Enteroviruses belong to the Picornaviridae family and are small icosahedral viruses with RNA genomes of positive polarity, containing a single open reading frame. They mostly cause mild or asymptomatic infections, but also a wide array of diseases including: poliomyelitis, encephalitis, gastroenteritis, aseptic meningitis, myocarditis, hand-foot-and-mouth disease, hepatitis and respiratory diseases, ranging from severe infections to the common cold. The projects described in this thesis have been carried out through reverse genetic studies of Enterovirus B and Rhinovirus C.                   In Papers I and II, a cassette vector was used to study recombination and translation of the RNA genome. It was found that the non-structural coding region could replicate when combined with the structural protein-coding region of other viruses of the same species. Furthermore, the genome could be translated and replicated without the presence of the structural protein-coding region. Moreover, it was found that when two additional nucleotides were introduced, shifting the reading frame, the virus could revert to the original reading frame, restoring efficient replication. In Paper III, a vector containing the genome of echovirus 5 was altered to produce an authentic 5’end of the in vitro transcribed RNA, which increased efficiency of replication initiation 20 times. This result is important, as it may lead to more efficient oncolytic virotherapy. An authentic 5’end was further used in Paper IV, where replication of Rhinovirus C in cell lines was attempted. Although passaging of the virus was unsuccessful, the genome was replicated and cytopathic effect induced after transfection. The restriction of efficient replication was therefore hypothesized to lie in the attachment and entry stages of the replication cycle. In Paper V, a cytolytic virus was found to have almost 10 times larger impact on gene expression of the host cell than a non-cytolytic variant. Furthermore, the lytic virus was found to build up inside the host cell, while the non-cytolytic virus was efficiently released.                   As a whole, this thesis has contributed to a deeper understanding of replication of enteroviruses, which may prove important in development of novel vaccines, antiviral agents and oncolytic virotherapies.

With global freshwater supplies under pressure, viable water reuse methods are being examined to assist in improving water supplies. Municipal effluent is an ideal source for water reclamation as it is consistent in quality and quantity. The health aspects of water reuse have been identified as an issue of concern, in particular the potential presence of enteric viruses. Managed Aquifer Recharge (MAR) is a method that can aid water reclamation by recharging water such as treated effluent into a suitable aquifer. Research into the removal of pathogenic contaminants by natural processes within aquifers, namely the action of autochthonous bacteria, has led to the consideration that MAR could be used to assist in the removal of microbial pathogens. Pathogens have been demonstrated to be removed during residence in groundwater, but the presence of active autochthonous groundwater bacteria are required for significant removal rates to occur. The aim of this research was to investigate the interaction between autochthonous groundwater bacteria (AGB) and the enteroviruses Poliovirus type 1, Coxsackievirus B3 and Adenovirus B41. It was established that these viruses decrease in number in the presence of AGB but the mechanisms causing this decrease are poorly understood. Experiments were designed to examine how the individual AGB caused decay of the viruses. In this study AGB were isolated and tested for their ability in increase the decay of the viruses. It was determined that 27 % (17/63) of the isolated AGB influenced viral decay. The AGB isolates varied in their influence with only 3 out of 17 isolates being able to cause of the decay of both poliovirus and coxsackievirus. Similar variations in decay were observed for adenovirus. Decay times for all three viruses varied amongst the AGB and between the viruses. Experiments were undertaken to characterise the mechanism causing the antiviral activity of four groundwater isolates (1G, 3A, 4B and 9G) under varying conditions and treatments to give insight into the compounds or mechanisms responsible for viral decay. This would indicate whether compounds produced by the AGB responsible for viral decay were closely associated to bacterial cells (perhaps membrane bound), independent of metabolic activity, heat labile or were enzymatic in nature. The influence of enzyme inhibiters and heat treatment indicated that viral degradation is caused by compounds that are enzymatic in nature. As viral numbers were monitored by nucleic acid copy numbers rather than via infectivity assays, the viral protein coats must be the first step in degradation followed by the removal of the viral nucleic acid. This two step process would require both protease and nuclease enzymes to result in loss of viral numbers as measured by RT-PCR/PCR. Further characterisation and identification of these four bacterial isolates was also carried out. Three out of the four isolates were sequenced and analysed using partial 16S rRNA gene sequences to determine their phylogenetic relationships compared to related organisms. Isolate 3A was placed in the order Burkholderiales. Isolate 4B was placed in the family Xanthomonadaceae. Isolate 9G was placed in the family Rhizobiaceae. Isolate 1G was only partially sequenced and preliminary identification placed it in the phylum Bacteriodetes. Understanding of the processes carried out by AGB within an aquifer during MAR using reclaimed waters will aid in increasing the viability of this water reuse process. If important natural processes could be utilised to remediate any potential pathogens, the health concerns with reclaimed waters could be addressed and solved simply through prescribed retention times within the aquifer. Key species of AGB may even be utilised as markers to assess the suitability of an aquifer for MAR.

La présente étude vise à étudier le potentiel de bifidobactéries à protéger les cellules contre l’infection par le Coxsackie B4 (CV-B4). Le criblage de bifidobactéries a identifié deux des cinq souches qui protégeaient les cellules HEp-2 lorsque les bifidobactéries sont pré-incubées avec les particules virales avant l'inoculation sur les cellules Hep-2. En revanche, aucun effet protecteur n'a été observé en incubant les cellules Hep-2 avec des bifidobactéries avant l'inoculation de CV-B4. Les lipoprotéines des parois cellulaires (LpAs) sécrétées par les souches sélectionnées sont testées pour leur activité antivirale. Les deux LpAs présentaient une activité antivirale quand ils sont incubés avec les particules virales avant d’être inoculées aux cellules HEp-2. Aucun effet protecteur n'a été induit par incubation des LpAs avec les cellules HEp-2 avant l'inoculation de CV-B4. La protéine recombinante présente une activité antivirale identique. Pour identifier les séquences peptidiques interagissant avec les particules virales, les protéines de LpAs sont alignées avec les séquences peptidiques du nord bord du canyon et avec l’empreinte de la région puff sur le Coxsackievirus et sur le récepteur de l’adénovirus (CAR). L'étude d'amarrage moléculaire in silico (Docking) utilisant le CV-B3 en tant que modèle a montré une faible énergie de liaison indiquant un système stable pour les peptides sélectionnés et par conséquent une interaction probable avec le CV-B. Les peptides de B.longum et de B.breve qui sont homologues à l’empreinte du rebord nord viral sur la séquence CAR, forment des liaisons d’hydrogène avec plusieurs résidus viraux dans la région du rebord nord du canyon, qui sont déjà décrits pour leur interaction avec le CAR.En conclusion, les protéines de LPAS bifidobactéries peuvent inhiber l'infection par le CV-B4 probablement par liaison aux acides aminés de la capside qui interagissent avec le CAR. / The present study aims at investigating the potential of bifidobacteria in protecting cells from Coxsackievirus B4 (CV-B4) infection. The bifidobacterial screening identified two out of five strains that protected HEp-2 cell viability when bifidobacteria were incubated with the viral particles prior inoculation. In contrast, no effect was shown by incubating HEp-2 cells with bifidobacteria prior CV-B4 inoculation. Cell-wall lipoproteins secreted by the selected strains (LpAs) were assayed for their anti-viral activity. The two LpAs exhibited anti-viral activity when they were incubated with the viral particles prior inoculation to HEp-2 cells. No effect was induced by incubating LpAs with HEp-2 cells prior CV-B4 inoculation. The recombinant LpAs derived-protein exhibited identical anti-viral activity. To identify the peptide sequences interacting with the virus particles, LpAs proteins were aligned with the peptide sequences of north canyon rim and puff footprint onto coxsackievirus and adenovirus receptor (CAR). The in silico molecular docking study using CV-B3 as template showed a low energy binding indicating a stable system for the selected peptides and consequently a likely binding interaction with CV-B. B.longum and B.breve peptides homologous to the viral north rim footprint onto CAR sequence formed hydrogen bonds with several viral residues in the north rim of the canyon, which were already predicted as interacting with CAR. In conclusion, proteins from bifidobacterial LpAs can inhibit the infection with CV-B4 likely through binding to the capsid aminoacids that interact with CAR.

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Bakgrund: Diabetes Mellitus typ I är ett globalt hälsoproblem som skördar många liv varje år och påverkar livskvaliteten för de drabbade. Diabetes typ I är en autoimmun sjukdom som leder till destruktion av insulinproducerande betaceller i pankreas och således rubbad glukosreglering. Huvudsakliga patogena immunceller inkluderar autoantikroppar, exempelvis riktade mot glutaminsyra dekarboxylase 65, och autoreaktiva T-celler. Diagnos sker generellt baserat på förhöjda halter plasmaglukos och eventuellt stimulering av C-peptid för att utreda status för den endogena betacellsfunktionen. Diabeteskomplikationer är en vanlig dödsorsak hos diabetespatienter. År 2019 orsakades 4,2 miljoner dödsfall av diabetes eller diabeteskomplikationer. I dagsläget är administrering av exogent insulin enda behandlingsmöjligheten för typ I diabetespatienter. Det har dock länge forskats på alternativ i form av preventiv behandling men i dagsläget finns inga preventiva behandlingar på marknaden. Syfte: Litteraturstudiens syfte var att undersöka prospektiva möjligheter till diabetespreventiv behandling inom områdena glutaminsyra dekarboxylase 65 vaccin och coxsackievirus B vaccin med avseende på effekt samt jämföra dessa två prospektiva behandlingsmöjligheter. Metod: Arbetet har utförts genom granskning av artiklar från databasen PubMed. För litteraturgranskning av studier om GAD-behandling valdes tre kliniska studier utifrån sökning med ”type 1 diabetes”, ”diabetes mellitus”, ”type 1”, ”GAD” och ”vaccine” som sökord. För artiklar om CVB och CVB-vaccin användes ”type 1 diabetes”, ”vaccine” och ”coxsackievirus” som sökord. Resultat: Kliniska studier på GAD-behandling visar ingen signifikant skillnad mellan GAD-alum och placebo i helgruppsanalyser. Vid vissa stratifierade analyser för exempelvis kön, ålder, eller antal riskfaktorer detekteras signifikanta skillnader genom ökad mängd stimulerad C-peptid eller progression till klinisk diabetes. Den prospektiva kohortstudien över diabetesincidens påvisar att CVB är en riskfaktor för diabetes hos människa. Vidare visar de prekliniska studierna på signifikant minskad diabetesincidens i CVB-vaccinerade studiepopulationer jämfört med placebo. Slutsats: Varken behandling med GAD-alum eller CVB-vaccin är möjligt att använda som preventiv behandling i nuläget. Dock visar studierna på lovande framtidsmöjligheter för CVB-vaccin som primärprevention och GAD-alum som sekundär- eller tertiärprevention. / Background: Diabetes Mellitus type I is a global health issue, causing numerous deaths each year and also influencing the quality of life of those affected. Type I diabetes is an autoimmune disease where the individuals own immune system causes destruction of insulin producing beta cells in the endocrine islets of pancreas. Main immunological features include, autoantibodies directed towards glutamic acid decarboxylase 65, and autoreactive T-cells. Diagnosis is generally based on elevated levels of plasma glucose and stimulated C-peptide, together disclosing the status of the beta cell function. The lack of endogen insulin causes disturbances in the glucose metabolism which leads to prevailing tissue damage in cells and organs of the diabetic individual’s body. Furthermore, insufficient control of plasma glucose is related to development of diabetes complications. Diabetic complications are known to be a major cause of death in diabetic patients. Diabetes and diabetic complications caused 4,2 million deaths in 2019. Insufficient adherence to treatment regimen during a long period of time is known to increase the risk for some common diabetes complications. Administration of exogenous insulin is the only current treatment available for type I diabetes, albeit recurrent attempts to find a cure or successful preventive treatment for diabetes mellitus type I. Recent promising research on diabetes preventive treatment includes the autoantigen glutamic acid decarboxylase-65 and vaccine against coxsackievirus B. Aim: The purpose of this literature study was to examine prospective possibilities for diabetes preventive treatments. Further, the purpose was to compare the promising preventive treatments of GAD65-vaccine and CVB-vaccine concerning effect and prospective treatment regimens. Methods: The thesis is a literature study based on articles found by searching the database PubMed. Clinical studies examining the effect of GAD-treatment was found by using key words such as ”type 1 diabetes”, ”diabetes mellitus”, ”type 1”, ”GAD” and ”vaccine”. Studies examining the effect of CVB and CVB-vaccines was primarily preclinical and prospective cohort studies, found by searching for the key words ”type 1 diabetes”, ”vaccine” and ”coxsackievirus”. Results: Clinical studies of GAD-treatment does not demonstrate a statistically significant difference between treatment with GAD-alum compared to placebo in full group analysis. Stratified groups occasionally prove significant differences in quantity of stimulated C-peptide or progression to clinical diabetes by age, gender or amount of risk factors for example. The prospective cohort study examining the incidence of diabetes, demonstrates that CVB is a risk factor for type I diabetes in humans. Furthermore, the preclinical studies detect a significant decrease in diabetes incidence in CVB-vaccinated mice compared with placebo. Conclusion: Neither treatment with GAD-alum nor CVB-vaccine is currently ready for use. However, the studies show a promising prospective possibility for CVB-vaccine as a primary prevention and GAD-alum as a secondary or tertiary prevention of type I diabetes.

Das Proteasom ist ein multikatalytischer, ATP-abhängiger Enzymkomplex, der kurzlebige und regulatorische Proteine in der Zelle abbaut. Im Rahmen der Proteinqualitätskontrolle werden durch das Proteasom auch fehlerhaft synthetisierte bzw. falsch gefaltete oder chemisch geschädigte Proteine degradiert. Zellen hämatopoetischen Ursprungs exprimieren sogenannte Immunoproteasomen, die durch drei alternative katalytische Untereinheiten (LMP2, MECL-1 und LMP7) charakterisiert sind. Unter dem Einfluss von Interferonen kommt es auch in nicht-hämatopoetischen Zellen zur de novo Assemblierung von IP. Sie weisen im Vergleich zu Standardproteasomen einen erhöhten Substratumsatz sowie veränderte Schnittpräferenzen auf. Dadurch können Standard- und Immunoproteasomen verschiedene MHC Klasse I-restringierte antigene Peptide generieren. Die vorliegende Arbeit untersucht die Relevanz der LMP2- bzw. der LMP7- Untereinheit im Rahmen der Coxsackievirus B3 Myokarditis. LMP7-/- Mäuse zeigen eine suffiziente CD8+ T Zell Antwort, die zur vollständigen Viruselimination nach der akuten Entzündungsphase beiträgt. Die reguläre Expression pro-inflammatorischer Zytokine und antiviraler Signalwege sowie CVB3-spezifischer IgG-Antikörper spricht gegen eine spezielle Funktion von IP bei der Induktion einer effektiven Immunantwort in diesem Modell. Es konnte jedoch gezeigt werden, dass der verminderte Einbau aller IP-Untereinheiten in LMP7-defizienten Mäusen mit einer schweren Inflammation und Myokardschädigung einhergeht. Der verringerte Substratumsatz führt zur Akkumulation von polyubiquitinylierten, oxidativ geschädigten Proteinen sowie zur verstärkten Apoptose IP-defizienter Kardiomyozyten und inflammatorischer Zellen. / The standard proteasome is the major ATP-dependent multi-catalytic protein complex that is important for the proteolytic processing of short-lived and regulatory proteins. It also degrades exogenous or improperly synthesized, misfolded, and damaged proteins. Cells of hematopoietic origin predominantly express an alternative variant - the immunoproteasome, which is characterized by three specific catalytically active subunits (LMP2, MECL-1 and LMP7). In non-immune cells, these immunosubunits are also induced and incorporated into newly assembling IPs upon exposure to interferons. As compared to standard proteasomes, IPs display altered cleavage site preferences, resulting in the generation of a different spectrum of antigenic peptides for MHC class I presentation. The present thesis investigates the impact of LMP2- and LMP7 within the context of viral heart disease, making use of the well-established murine model of coxsackievirus B3 infection. LMP7-deficient mice demonstrate a potent CD8+ T cell capacity to control CVB3 infection, resulting in viral clearance after the acute stage of disease. The expression of pro-inflammatory cytokines, innate antiviral mediators, and CVB3-specific IgG antibodies argue against a specific role of IPs in the induction of an effective immune response against CVB3 infection. However, the impaired incorporation of all three immunosubunits in LMP7-deficient hearts coincides with severe inflammation and myocardial tissue damage. Exposure to IFN-γ gives rise to prolonged accumulation of oxidant-damaged, poly-ubiquitylated proteins in IP-deficient cardiomyocytes and inflammatory cells. Along with the restricted degradation of toxic protein aggregates, inflammatory cells and the adjacent myocardium are prone to increased apoptotic cell death.

It has been suggested that the rising amounts of chemicals in the environment may affect host resistance and increase susceptibility to infections. Studies have also shown that infections can change the toxicity of pollutants. The aim of this thesis was to study interactions between environmental pollutant exposure in terms of polybrominated diphenyl ethers (PBDE) and a common human coxsackievirus B3 (CVB3) infection adapted to Balb/c mice. The studies focused on virus levels, cytokines, metabolising cytochrome P450 (CYP) enzymes and tissue distribution of PBDE. A novel finding was an organ-specific effect of CVB3 infection on the metabolising capacity of PBDE. The PBDE metabolising enzyme CYP2B10 was down-regulated by the CVB3 infection in the liver, up-regulated in the lungs, but not affected in the pancreas. Accordingly, CVB3 infection increased the concentration of PBDE in the livers of infected mice. However, serum levels of PBDE were not affected by the infection, indicating that serum does not reflect the actual organ exposure of PBDE in infected individuals. The change in metabolising capacity was likely mediated by infection-induced cytokines and associated effects on the nuclear factor-κB (NF-κB) pathway. PBDE drastically decreased serum levels of several cytokines and chemokines, an event that may create a slot for viruses to replicate. Accordingly, some results show that infected mice exposed to a high dose of PBDE had higher virus levels than mice exposed to a low dose. In conclusion, infected individuals showed organ-specific changes in metabolism and tissue levels of PBDE, which potentially could change the toxicity of PBDE. PBDE also seems to affect the fate of the infection. NF-κB activated pathways may mediate one possible mechanism underlying these effects. Thus, further investigations of this pathway are warranted. In addition, future studies should address how PBDE exposure affects viral replication.

INKT cells are non-conventional T lymphocytes that are restricted to glycolipid presenting CD1d molecule. iNKT cells express an invariant TCR a chain (Va14-Ja18 in mice and Va28-Ja18 in humans). Their particularity is to rapidly produce copious amounts of cytokines (IFN-? and IL-4) after activation and to activate other cells of the immune system such as dendritic cells, NK cells and T lymphocytes. iNKT cells, therefore, form a bridge between innate and adaptive immune responses. Type 1 diabetes is an autoimmune disease characterized by the destruction of pancreatic ß cells whose role is to produce insulin. While diabetes development can clearly be associated with genetic polymorphisms, environmental factors were also implicated in the etiology of the disease. Numerous studies suggest that viral infections, particularly infections with Coxsackievirus B4 (CVB4), could be implicated in the development of type 1 diabetes. Our study was performed with NOD mice that develop type 1 diabetes around 15 weeks of age and with proinsulin 2 knockout NOD mice (Pro-ins2-/-) which become diabetic around 8 weeks of age. Our results show that CVB4 infection induces accelerated diabetes in around half of NOD and Pro-ins2-/- mice compared to uninfected mice. However, the activation of iNKT cells with their agonist, aGalactosylceramide (aGalCer), at the time of infection greatly decreases diabetes incidence. CVB4 infection induces a strong recruitment of macrophages into the pancreas. Interestingly, iNKT cell activation modifies the function of these macrophages. Indeed, pancreatic macrophages of CVB4 infected mice strongly express IL-1, IL-6 and TNF-a, indicating their pro-inflammatory character. On the contrary, macrophages of mice infected with CVB4 and treated with aGalCer express low levels of these cytokines, but strong levels of suppressive enzymes iNOS (inducible NO synthase), IDO (Indoleamine 2,3-dioxygenase) and arginase I. The use of inhibitors of these enzymes showed that diabetes prevention is induced by IDO. We have also observed that autoreactive T cells strongly infiltrate the pancreatic islets after CVB4 infection. It is interesting to note that the high diabetes incidence of CVB4 infected mice is associated with an increased frequency of IFN-? producing autoreactive T cells in pancreatic islets. On the contrary, the frequency of these cells is very low in infected mice treated with aGalCer. The inhibition of IFN-? production is dependent on IDO enzyme, since the use of its inhibitor strongly increases IFN-? production by anti-islet T cells and diabetes incidence. To summarize, our results show that iNKT cell activation during the infection with CVB4 induces immunosuppressive macrophages in the pancreas. These cells inhibit the function of autoreactive T cells and prevent diabetes development.