, it was observed that substitution of amino acid residues 8, 18 and 29 abolished the ability of TMEV to induce cytopathic effect (CPE), while substitution of residues 4, 14 and 23 only attenuated the ability of TMEV to induce CPE. To determine whether amino acid substitution mutations would affect the localisation of the 2C protein, 2C proteins with substitution mutations at amino acids 4, 8, 14, 18, 23 and 29 were transiently expressed in BHK-21 cells and detected by indirect imrnunostaining and examination by laser-scanning confocal and epifluorescence microscopy. The 2C mutant 4, 8 and 29 proteins showed slightly altered localisation patterns compared to the wild type protein with a significant portion of the proteins localising in a perinuclear stain suggesting possible localisation to the nuclear envelop. The 2C mutant 14 and 18 proteins localised to a diffuse pattern in BHK-21 cells while the 2C mutant 23 protein located to small punctate structures that partially overlapped with the ERp60 stain but were completely separate from the β-COP stain. Finally, a hydrophilic, antigenic region of the 2C protein was expressed in frame with an N-terminal GST tag and was successfully purified on a pilot-scale and detected by Western analysis. This 2C178 peptide will be used to generate antibodies against the 2C and 2BC proteins for use in future studies. This study has furthered our knowledge of the localisation of the picornavirus 2B, 2C, 2BC and 3A proteins in host cells and identified a possible link between this localisation and an ability of TMEV to replicate in BHK-21 cells.