Foot-and-mouth disease virus (FMDV) is a highly infectious virus affecting cloven-hoofed animals. The most prominent of its clinical signs is the development of vesicular lesions on the feet and in or around the mouth, which are a consequence of extensive FMDV-induced epithelial cell death. Currently, there is no certain biological knowledge on why extensive epithelial cell death occurs in some FMDV-infected tissues, but not in others. Using the epithelial tissues of tongue and dorsal soft palate as examples of a tissue where lesions occur and one that does not visibly exhibit FMDV-induced cell death, this work aims to identify the potential drivers of epithelial cell death and survival. A partial differential equation (PDE) model informed by experimental data on epithelial structure, is used to test epithelium thickness and cell layer structure as potential determinants. A second PDE model investigates FMDV-interferon (IFN) dynamics and their impact on the levels of cell death and survival, while an experimental study is undertaken to provide data for model validation. The work carried out casts light on the important role of a variety of factors including FMDV replication, IFN production and release, and IFN antiviral action.

Background Climate variation has affected diverse physical and biological systems worldwide. Population health is one of the most important impacts of climate variation. Although the impact of climate variation on infectious diseases has been of significant concern recently, the relationship between climate variation and infectious diseases, including vector-borne diseases and enteric infections, needs greater clarification. Australia is grappling with developing politically acceptable responses to global warming. In China, few studies have been conducted to examine the effect of climate variation, including global warming, on population health. As residents of developing countries may suffer more from climate change compared with people living in more developed countries, this thesis has significance for both countries. Aims This study aims to contribute to a better understanding of the impact of climate variation on population health, and to provide scientific evidence for policy makers, researchers, public health practitioners and local communities in the development of public health strategies at an early stage, in order to prevent or reduce future risks associated with ongoing climate change. The objectives of this study include: (1) to quantify the association between climate variation and selected vectorborne diseases and enteric infections in different climatic regions in Australia and China; (2) to project the future burden of selected vector-borne diseases and enteric infections based on climate change scenarios in different climatic regions in Australia and China. Methods This ecological study has two components. The first uses time-series analyses to quantify the relationship between meteorological variables and infectious diseases, whereas the second projects the burden of selected infectious diseases using future climate and population scenarios. Temperate and subtropical climatic zones in both Australia and China were selected as the primary study areas, and a study of an Australian tropical region was also conducted. Study of Australia’s temperate zones was conducted in Adelaide, South Australia, as well as the Murray River region in that State. The study of China’s temperate zone was carried out in Jinan, Shandong Province. Subtropical studies were conducted in Baoan, Guangdong Province, China, and Brisbane in Queensland, whilst research for the tropics centred on Townsville, also in Queensland, Australia. The selected infectious diseases - one vector-borne disease and one enteric infection in each country - are Ross River Virus (RRV) infection and salmonellosis in Australia, and malaria and bacillary dysentery in China. Study periods vary from eight to sixteen years (depending upon the availability of data). Climate data, infectious disease surveillance data and demographic data were collected from local authorities. Data analyses conducted in the ecological studies include Spearman correlation analysis, time-series adjusted Poisson regression and the Seasonal Autoregressive Integrated Moving Average (SARIMA) model with consideration of lag effects, seasonality, long-term trends, and autocorrelation, on a weekly or monthly basis depending on data availability, and Hockey Sticky model to detect potential threshold temperatures. In the burden of disease component, analyses include the calculation of an indicator of the burden of disease - Years Lost due to Disabilities (YLDs) - and use scenario-based models to project YLDs for the selected diseases in 2030 and 2050 in Australia and 2020 and 2050 in China respectively. The projections consider both different scenarios of projected temperature and future population change. Results Relationship between climate variation and selected infectious diseases In all the study regions in Australia, maximum temperature, minimum temperature, rainfall and humidity are all significantly related to the number of RRV infections, with lag effects varying from 0 to 3 months. Additionally, high tides in the two seaside regions with tropical (Townsville) or subtropical (Brisbane) climates, and river flow in the temperate region (Murray River region), are related to the number of cases without any lag effects. A potential 1°C increase in maximum or minimum temperature may cause 4%~23% extra cases of RRV infection in the temperate region, 5~8% in the subtropical region, and 6%~15% in the tropical region. Maximum temperature, minimum temperature, humidity and air pressure are significantly related to malaria cases in the temperate city Jinan and subtropical city Baoan in China, with a lag effect range of 0 to 1 month. An association between rainfall and malaria cases was not detected in either region. A potential 1°C increase in maximum or minimum temperature may lead to 4%~15% extra malaria cases in the temperate region, and 12%-18% in the tropical region in China. Maximum temperature, minimum temperature, rainfall and humidity are all significantly related to the number of salmonellosis cases in the three study cities in Australia, with lag effects varying from 0 to 1 month. A potential 1°C increase in maximum or minimum temperature may cause 6%~19% extra salmonellosis cases in the temperate region (Adelaide), 5%~10% in the subtropical region (Brisbane), and 4%~15% in the tropical region (Townsville). The thresholds for the effects of maximum and minimum temperatures are 20ºC and 12ºC respectively in Adelaide. No threshold temperatures are detected in Townsville and Brisbane. Maximum temperature, minimum temperature, humidity, air pressure and rainfall are significantly related to bacillary dysentery cases in the temperate city Jinan and subtropical city Baoan in China, with the lag effect range of 0 to 2 months. A potential 1°C increase in maximum or minimum temperature may cause 7%~15% extra bacillary dysentery cases in the temperate region and 10% ~ 19% in the subtropical region in China. The thresholds for the effects of maximum and minimum temperatures on bacillary dysentery are 17ºC and 8ºC respectively in Jinan. No threshold temperatures are detected in Baoan. Projection of YLDs from target diseases In Australia, considering both climatic and population scenarios, if other factors remain constant, compared with the YLDs observed in 2000, the YLDs for salmonellosis might increase by up to 48% by 2030, and nearly double by 2050 in South Australia, while the YLDs might double by 2030 and increase by up to 143% by 2050 in Brisbane, Queensland. The YLDs for RRV infection might increase by up to 66% by 2030, and nearly double by 2050 in South Australia. They might increase by up to 61% by 2030 and double by 2050 in Brisbane, Queensland. In China, considering both climatic and population scenarios, if other factors remain constant, compared with the YLDs observed in 2000, the YLDs for bacillary dysentery might double by 2020 and triple by 2050 in both Jinan and Baoan. The YLDs for malaria might increase by up to 108% by 2020 and nearly triple by 2050 in Jinan, the temperate city, and increase by up to 144% by 2020 and nearly triple by 2050 in Baoan, the subtropical city. Conclusions 1. Both maximum and minimum temperatures are important in the transmission of vector-borne diseases in various climatic regions in both Australia and China. River flow or high tides may also play an important role in the transmission of such diseases. 2. Both maximum and minimum temperatures play an important role in the transmission of enteric infections in various climatic regions in both Australia and China, with a threshold temperature detected in the temperate regions but not in subtropical and tropical regions. 3. The effects of rainfall and relative humidity on selected infectious diseases vary in different study areas in Australia and China. 4. The burden of temperature-related infectious diseases may greatly increase in the future if there is no effective preventive intervention. Public health implications 1. Implication for health practice • Public health practitioners, together with relevant government organisations, should monitor trends in infectious diseases, as well as other relevant indexes, such as vectors, pathogens, and water and food safety. They should advise policy makers of the potential risks associated with climate change and develop public health strategies to prevent and reduce the impact of infectious disease associated with such change. • Doctors and other clinical practitioners should be prepared and supported in the provision of health care for any expected extra cases associated with climate variation and should play an important role in relevant health education on climate change. • Community participation is of significance to adapt to and mitigate the risk of climate change on population health. Community involvement helps to deliver programmes which more accurately target local needs. Therefore, community should be involved in the partnerships of climate change as early as possible. • Relevant education programs on the potential health impact of climate change should be conducted by government at all levels for different stakeholders, including industries, governments, communities, clinicians and researchers. • Advocacy for adapting to and mitigating climate change should be a longstanding public health activity. 2. Implication for researchers • The main task for researchers is to identify the independent contribution made by key climatic variables and whether there are exposure thresholds for infectious disease transmission. Further studies should include various infectious diseases in different climatic regions. • Developing countries and rural regions are more vulnerable to the impact of climate change so more research should be conducted for people living in those regions. • Studies using summary measures that combine prevalence of disease, quality of life and life expectancy, such as Disability Adjusted Life Years (DALYs), to assess the burden of disease due to climate change is necessary to assist in decision making. • More research should be conducted on the assessment of adaptive strategies and mitigation to future climate change. 3. Implication for policies • Public and preventive health strategies that consider local climatic conditions and their impact on vector and food borne diseases are important in reducing such impact due to climate change in the future. • The extra health burden that may be caused by future climate change may have a great impact on the currently overloaded public health system in both developed and developing countries. Long-term planning about health resource allocation, infrastructure establishment, and relevant response mechanisms should be developed at relevant government levels. • Effective prevention and intervention strategies will be possible only if the efforts of relevant sectors, including governments, communities, industries, research institutions, clinical professionals and individuals, have coordinated responses. • International and regional collaborations are necessary to address this global issue. In addition, strategies of an international dimension should be translated into regional and local actions. This is extremely important to developing countries such as China and India. • Sustainable development policies with consideration given to reducing green house gases and environmental degradation need immediate action which will benefit future generations. Health priorities should include the prevention of climate change. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1290777 / Thesis(Ph.D.)-- School of Population Health and Clinical Practice, 2007

Hepatitis C virus (HCV) infection globally affects 130-150 million people. It causes both acute and chronic infections. Due to the severe side effects and low success rates of interferon based treatments, which formed the standard treatment for HCV, the treatment paradigm shifted to direct acting antivirals (DAAs). DAAs have revolutionized the treatment of hepatitis C virus infection. Clinical trials with combinations of DAAs have recorded >90% response with shorter treatment durations and fewer side effects than earlier treatments involving IFN. Outside the controlled setting of a clinical trial, however, response rates with DAA combinations are much lower (<70%). DAAs can fail if HCV accumulates mutations that confer drug resistance. Interestingly, the pre-existence of mutant frequency in the virus appears not to influence treatment outcome. A better predictor for DAA treatment outcome is yet to be unravelled. Surprisingly, individuals who respond poorly to IFN appear to be more likely to fail DAA treatment. IFN is a generic antiviral that improves immune responses and is expected not to have any bearing on DAA treatment outcomes. Why individuals with poor IFN sensitivity fail DAA treatment remains a mystery. In a recent study of the IFN signalling network, HCV has been shown to compromise IFN activity. It induces bistability in the network leading to distinct phenotypic responses of cells to IFN exposure. In particular, individuals who respond poorly to IFN tend to have a higher percentage of cells that are refractory to IFN; these cells allow viral persistence despite IFN exposure. We hypothesized here that in such individuals, greater ongoing replication would allow increased development of resistance and thus lead to the failure of DAAs. We constructed a model of viral dynamics that accounts for the distinct phenotypic responses of cells to IFN, viral replication and mutation, and the development of resistance to DAAs. Our model predicted that although the relative prevalence of pre- existing mutants is unaffected by IFN sensitivity, in agreement with observations, the growth of drug resistant mutants is accelerated in individuals with poor IFN sensitivity. Based on a distribution of IFN sensitivity across individuals, our model accurately described clinical observations of the response rates to different current treatment protocols. With this model, we predict that the common strategy of increasing the genetic barrier by adding more drugs to the combination was not necessary to avert the development of drug resistance. Instead, an optimised increase in DAA dosage alone or DAA+PR or PR dosage depending on the patient’s IFN sensitivity could help achieve success.

Introduction: At the end of 2015, zika virus became the protagonist of an epidemic of congenital anomalies never observed. The northeastern region of Brazil was the most affected. Congenital Zika Syndrome is characterized by severe microcephaly, critical brain damage, ophthalmologic, auditory, cardiac and orthopedic anomalies, as well as severe developmental delay with irritability, spasticity and convulsions. Owning to the fact that it is a new pathology, little is known about its long-term evolution, since affected children are aged around 3 years. Goal: To follow-up of a cohort of infants born with microcephaly and / or anomalies associated with congenital zika virus infection, from birth to 18 months of age, evaluating their growth, development, feeding and occurrence of associated morbidities. Methodology: This was a longitudinal, observational and descriptive study of a cohort of infants born in Sergipe during the outbreak of microcephaly and referred to two public health services. The children were followed up through 18 months of age in childcare consultations, together with expert evaluations and complementary examinations. The data was collected from August / 2017 to January / 2018 with using a research form. Statistical analyzes were carried out in R Core Team 2018 software. Results: The cohort comprised 84 children with Congenital Zika Syndrome. There was a predominance of females (53.8%) and only 9 newborns had no diagnosis of microcephaly but had other alterations compatible with Congenital Zika Syndrome. The Z scores for head circumference, weight and length remained stable over time, remaining below the expected standard for the three anthropometric indexes. The evolution of Z scores for weight / length showed a downward trend, although the average remained in the eutrophic pattern. In addition to the occurrence of other neurological impairments, such as seizures (69%), spasticity (48,8%), and irritability (64,3%), the infants presented severe developmental delays with delayed acquisition of all markers. The prevalence of exclusive breastfeeding until 6 months was law (14.3%) and a significant percentage of feeding difficulty (57,1%). This aspect reflected the delay in the introduction of complementary feeding (mean age of 7.1 months) and non-progression to the family diet in 22.6%. As to the complementary evaluation, cerebral malformations compatible with congenital Zika infection were detected in all children, ocular involvement was diagnosed in 42 infants (54.5%), and in half (50.7%) cardiac anomalies were observed. The main clinical morbidity observed was upper airways infection, followed by intestinal constipation. Conclusions: Infants with Congenital Zika Syndrome exhibited anthropometric growth impairment, as well as a severe delay in the acquisition of neuromotor development markers. It was found low prevalence of exclusive breastfeeding until 6 months, with a high frequency of feeding difficulties. There was also a significant number of infants who presented irritability, convulsion and spasticity. This study reinforces the need for specialized multiprofessional follow-up aimed at rehabilitation therapies and support to the family members involved. / Introdução: Ao final de 2015, o Zika vírus tornou-se protagonista de uma epidemia de anomalias congênitas jamais observada, sendo a região nordeste do Brasil a mais atingida. A Síndrome da Zika Congênita caracteriza-se por microcefalia com grave dano ao tecido cerebral, alterações oftalmológicas, auditivas, cardíacas e ortopédicas, além de crítico atraso do desenvolvimento, com irritabilidade, espasticidade e convulsões. Tratando-se de nova condição clínica, pouco se sabe sobre sua evolução em longo prazo, uma vez que as crianças acometidas estão com média de 3 anos de idade. Objetivo: Realizar o acompanhamento de uma coorte de bebês com Síndrome da Zika Congênita, do nascimento aos 18 meses de vida, avaliando seu crescimento, desenvolvimento, evolução da alimentação e ocorrência de morbidades. Metodologia: Trata-se de estudo longitudinal, observacional e descritivo do acompanhamento de uma coorte de lactentes nascidos em Sergipe durante o surto de microcefalia e referenciados para dois serviços públicos de saúde. As crianças foram avaliadas até os 18 meses de vida em consultas de puericultura somadas a interconsultas com especialistas e realização de exames complementares. Os dados foram coletados de agosto/2017 a janeiro/2018 através de um formulário de pesquisa. As análises estatísticas foram realizadas com o auxílio do software R Core 2018. Resultados: Compuseram a coorte 84 crianças com características clínicas da Síndrome da Zika Congênita. Houve predomínio do sexo feminino (53,8%) e somente 9 recém-nascidos não tiveram diagnóstico de microcefalia, mas apresentavam outras alterações compatíveis com a Síndrome da Zika Congênita. Os escores Z para perímetro cefálico (PC), peso e comprimento apresentaram pouca variação ao longo do tempo. As médias de escore Z na primeira e última consulta foram as seguintes: PC (-6,0; -5,9); Peso (-1,9; -1,6) e Comprimento (-2,5; -1,7). A evolução dos escores Z para peso/comprimento, revelou tendência de queda, apesar da média ter se mantido no padrão de eutrofia. As crianças manifestaram grave atraso do desenvolvimento com retardo na aquisição de todos os marcos pesquisados, além da ocorrência de outros comprometimentos neurológicos tais quais convulsão (69%), espasticidade (48,8%) e irritabilidade (64,3%). Encontrou-se baixa prevalência de aleitamento materno exclusivo até os 6 meses (14,3%) e percentual significativo de relatos de dificuldade alimentar (57,1%), aspecto que refletiu no atraso da introdução da alimentação complementar (idade média de 7,1 meses) e na não progressão para a alimentação da família em 22,6%. Quanto aos exames e avaliações complementares, em todos os lactentes foram detectadas malformações cerebrais compatíveis com a infecção congênita pelo Zika vírus, em 54,5% foi diagnosticado comprometimento ocular e em metade (50,7%) foi observado alguma alteração cardíaca. A principal morbidade clínica apresentada pelas crianças foram as infecções das vias aéreas superiores, seguido de constipação intestinal. Conclusões: Os lactentes com Síndrome da Zika Congênita exibiram comprometimento do crescimento antropométrico, além de grave atraso na aquisição de marcos do desenvolvimento neuromotor. Constatou-se baixa prevalência de aleitamento materno exclusivo até os 6 meses, com alta frequência de dificuldades alimentares. Observou-se também número significativo de lactentes que evoluíram com irritabilidade, convulsão e espasticidade. Os achados deste estudo reforçam a necessidade de acompanhamento multiprofissional especializado para estas crianças, voltado para terapias de reabilitação e apoio aos familiares envolvidos. / Aracaju

L'identification de biomarqueurs et de nouvelles cibles thérapeutiques constitue un enjeu majeur de la recherche biomédicale visant au développement de la médecine personnalisée. L'objectif de cette thèse est d'étudier, à l'aide de puces à ADN, les modulations transcriptionnelles associées à la pathogénèse et à la réponse thérapeutique dans le cas de deux pathologies: l'infection par le Virus de l'Hépatite C (VHC) et la Polyarthrite Rhumatoïde (PR).Des biomarqueurs prédictifs de la réponse au traitement standard interféron ont été identifiés grâce à un modèle cellulaire ex vivo. Par ailleurs, l'analyse de données d'expression de deux modèles d'infection par le VHC (réplicon et infectieux) a permis de mettre en évidence les modulations transcriptionnelles résultant de l'activité antivirale de la chloroquine, une alternative potentielle anti-VHC. Dans le cas de la PR, nous avons identifié des biomarqueurs dont l'expression est corrélée au succès thérapeutique de l'anti-TNF Enbrel. / The identification of biomarkers and new therapeutic targets is a major challenge of biomedical research for the development of personalized medicine. The objective of this thesis is to study, using DNA microarrays, transcriptional modulations associated with the pathogenesis and therapeutic response in the case of two diseases: infection with Hepatitis C Virus (HCV) and Rheumatoid Arthritis (RA).Predictive biomarkers of response to standard interferon treatment were identified using an ex vivo cell model. Furthermore, analysis of expression data of two models of infection with HCV (replicon and infectious) has highlighted the transcriptional modulations resulting from the antiviral activity of chloroquine, a potential anti-HCV alternative. In the case of RA, we have identified biomarkers whose expression correlates with the therapeutic success of Enbrel anti-TNF drug.

Introduction The rapid expansion of the novel SARS-CoV-2 virus has raised serious public health concerns due to the possibility of misdiagnosis in regions where arboviral diseases are endemic. We performed the first study in northern Peru to describe the detection of SARSCoV-2 IgM antibodies in febrile patients with a suspected diagnosis of dengue and chikungunya fever. Materials and methods A consecutive cross-sectional study was performed in febrile patients attending primary healthcare centers from April 2020 through March 2021. Patients enrolled underwent serum sample collection for the molecular and serological detection of DENV and CHIKV. Also, serological detection of IgM antibodies against SARS-CoV-2 was performed. Results 464 patients were included during the study period, of which (40.51%) were positive for one pathogen, meanwhile (6.90%) presented co-infections between 2 or more pathogens. The majority of patients with monoinfections were positive for SARS-CoV-2 IgM with (73.40%), followed by DENV 18.09% and CHIKV (8.51%). The most frequent co-infection was DENV + SARS-CoV-2 with (65.63%), followed by DENV + CHIKV and DENV + CHIKV + SARSCoV-2, both with (12.50%). The presence of polyarthralgias in hands (43.75%, p<0.01) and feet (31.25%, p = 0.05) were more frequently reported in patients with CHIKV monoinfection. Also, conjunctivitis was more common in patients positive for SARS-CoV-2 IgM (11.45%, p<0.01). The rest of the symptoms were similar among all the study groups. Conclusion SARS-CoV-2 IgM antibodies were frequently detected in acute sera from febrile patients with a clinical suspicion of arboviral disease. The presence of polyarthralgias in hands and feet may be suggestive of CHIKV infection. These results reaffirm the need to consider SARS-CoV-2 infection as a main differential diagnosis of acute febrile illness in arboviruses endemic areas, as well as to consider co-infections between these pathogens. Copyright: / Revisión por pares

Over the past decade, and accelerated due to the COVID-19 pandemic, there has been increasing adoption of decentralized diagnostic testing, where the testing is brought closer to the patient. This trend has largely been fueled by the development of more accurate diagnostic tools and faster and more reliable data connectivity. Decentralized testing has been shown to greatly reduce turnaround times while increasing accessibility to users in remote regions. However, there are challenges that limit its widespread adoption. In this dissertation, we detail the development of tools and technologies to overcome these barriers and expedite the shift towards decentralized diagnostic testing. First, we demonstrate the ability to develop point-of-care (POC) diagnostic tests with performance that rivals that of traditional lab-based methods. We developed a rapid, multiplexed, microfluidic serological test for Lyme disease, a tick-borne disease caused by the Borrelia burgdorferi bacterium. The recommended testing, the standard 2-tiered (STT) approach, is not sensitive for early-stage infections, is labor-intensive, has long turnaround times, and requires the use of two immunoassays (enzyme-linked immunosorbent assay (ELISA) and the Western Blot). We developed a standalone multiplexed sandwich ELISA assay and adapted it to the mChip microfluidic platform. We validated the assay on a rigorously characterized panel of human serum samples and demonstrated that our approach outperforms the STT algorithm on sensitivity while matching its specificity. The form factor of this technology is amenable to use in physician’s offices and urgent care clinics. We also showed exploratory work towards adapting the mChip platform for diagnosis of Zika disease, a mosquito-borne disease caused by the Zika virus, and acute kidney injury, a syndrome characterized by loss of kidney excretory function. Next, we worked on increasing the adoption of rapid diagnostic tests for self- and partner-testing designed to be used in at-home settings. We developed a smartphone application to be used alongside the INSTI Multiplex test for detecting HIV and syphilis infections. The application was designed to provide users with i) instructions on running the test, ii) an automated deep-learning-based image interpretation algorithm to interpret the rapid test results from a smartphone image, iii) a way to save test results and display/share them, and iv) resources for follow-up care. We adopted a user-centered, iterative design process where we worked with a cohort of study participants composed of men who have sex with men and transgender women at high risk for contracting sexually transmitted infections. We then field tested the application with 48 participants over a duration of three months and found high acceptability for the application, both in terms of functionality and helpfulness. Finally, we sought to address a key limitation with deep-learning-based image classification techniques, specifically, the requirement for large numbers of annotated images for training. We developed a deep-learning image interpretation algorithm that could be quickly adapted to new rapid test kits using only a fraction of the images that would otherwise be needed for training the model. The interpretation algorithm followed a three-step, modular process. First, the rapid test kit and the membrane were extracted from the smartphone image. Second, the constituent zones were cropped from the extracted membrane. Finally, a classifier detected the presence or absence of a line in the individual zones. Fast adaptation was demonstrated by adapting a base model, trained using images of a single COVID-19 rapid test kit, to four different rapid test kits, each with different form factors, using few-shot domain adaptation. After training with 20 or fewer images, the classification accuracies of all the adapted models were > 95%. This approach can provide a digital health platform for improved pandemic preparedness and enable quality assurance and linkage to care for consumers operating new LFAs in widespread decentralized settings. Together, these methods provide a suite of tools that could expedite the shift towards decentralized, POC testing.

The rubella virus (RV) was the first virus shown to be teratogenic in humans. The wealth of data on the clinical symptoms associated with congenital rubella syndrome is in stark contrast to an incomplete understanding of the forces leading to the teratogenic alterations in humans. This applies not only to RV, but also to congenital viral infections in general and includes (1) the mode of vertical transmission, even at early gestation, (2) the possible involvement of inflammation as a consequence of an activated innate immune response, and (3) the underlying molecular and cellular alterations. With the progress made in the development of pluripotent stem cell-based models including organoids and embryoids, it is now possible to assess congenital virus infections on a mechanistic level. Moreover, antiviral treatment options can be validated, and newly emerging viruses with a potential impact on human embryonal development, such as that recently reflected by the Zika virus (ZIKV), can be characterized. Here, we discuss human cytomegalovirus (HCMV) and ZIKV in comparison to RV as viruses with well-known congenital pathologies and highlight their analysis on current models for the early phase of human development. This includes the implications of their genetic variability and, as such, virus strain-specific properties for their use as archetype models for congenital virus infections. In this review, we will discuss the use of induced pluripotent stem cells (iPSC) and derived organoid systems for the study of congenital virus infections with a focus on their prominent aetiologies, HCMV, ZIKV, and RV. Their assessment on these models will provide valuable information on how human development is impaired by virus infections; it will also add new insights into the normal progression of human development through the analysis of developmental pathways in the context of virus-induced alterations. These are exciting perspectives for both developmental biology and congenital virology.

Im Kampf gegen eine Virusinfektion spielen CD8+ T Zellen des adaptiven Immunsystems eine besondere Rolle. Sie patroullieren im Körper und entdecken spezifische Virusepitope, welche mittels MHC Klasse I Molekülen auf der Oberfläche infizierter Zellen präsentiert werden. Wird eine virus-infizierte Zelle erkannt, kann diese schnell und effizient eliminiert. Für die Generierung viraler Peptide, welche auf MHC Klasse I Komplexe geladen werden, ist das Ubiquitin-Proteasom-System von essentieller Bedeutung. Kürzlich wurden weitere Funktionen des Immunoproteasoms aufgedeckt wie zum Beispiel der Schutz gegen oxidativen Stress. Innerhalb der vorliegenden Arbeit konnte die Fähigkeit des Immunoproteasoms gegen eine Akkumulation oxidativ geschädigter Proteine zu schützen mit der Generierung von MHC Klasse I Liganden kombiniert und neu interpretiert werden. Es konnte gezeigt werden, dass während einer Virusinfektion in Nicht-Immunzellen die Produktion reaktiver Sauerstoffspezies durch die alternative NADPH Oxidase Nox4 eine bedeutende Rolle spielt. Die Aktivierung von Nox4 resultiert in der Akkumulation oxidativ geschädigter Proteine. Innerhalb von zwei Stunden nach dem Eintreten von Viruspartikeln in die Zellen wurden strukturelle Virusproteine oxidiert und anschließend ubiquityliert. Die gleichzeitige, virus-induzierte Expression von Immunoproteasomen führte zu einem schnellen und effizienten Abbau ubiquitylierter Virusantigene. Infolgedessen konnten immundominante Virusepitope vermehrt freigesetzt werden. Folglich wurde ein soweit unbekannter Mechanismus gefunden, welcher Substrate für das Proteasom zur Generierung von MHC Klasse I Liganden bereitstellt. Zusammenfassend konnte innerhalb dieser Arbeit gezeigt werden, dass das Immunoproteasom den Schutz vor oxidativen Stress mit der Generierung antigener Peptide verbindet, wodurch eine effektive adaptive Immunantwort etabliert werden kann. / An efficient immune control of virus infection is predominantly mediated by CD8+ T cells which patrol through the body and eliminate infected cells. Infected cells are recognized when they present viral antigenic peptides on their surface via MHC class I molecules. To make antigenic peptides available for loading on MHC class I complexes, the ubiquitin proteasome system plays a crucial role. Moreover, the induction of the i-proteasome is known to support the generation of MHC class I ligands. Recently, new functions of the i-proteasome have been discovered. Evidence is increasing that the i-proteasome is involved in the protection of cells against oxidative stress. Within this thesis the characteristic of the i-proteasome to protect cells against the accumulation of oxidant-damaged proteins could be linked to its role in improving the generation of MHC class I ligands. It could be demonstrated that during a virus infection in non-immune cells the production of reactive oxygen species by the alternative NADPH oxidase Nox4 is of critical importance resulting in the accumulation of potentially toxic oxidant-damaged proteins. Indeed, within two hours of infection structural virus proteins were oxidized and subsequently poly-ubiquitylated. The concomitant formation of i-proteasomes led to a rapid and efficient degradation of ubiquitylated virus antigens thereby improving the liberation of immunodominant viral epitopes. In conclusion, a so far unknown mechanism to fuel proteasomal substrates into the MHC class I antigen presentation pathway has been revealed. A new protein pool consisting of exogenously delivered viral proteins provides proteasomal substrates in the very early phase of a virus infection. Within the scope of this thesis the i-proteasome has been shown to link the protection against oxidative stress, initiated directly by pathogen recognition, with the generation of antigenic peptides. Together, an effective adaptive immune response is triggered.

Zikaviruset är ett virus som fått stor uppmärksamhet i framför allt Sydamerika från 2015 och framåt då allt fler fall uppmärksammats. Detta arbete har utförts som en litteraturstudie med mål att sammanfatta kunskapsläget kring Zikavirusets morfologi, spridning, historia, komplikationer, diagnostik samt rådande behandlingsmöjligheter. Som källor används information från Folkhälsomyndigheten, CDC, PAHO och WHO samt MeSH-sökningar via PubMed. Viruset tillhör familjen Flaviviridae. Liknande andra virus i samma grupp kan infektionen ge feber, makulopapulösa hudutslag, konjunktivit, ledvärk, huvudvärk och myalgi. Det beskrevs först redan på slutet av 1940-talet i Afrika och har sedan rapporterats ha spridit sig till Asien, Oceanien, Stilla havsöarna och nu senast med utbrott i Sydamerika. Virusinfektionen har blivit mycket omdiskuterad då allt mer bevis kunnat läggas fram för att den kan leda till Guillain-Barrés syndrom samt även utöva teratogena effekter med mikrocefali som följd. Man har kartlagt spridning framför allt via myggarten Aedes men bevis finns även för att sexuell spridning kan ske samt att sjukdomen förefaller även kunna spridas från mor till foster. Diagnostiken baseras på RT-PCR och serologiska tester. I nuläget finns ingen aktiv behandling. Sammanfattningsvis har Zikavirus spridit sig snabbt genom Syd- och latinamerika sista åren och visat sig utgöra ett hot mot folkhälsan i dessa områden varför ett framtagande av ett fungerande vaccin är önskvärt.