Type 1 diabetes (T1D) is due to a selective loss of the insulin producing β-cells. However, the process responsible for this loss is still unknown. There is accumulating evidence that enteroviruses (EVs) are involved in T1D. In addition to direct virus-induced cytolysis, EVs could facilitate β-cell destruction by inducing inflammatory cytokines. Induction of such genes has previously been shown in EV-infected islets in vitro. Modulation of inflammatory mediators expressed in the islets could be a possible strategy to reduce β-cell destruction. In the first paper we screened uninfected isolated human islets for genes with the potential to induce or modulate an immune response. We found that several of the genes expressed in the islets encode proteins with a powerful biological activity, such as IL-1β, IL-8, MIP-2α, MCP-1 and MIF. This indicates that the islets themselves can express several triggers of inflammation, and if expressed in vivo these mediators would probably contribute to β-cell destruction. The vitamin B3 derivate, nicotinamide (NA), has been shown to modulate expression of factors important for coagulation and inflammatory responses. Addition of NA into isolated islet cultures resulted in a reduced expression of the pro-inflammatory chemokine MCP-1 and the coagulation activator tissue factor, suggesting that NA may have implications for both inflammatory responses and the pro-coagulant activity of islets. We successfully isolated EVs from three newly diagnosed T1D patients. All isolates showed tropism for human islets and β-cells in vitro and clearly affected islet function. We also found that EV infection induced islet secretion of the chemokines IP-10 and MCP-1and that this induction could be blocked or reduced by addition of NA to the culture medium. Interestingly, NA also reduced viral replication and virus-induced islet destruction. To conclude, this thesis provides new information about expression and modulation of inflammatory mediators in infected and uninfected human islets that could trigger inflammatory reactions leading to β-cell destruction. Moreover, it further strengthens the causal relationship between EV and T1D.

Human enteroviruses (HEVs), particularly Coxsackie B viruses (CVBs), might trigger the onset of type 1 diabetes (T1D), either by direct infection of the insulin-producing beta-cells or by an indirect inflammatory response. The overall aim of this thesis was to study the tropism of HEVs in isolated human pancreatic cell clusters in vitro including virus effects on islet function, gene-expression and ultrastructure. Furthermore, the expression of the major CVB-receptor, CAR, was investigated in pancreatic tissue from T1D-related subjects and CVB-infected islets. Also, tissues and isolated islets from two adult organ-donors who died close to disease onset were studied.The results showed that beta-cells were destroyed through lytic infections with different strains of CVBs and that islets function did not depend on replication per se but on the degree of islet destruction. Virus particles were observed in beta-cells in association with insulin granules, however no virus replication or particles could be observed in the exocrine cell clusters, as opposed to in mice models. The virus-infected islets had a decreased expression of insulin mRNA and CAR mRNA/protein, possibly reflecting virus-killed beta-cells. Infected beta-cells contained a high number of insulin granules, which might indicate an impaired function.The in vivo studies showed presence of virus proteins in the islets of both donors who died close to onset of T1D and elevated expression of innate immunity genes, potentially indicating viral infection, but direct evidence is lacking. Both donors were immune-reactive for insulin but the isolated islets had an impaired or completely lacking glucose response. Ultrastructural analysis showed both damaged beta-cells and normal-looking beta-cells, indicating that the latter might still have the potential to function but were blocked. CAR-expression was significantly increased in T1D-related subjects which might indicate tissue damage and/or inflammation in these subjects.To conclude, these results showed that CVBs could infect human primary beta-cells, likely by binding to CAR and lead to functional abnormalities, indicating that they could cause T1D in vivo. Exocrine cells were not permissive to CVB, which raises the question if mice-models should be used to study human pancreatitis. Also, unique materials from two T1D organ-donors were described.

Les Entérovirus, et notamment les coxsackievirus B (CV-B), sont une cause commune de myocardite. Cette maladie peut évoluer vers une myocardite chronique jusqu’au stade de cardiomyopathie dilatée (CMD). Le mécanisme moléculaire permettant le passage de l’infection aigue à l’infection persistante dans le tissu cardiaque humain reste méconnu. Pour étudier les activités de réplication des CV-B persistant, un réplicon a été généré à partir d’une souche cardiotrope. Il a permis de caractériser les activités de réplication de CV-B persistant dans des cellules cardiaques humaines. Une analyse par séquençage à moyen débit a permis de mettre en évidence la sélection de variants tronqués dans le cœur pouvant expliquer la progression de la myocardite virale vers la CMD. De plus, l’existence de populations majoritaires tronquées de 19 à 50 nucléotides associées à des formes virales minoritaires complètes a été mise en évidence chez 8 patients atteints de CMD. La proportion de populations tronquées s’est révélée négativement corrélée au ratio ARN+/ARN- et à la charge virale (R2=0,748; P=0,016; R2= 0,36, P=0,038, respectivement). Des études immuno-histologiques et par hybridation in situ des tissus cardiaques ont montrées que le clivage de la dystrophine était uniquement retrouvé dans les cardiomyocytes infectés par les CV-B. La transfection d’ARN de synthèse complets et tronqués dans des cultures de cardiomyocytes humains primaires a mis en évidence une trans-complémentation entre les 2 formes virales induisant de faibles activités de réplication. Nos résultats démontre l’existence d’un nouveau mécanisme moléculaire de coopération entre des populations persistantes d’entérovirus B tronquées et complètes qui contribue à la physiopathologie de la CMD. / Enteroviruses, especially group B coxsackieviruses (CV-B) are considered to be a common cause of acute human myocarditis, a disease that is a precursor of chronic myocarditis cases as well as dilated cardiomyopathy (DCM). The molecular mechanisms related to the switch from the acute to the CV-B chronic persistent infection in human cardiac tissues are still unknown. To study the replication activities of CV-B a replicon from a cardiotropic prototype strain was generated and was used to study persistent CV-B replication activities into human cardiac cells. Using NGS analyses, our results evidenced that the molecular selection of TD viral forms in heart could explain pathophysiological progression from acute viral myocarditis to DCM. Moreover, we demonstrated in 8 end-stage DCM patients the existence of CV-B major populations characterized by 5’NTR deletions ranging from 19 to 50 nucleotides that were associated with minor full-length viral forms. The amounts of persistent deleted populations appeared to be negatively correlated to RNA(+)/RNA(-) minus ratio and viral load values (R2=0.748; P=0.016; R2= 0.36, P=0.038, respectively). In situ hybridization and immunohistological assays in cardiac tissues demonstrated that the dystrophin disruption was only present in EV-B infected cardiomyocytes. Transfection of deleted and full-length RNA-populations in cultured primary human cardiomyocytes evidenced a trans-acting genomic complementation system between the two viral forms resulting in low viral replication activities. Our findings suggest a new molecular mechanism through which persistent low replicative EV-B deleted and full-length collaborative populations contribute to the pathogenesis of idiopathic DCM cases.

Enterovirus D68 (EV-D68) is a virus that normally causes disease in children. While this virus typically causes a respiratory infection, in 2014, a large outbreak of the virus was associated with patients that had paralysis of the arms or legs. Even though the virus was discovered in 1962, little was known about the life cycle of the virus or its ability to cause disease. An animal model of disease was needed to understand how the virus causes disease and to develop antiviral compounds to target the virus life cycle. We adapted the virus by serial-passage in lung tissues from mice deficient in interferon receptors. Using the adapted virus, we established a model of respiratory disease where the virus was able to replicate and cause moderate damage to the lung tissue. We created a separate model of disease where the virus caused paralysis and mortality in infected mice, similar to symptoms seen in infected children. Lastly, we evaluated several antiviral compounds to determine if they were able to protect the mice from virus replication and mortality. Guanidine was able to reduce the amount of virus in each tissue as well as protect mice from paralysis and mortality. In addition, human intravenous immunoglobulin (hIVIG), a mixture of pooled antibodies from human donors, did not reduce the amount of virus in the lungs, but did protect mice from paralysis and mortality.

Ce travail a analysé tous les cas de HFMD déclarés à Hai Phong pendant l’épidémie de 2011 et 2012 qui a été la plus importante au Vietnam et la première enregistrée dans le nord du pays. Hai Phong a connu la plus forte incidence au Nord Vietnam. C’était donc un bon modèle pour étudier la dynamique de cette maladie sans interférence et reliquats de précédentes épidémies ou de patients immunoadaptés.La première section est consacrée à une revue de la littérature sur EV-A71 et les entérovirus. La seconde section est divisée en trois chapitres, chacun abordant un aspect spécifique du projet.Le premier chapitre aborde la dynamique de la maladie et le rôle des directives officielles pour la gestion de l’épidémie de 2011-2012. Outre les éléments de base, cette étude apporte des résultats sur l’influence des directives HFMD durant l’épidémie, ce qui n’avait pas encore été fait. La publication des directives a conduit à un accroissement du score de sévérité et d’une réduction du délai entre le premier pic de fièvre et l’admission. Cet effet est associé à un accroissement de la sensibilisation qui a conduit à déclarer la plupart des patients avec des symptômes sévères pour assurer de meilleurs traitements et suivis. Le travail décrit dans ce chapitre a aussi démontré que trois vagues avec des caractéristiques différentes et causées par trois virus différents s’étaient succédées. La vague 1 et la vague 3 ont été causées respectivement par EV-A71 et par une combinaison de CV-A6 et CV-A16 alors que la vague 2 a été causée par un virus inconnu. Ce travail est aussi une analyse intégrative incluant une analyse spatiotemporelle. La maladie semble s’être étendue vers l’est en suivant les rivières pour atteindre les des zones plus peuplées à partir desquelles elle s’est répandue par les routes secondaires locales. Etant donné l’âge moyen des patients, environ 2 ans, la source de contamination doit être cherchée chez les adultes asymptomatiques contaminés lors de leurs activités professionnelles et des mobilités locales.Le deuxième chapitre aborde la phylogénie et la distribution spatiotemporelle de EV-A71 dans le nord du Vietnam et apporte un éclairage sur l’évolution et la dynamique de cet entérovirus. La protéine de capside VP1 a été ciblée. La première conclusion de ce chapitre est que l’épidémie de 2011 et 2012 n’a pas été causée par une souche exogène mais par des souches d’EV-A71 déjà présentes au Nord Vietnam. Ceci indique qu’elles peuvent se maintenir à faible niveau, asymptomatique, en stase génomique et avec une structuration géographique. La cause de l’épidémie devrait donc être recherchée dans le tissu socio-économique plutôt que dans une émergence extérieure. Une autre conclusion de ce chapitre est la corrélation observée ente les groupes de variants I/V et phylogénie, pathogénicité et groupe ethnique. Les profils des mutations I/V aux positions 249, 262 et 284 sur la protéine VP1 pourraient jouer un rôle dans la pathogénicité, ce qui est appuyé par la corrélation entre variants I/V et sévérité/ethnicité.Le dernier chapitre aborde la modélisation mathématique d’une maladie multiphases telle que HFMD. Il est essentiel de détecter aussi tôt que possible une nouvelle vague associée à un nouvel agent. Grace à la grande taille de la cohorte disponible pour ce travail (environ 9000 patients), nous avons pu développer un système d’équations différentielles apportant une forte correspondance avec les données observées. Le modèle a confirmé l’existence de trois vagues en 2011-2012, ayant des niveaux de virulence différents. Il permet aussi de caractériser chaque vague, de détecter l’apparition d’une nouvelle vague et d’associer des groupes patients à un tableau clinique.En conclusion, ce travail de thèse a permis de souligner plusieurs éléments clés à aborder de façon coordonnée afin de faciliter une surveillance efficace de l’HFMD au Vietnam. / This work analyzed all HFMD cases reported in Hai Phong in 2011 and 2012 outbreak which was the largest to have ever occurred in Vietnam and the first recorded in the northern part of the country. Hai Phong city experienced the highest HFMD incidence in North Vietnam. It was thus a good model for investigating the dynamic of the disease without interference and potential remains from previous outbreaks or patient immunological adaptation.The first section is dedicated to a review of the literature on EV-A71 and enteroviruses. The second section is divided in three chapters, each one addressing a specific issue of the project.The first chapter addresses the dynamic of the disease and the role of official guidelines in the handling of the 2011-2012 epidemic. Beside basic epidemiological features, the study also provides findings relating to the influence of HFMD guidelines during the outbreak period that has never been described before. The guideline release led to a significant increase of the severity score and reduced delay between onset and admission. This effect is linked to an increased awareness leading to patients being mostly declared with severe symptoms in order to ensure a better treatment and surveillance. The work presented in this chapter also demonstrated that three waves occurred with different characteristics and caused by three different viruses. Wave 1 and wave 3 were caused by EV-A71 and a combination of CV-A6 and CV-A16, respectively while Wave 2 was caused by an unknown virus. This work is also an integrative analysis including a spatiotemporal analysis. The disease seems to have expanded following the eastbound river system to reach densely populated settlements from where it secondarily expanded through local roads. Owing to the average age of the patients, around 2, the source of contamination must be sought for within asymptomatic adults being contaminated during their occupational activities and in local movements.The second chapter addresses the phylogeny and spatiotemporal distribution of EV-A71 in North Vietnam and provides an insight on the evolution and dynamic of the EV-A71 enterovirus. The VP1 capsid protein was used as target. The first conclusion of this chapter is that the 2011-2012 outbreak was not caused by an incoming strain but by EV-A71 strains which were already present in North Vietnam. This indicates that they can remain in a low level, asymptomatic state, in genomic stasis and with a geographic structuration. The cause for outbreaks should thus be sought for in the socio-economic patterns rather than in exogenous emergence. Another outcome of this chapter is the observed correlation between I/V variant groups and phylogeny, pathogenicity and ethnicity. The I/V pattern at positions 249, 262 and 284 on the VP1 protein might play a role in pathogenicity. The observed correlation of the I/V variant populations with severity and ethnicity strengthen this hypothesis.The last chapter addresses the mathematical modelling of a multiphase disease such as HFMD. It is essential to detect as soon as possible the emergence of new wave, associated to a novel agent. Owing to the large size of the cohort available for this work (ca. 9000 patients), we have been able to develop a differential equation model providing a very high fit with the observed data. The model confirmed that three waves were present in 2011-2012 with differing virulence. It also allows to characterize each wave, detect the start of a new one and associate groups of patients with specific patterns of symptoms.As a conclusion, this PhD work as underlined some key issues to be addressed in a coordinated way in order help developing an efficient surveillance and monitoring system for HFMD in Vietnam.

Les entérovirus (EV) sont des agents étiologiques de nombreuses pathologies chez les adultes et les enfants, y compris la poliomyélite qui a été éradiquée en France. Aujourd’hui, la surveillance d’EV se déroule dans le cadre de la vigilance post-éradication, et fournit des données épidémiologiques importants sur des entérovirus non polio.A Marseille, la surveillance a amené à l’analyse de 654 souches isolées entre 1985 et 2005. Les EV de l'espèce B étaient prédominants, parmi lesquels l’echovirus 30 (E30) a été le plus fréquemment isolé et l’E13 a émergé lors de l’épidémie en 2000. Notre analyse des souches cliniques sur 20 ans renforce la stratégie de sérotypage par la VP1. L'analyse phylogénétique a identifié des souches de différents sérotypes, avec des régions nonstructurales génétiquement proches associées aux VP1 divergents. Ceci contredit le modèle actuel de la recombinaison et pourrait être à l’origine de l'émergence d’E13 épidémique.Deux épidémies majeures d’E30 ont été décrites en 2000 et 2005. Entre elles, le protocole de diagnostic d’EV a été modifié: en 2000, la détection s’est fait par la culture cellulaire et la RT-PCR classique; en 2005, la technique de la RT-PCR en temps réel a été utilisée. Ainsi, l’épidémie de 2005 a été caractérisée par une réduction significative du délai nécessaire de livrer les résultats du diagnostic et de la durée du séjour hospitalier.Nous avons également adapté un système moléculaire pour la détection d'EV71. EV71 est associé à des épidémies du syndrome pied, main, bouche en Asie, mais peut aussi engendrer des complications neurologiques fatales. Nous avons testé 365 échantillons positifs pour l’EV. 3 cas d'EV71 du génogroupe C2 ont été détectés entre 2009 et 2011 chez les enfants sans histoires de voyage récent, ce qui confirme la circulation actuelle de ce génogroupe en France.Les entérovirus ont le potentiel de provoquer des épidémies fréquentes, à cause de leur diversité génétique importante et de leur capacité de réémergence. Il est nécessaire de maintenir la surveillance d'EV par la détection et l'analyse des virus en circulation, et de développer d’autres techniques rapides de détection et d’identification. / Enteroviruses are single-stranded RNA viruses associated with a myriad of pathologies in adult and paediatric populations, the most notable of which, poliomyelitis, has been eradicated in France. Today, enterovirus surveillance is carried out in the context of post-eradication monitoring, and provides important epidemiological data for nonpolio enteroviruses.In Marseille, surveillance efforts culminated in the compilation and analysis of 654 strains isolated between 1985 and 2005. Predominant serotypes belonged to the B species: Echovirus 30 (E30) was the most frequently isolated serotype and E13 emerged during the 2000 epidemic. Our analysis of clinical strains over 20 years lends credence to the VP1 serotyping strategy. Phylogenetic analysis identified strains of different serotypes which were genetically similar in the nonstructural regions despite distinct VP1 regions. This observation contradicts the current model of recombination and could explain the emergence of epidemic E13.Two large outbreaks of E30 were described in 2000 and 2005, in between which EV diagnostic protocol was changed: in 2000, detection was performed using cell culture and classic RT-PCR techniques; in 2005, this was done via real-time RT-PCR. As a result, the 2005 outbreak was characterised by a significant decrease in the time needed to deliver diagnostic results, as well as in the length of hospital stay.We also adapted a real-time molecular assay for the detection of EV71. EV71 is associated with major outbreaks of hand, foot and mouth disease in the Asia-Pacific region, but can also cause fatal neurological complications. We screened 356 EV-positive samples and detected three cases of genogroup C2 EV71 infection between 2009 and 2011 in young children with no history of travel, confirming the current circulation of EV71 in France.Enteroviruses have the potential to cause frequent epidemics, due to their great genetic diversity and their propensity for re-emergence. This underscores the need to maintain EV surveillance by analysing past and present circulating viruses, as well as to develop more rapid detection and identification techniques.

Title from PDF of title page. / Document formatted into pages; contains 57 pages. / Thesis (M.S.P.H.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The Centers for Disease Control and Prevention estimated 23,000,000 cases of viral gastroenteritis caused by Norovirus in 2000, 40% of which were transmitted by food including: a variety of fresh produce, cake, deli meats, fruit salad, cheeses and ice. (CDC, 2003). An estimated 83,391 cases of Hepatitis A virus was reported in 2000, of which 5% was attributed to foodborne transmission (CDC, 2003). These figures underscore an urgent need for a method that can isolate virus from a variety of food matrices. The aim of this study was to develop an overall assessment of the inhibitory effects of a variety of food matrices on Real Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR). / ABSTRACT: Additionally, to compare a sequence specific hybridization probe amplification format to a non sequence specific SYBR Green format using the Roche LightCycler. The secondary aim was to evaluate the effectiveness of a food virus concentration and isolation protocol under development at the Florida Department of Health Bureau of Laboratories, Tampa. Three food specimens consisting of prepackaged smoked ham, fresh cilantro, and Thompson's green grapes were seeded with three dilutions of poliovirus 3 (Sabin strain). A viral concentration procedure under development at the Florida Department of Health Bureau of Laboratories, Tampa was used to isolate the virus. Real Time RT-PCR was carried out on the Roche LightCycler in SYBR Green and Hybridization probe formats. Spiking the virus-negative samples of each matrix with a dilution series of poliovirus 3 created post flocculation spikes. / ABSTRACT: This post-flocculation dilution series amplification allowed a standard curve to be created unique to each food matrix. The flocculation and concentrations specimens were then amplified and the standard curves from the post-flocculation seed were used to calculate the loss associated with the concentration procedure. This study reports significant differences (p[0.05) in recovery detected between the various matrices, and Real Time RT-PCR formats. The concentration protocol under development at the Florida Department of Health Bureau of Laboratories, Tampa, demonstrates a 12-78% recovery of seeded virus in a simulated "real world" virus contamination event among the various matrices. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by loss of insulin-producing beta cells resulting in life-long insulin deficiency. Beta cell destruction by autoreactive CD8+ effector T-cells is thought to be the main cause of loss of insulin output. Autoreactive T-cells are similarly to autoantibodies, which have been established as markers of risk and progression of the disease, directed towards autoantigens of T1D. These are most notably, insulin, 65 kDa glutamic acid decarboxylase (GAD65, also known as GAD2), insulinoma-associated protein 2 (IA­2, also known as PTPRN or ICA512) or zinc transporter 8 (ZNT8). Most of the known T1D autoantigens are components of insulin secretory granules (SGs). T1D arises from an interplay of genetic and environmental factors, which are thought to act as triggers in susceptible individuals. Predisposing alleles in genetic loci for human leukocyte antigen (HLA) account for by far the highest contribution to the risk of disease development, followed by an array of polymorphisms thought to play a role in either immune cells or beta cells. Of environmental factors that potentially add to the risk of disease progression, the most evidence-supported are Enteroviruses (EVs). Most notably, their genome and viral proteins, as well as higher expression of cellular proteins involved in viral response were detected more often in blood and pancreata of patients with T1D than in healthy population. In addition, recent evidence from a large long-term observational study has implicated prolonged shedding of specifically species Enterovirus B in the stools of children as a risk factor in development of beta cell autoimmunity in children with high genetic risk of T1D. For these reasons, many researchers have studied the potential mechanisms of EV involvement in T1D pathogenesis. In our laboratory, we have investigated the effects of coxsackievirus B5 (CVB5) infection on murine insulinoma MIN6 cells. Previously, we have reported that glucose-stimulated translation of SG proteins can be carried out in a cap-independent manner and is not shut down as part of the early effects of CVB5 infection on MIN6 cells. We have also observed that mature forms of SG proteins are being degraded during viral infection. As intracellular protein degradation is one of the major pathways to supply peptides for presentation on HLA I for immune recognition, we hypothesized that concomitant production and degradation of SG proteins upon viral infection could lead to altered presentation of mainly peptides derived from insulin SG component proteins and potentially drive the response of autoreactive T-cells. To address this hypothesis, we aimed to identify appropriate conditions to study the impact of EV infection on antigen presentation of ECN90 cells. To that end, we established a panel of markers examined by SDS-PAGE and immunoblotting. Stage of viral infection was assessed based on the detection of the viral protein VP1 and cleavage of cellular factors such as eukaryotic translation initiation factor 4 G (eIF4G), poly(A)-binding protein (PABP1), polypyrimidine tract-binding protein 1 (PTBP1), poly (ADP-ribose) polymerase (PARP) and caspase 3, which is mediated by viral proteases. Furthermore, we assessed the levels of ICA512 and chromogranin A and their pro-forms to estimate the size of insulin SG stores, and the expression of HLA I and β2 microglobulin to confirm sufficient antigen presentation. Peptides presented on both HLA I and II were isolated by immunoaffinity purification and identified by liquid chromatography-tandem mass spectrometry analysis. About 500 unique HLA I-presented peptides were found on average per replicate and condition with purity of 89% (peptides predicted to bind HLA alleles expressed by ECN90 cells). The distribution of unique peptides presented by infected ECN90 cells significantly differed from those presented by control cells as 54 unique peptides were present only in all infected samples and none of uninfected and 13 peptides were only found in uninfected cells. In total, we identified 26 unique peptides from known T1D autoantigens associated with SGs (e.g. insulin, chromogranin A, ICA512) in both conditions. The majority of them were predicted to bind HLA I alleles B*40:01 and A*02:01, while two identified viral peptides were found to bind B*40:01 and A*03:01 alleles. Both of the viral peptides and almost half of the peptides originating from known T1D autoantigens have not been described before. In addition, on average 300 unique HLA II peptides were found per replicate and condition. Similarly to HLA I peptides, the distribution of unique peptides across infected and control cells differed as well, showing that antigen presentation was altered in infected cells. We identified two viral HLA II-eluted peptides and peptides originating from only two known T1D autoantigens, 35 originated from insulin and 157 from chromogranin A. As most of the newly identified HLA I peptides originating from T1D autoantigens and one peptide from viral proteins were restricted by the allele HLA-B*40:01, our further efforts were invested in the development of a recombinant disulfide-stabilized biotinylated peptide-receptive HLA molecule of this allele. This technology has been extensively validated, and will allow us to test the wide array of novel peptides identified by us for the ability to bind this allele, as well as asses frequencies and responses of specific T-cells in subject populations relevant for T1D.

BACKGROUND: The type I interferon (IFN) response is a critical component of the innate immune response to infection by RNA viruses and is initiated via recognition of viral nucleic acids by RIG-like receptors (RLR). Engagement of these receptors in the cytoplasm initiates a signal transduction pathway leading to activation of the transcription factors NF-κB, ATF-2 and IRF-3 that coordinately upregulate transcription of type I IFN genes, such as that encoding IFN-β. In this study the impact of poliovirus infection on the type I interferon response has been examined. METHODS: The type I IFN response was assessed by measuring IFN-β mRNA levels using qRT-PCR and normalizing to levels of β-actin mRNA. The status of host factors involved in activation of the type I IFN response was examined by immunoblot, immunofluorescence microcopy and qRT-PCR. RESULTS: The results show that poliovirus infection results in induction of very low levels of IFN-β mRNA despite clear activation of NF-κB and ATF-2. In contrast, analysis of IRF-3 revealed no transcriptional induction of an IRF-3-responsive promoter or homodimerization of IRF-3 indicating it is not activated in poliovirus-infected cells. Exposure of poliovirus-infected cells to poly(I:C) results in lower levels of IFN-β mRNA synthesis and IRF-3 activation compared to mock-infected cells. Analysis of MDA-5 and IPS-1 revealed that these components of the RLR pathway were largely intact at times when the type I IFN response was suppressed. CONCLUSIONS: Collectively, these results demonstrate that poliovirus infection actively suppresses the host type I interferon response by blocking activation of IRF-3 and suggests that this is not mediated by cleavage of MDA-5 or IPS-1.

Worldwide, 3.575 million people die each year from water-related diseases. The water and sanitation crisis claims more lives than any warfare and is predicted to be one of the biggest global challenges of this century. The rapid, accurate detection of viral pathogens from environmental samples is an ongoing and pertinent challenge in biological engineering. Currently employed methods are lacking in either efficiency or specificity. Here we explore a novel method for virus detection and concurrently use this method to learn more about the very early stages of the virus infection process. The method combines Fourier transform infrared (FTIR) spectroscopy, a method of visualizing molecules based on changes in vibration of particles, and mammalian cells as the biosensor. This method is used to detect and investigate viruses from the family picornaviridae, chosen due to their public health burden and their widespread presence in environmental samples, especially water sources. This family includes the Polioviruses, echoviruses and Coxsackieviruses, among others, many of which are human pathogens.The research outlined in this dissertation is aimed at developing and implementing a new cell-based biosensor that combines the advantages of FTIR spectroscopy with the ability of buffalo green monkey kidney (BGMK) cells to sense diverse stimuli, including infective enteroviruses. The goal of developing this biosensor is outlined in the first paper. The second paper focuses on the application of advanced statistical methods to analyze the spectra to discriminate different viral infections in BGMK cells. Finally, we designed a non-reactive metal biochamber to use with attenuated total reflectance-FTIR. This allowed near-continuous acquisition of real-time spectral data for the study of biochemical changes in mammalian cells caused by poliovirus (PV1) infection. This system is capable of tracking changes in cell biochemistry in minute intervals for many hours at a time.This work demonstrates the feasibility of FTIR spectroscopy in combination with the broad sensitivity of mammalian cells for potential use in the detection of infective viruses from environmental samples. We envision this method being extended to high throughput, automated systems to screen for viruses or other toxins in drinking water systems and medical applications.