No grupo das doenças infecciosas emergentes e reemergentes, os arbovírus transmitidos por mosquitos, são considerados importantes desafios para a saúde pública. O alastramento mundial do vírus Chikungunya (CHIKV, Togaviridae, Alphavirus), acabou resultando na introdução do CHIKV no Brasil, através da transmissão zoonótica por mosquitos do gênero Aedes spp, particularmente Ae. aegypti e Ae. albopictus, duas espécies invasoras e cosmopolitas. Outro Alphavirus, o vírus Mayaro (MAYV) presente na região amazônica da América do Sul, vem apresentando indícios de uma real urbanização, elevando a preocupação sobre sua possível transmissão por mosquitos urbanos. Diante desse cenário, fica clara a necessidade da realização de estudos sobre estratégias de controle e prevenção da infecção por MAYV e CHIKV, uma vez que não há vacinas ou terapia antiviral específica para a infecção por esses arbovírus. Este projeto descreve pela primeira vez a eficiente expressão, purificação e análise de partículas semelhantes a vírus (VLP, virus-like particles) dos Alphavirus CHIKV e MAYV em células de inseto S2 (Drosophila melanogaster). Para esse fim, clonamos os genes das proteínas estruturais dos vírus MAYV e CHIKV em vetores para a expressão recombinante em células S2. Essa plataforma de expressão de proteínas provou ser adequada para o processamento de glicoproteínas do CHIKV e MAYV para produção de VLP, uma vez que detectamos a presença de partículas no sobrenadante do cultivo por Western blotting e Microscopia eletrônica de transmissão (TEM). Ainda, foi possível selecionar células para uma maior produção de VLP e estabelecer um método de purificação das partículas. / In the group of emerging and reemerging infectious diseases, mosquito-borne arboviruses are considered major public health challenges. The transmission of Chikungunya (CHIKV, Togaviridae, Alphavirus) in America continent was first reported in Central America and Caribbean region The CHIKV epidemics reached Brazil through zoonotic transmission by Aedes spp mosquitoes, particularly Ae. Aegypti and Ae. albopictus, two invasive and cosmopolitan species. Another Alphavirus, the Mayaro virus (MAYV) present mainly in the Amazon region has been showing evidence of a real urbanization, increasing concerns about its transmission by urban mosquitoes. Therefore, it is clear that studies on strategies for the control and prevention of MAYV and CHIKV infection are needed. Currently no vaccines or antiviral therapy specific for CHIKV and MAYV infection are available. This work describes for the first time an efficient expression, purification and analysis of virus-like particles (VLP) of CHIKV and MAYV Alphaviruses in S2 (Drosophila melanogaster) insect cells. The genes coding for the structural proteins of the MAYV and CHIKV viruses were cloned into vectors for recombinant expression in S2 cells. This platform proved to be suitable for the processing of CHIKV and MAYV glycoproteins and to produce VLP, since we detected the presence of particles in the culture supernatant by Western blotting and Transmission Electron Microscopy (TEM). Furthermore, it was possible to select cells for greater production of VLP and to establish a method for particle purification.

Alphavirus et virus de l'hépatite E, appartiennent à l'alpha-like supergroupe de virus à ARN simple brin positif. Dans cette thèse, la caractérisation fonctionnelle de l'ARNm plafonnement enzyme et le domaine macro sont abordées, afin d'élucider leur rôle dans la réplication virale et de les évaluer en tant que cibles antivirales possibles.Les alphavirus possèdent un mécanisme unique de coiffe de l'ARNm viral impliquant la protéine non structurale nsP1. Nous présentons ici la caractérisation biochimique de nsP1d'alphavirus et son potentiel comme cible antivirale. Pour cela, différents tests enzymatiques ont été développés afin de mieux comprendre et de découpler les différentes étapes de la réaction catalysée par nsP1. Nous avons pu montrer pour la première fois chez les alphaviurs le guanylyltransfert de m7GMP sur l'extrémité 5'-diphosphate d'un ARN. Les techniques développées mises au point ont été mises à profit pour élucider le mode d'action d'une nouvelle classe d'antiviraux d'alphavirus.Le Macro domaine est un domaine protéique ancien et conservé et largement distribué dans tout le règne vivant. Nous déclarons que le domaine Macro de virus de l'hépatite E sert une protéine hydrolase ADP-ribose pour inverser la protéine ADP-ribosylation. L'abolition de l'activité diminue considérablement la réplication d'un réplicon sub-génomique du VHE. L'activité est également présente dans les macro domaines du SRAS-CoV et VEEV. Nos résultats montrent que les macro domaines viraux servent ADP-ribose protéine hydrolase et jouent un rôle important dans la réplication virale, peut-être grâce à la modulation de la réponse antivirale de l'hôte. / Alphavirus and Hepatitis E virus, belong to alpha-like supergroup of positive single stranded RNA viruses. In this thesis, the functional characterization of mRNA capping enzyme and Macro domain are addressed, in order to elucidate their role in the viral replication and to evaluate them as possible antiviral targets. Part I: Alphaviruses are known to possess a unique viral mRNA capping mechanism involving the viral non-structural protein nsP1. Here we report the biochemical characterization and antiviral investigation of alphavirus nsP1. Different enzymatic assays were developed to further understand and uncouple the different reaction steps catalyzed by nsP1. The final guanylyltransfer of m7GMP onto a 5'-diphosphate RNA oligonucleotide was observed for the first time in vitro with an alphavirus nsP1. Taking advantage of the developed techniques, the mode of action of a novel class of alphavirus antivirals, [1,2,3]triazolo[4,5-d]pyrimidin-7(6H)-ones, was deciphered. Part II: Macro domain is an ancient and highly evolutionarily conserved protein domain widely distributed throughout all kingdoms of life. Here, we report that the Macro domain from hepatitis E virus serves as an ADP-ribose protein hydrolase to reverse protein ADP-ribosylation. Abbrogation of this activity dramatically decreases replication of a HEV sub-genomic replicon. This activity is also present in Macro domains from SARS-CoV and VEEV virus. Collectively, our results show that viral Macro domains serve as ADP-ribose protein hydrolase and play important roles in viral replication, possibly through modulating the antiviral host response.

Eastern Equine Encephalitis virus has a human mortality rate of 30% of those cases diagnosed, while 30% of those surviving infection remain with neurological sequelae for life (CDC.gov, 2007). The use of sentinel chickens for surveillance of arboviruses that are known to use birds as a reservoir host, such as St. Louis Encephalitis (SLE), West Nile (WN) virus, Eastern Equine Encephalitis (EEE) and Highlands J (HJ) virus, in Florida began with the Sentinel Chicken Arboviral Surveillance Network in 1978 (Day and Stark, 1996). This network enables the activation of an early warning system for citizens, as well as, county epidemiologists and those in mosquito control, allowing for a coordinated effort of disease prevention. Methods currently used at the Florida Department of Health, Tampa Branch Laboratory include screening of submitted sera for antibodies to these arboviruses of epidemiologic importance by way of the hemagglutination inhibition test (HAI), and confirmation by the IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA) and Plaque Reduction Neutralization test if the MAC-ELISA proves to be negative. While these tests combined are providing the results needed, the time to result can be a week or greater depending on the initial screening result in the HAI tests. The Microsphere Assay Technology provides an accurate, more rapid (a day or two instead of a week or more) detection method including both a screening and confirmation protocol specifically designed to test for antibody to EEE in sentinel chicken sera. Two sera out of the thousands tested that were tested by HAI shown to be negative in standard testing, resulted as positive by the MIA method and therefore indicated a missed positive. The sensitivity and specificity, positive and negative predictive values of this new protocol as compared with MAC-ELISA as a reference standard indicated that both tests were remarkably similar; Providing sensitivity near 80%, specificity and PPV at 99%, and negative predictive values at 90% for MAC-ELISA and 94% for the MIA. Finally it was determined that Highlands J virus will not have any impact on the testing protocol and results of this test.

Ross River virus (RRV) is a mosquito-borne alphavirus and the aetiological agent of epidemic polyarthritis (EPA). Arthropod borne-Alphaviruses that are related to RRV, such as Chikungunya virus, Sindbis virus and Barmah Forest virus, are usually associated with epidemics of infectious arthritides in different parts of the world. In humans, RRV-induced disease symptoms include fever, rash, myalgia and pain and stiffness of the joints. Muscle and joint pain are the most debilitating symptoms in RRV patients and the best treatment available is non-steroidal anti-inflammatory drugs (NSAID). Previous studies in mice have demonstrated that RRV infection results in inflammation of skeletal muscle and joints and that macrophages play a primary role in disease. The present study was carried out to further elucidate the underlying mechanisms mediating RRV-induced muscle and joint pathology. Previous studies have reported that encephalitic alphaviruses trigger apoptosis of brain cells in mice and that blocking apoptosis reduces mortality rates. In the present study, the ability of RRV to induce muscle apoptosis was investigated in vitro, using a murine myoblast cell line (C1C12), and in vivo, using a mouse model of RRV disease. RRV-infected C1C12 myofibres displayed an array of morphological and biochemical makers of apoptosis. Apoptosis was also observed in the skeletal muscle of RRV-infected C57BL/6J mice. Blocking apoptosis by general caspase inhibition resulted in milder disease symptoms, reduced myofibre damage and decreased inflammation of muscle and joint tissues. The total number of cell infiltrates as well as the number of macrophages infiltrating muscle was significantly reduced by the treatment with a caspase inhibitor. The effects of RRV infection on the skeletal system were also investigated. Primary human osteoblast cells were infected with RRV and monitored for viral-induced cytopathic effect. Osteoblasts supported rapid virus growth and, by 48 hours after infection, succumbed to viral-induced necrosis. In addition, histological examination of bone tissue from RRV-infected C57BL/6J mice showed clear evidence of bone resorption. Tibias from infected mice showed an increased number of activated osteoclasts, a reduction in bone density and thinning of cortical bone. The expression of host factors involved in inflammatory responses and bone remodelling was studied in RRV-infected myofibres and osteoblast cell cultures and in the muscle and joint tissues from infected mice. RRV-infected muscle cells and tissue showed elevated mRNA levels for the chemokines CCL-2, CCL3, CCL5 and CXCL1, all of which are known to mediate the migration of monocytic cells. With the exception of CXCL1, these chemokines were also found to be up-regulated in RRV-infected osteoblast cultures and in joint tissues from infected mice. Muscle and joint tissue from infected mice also showed elevated mRNA levels for type I and type II interferons, TNF- and NOS2. In addition, joint tissues from infected animals contained high levels of IL-6 and IL-1, two cytokines known to mediate bone remodelling. Finally, the therapeutic potential of the drug bindarit was investigated using the mouse model of RRV disease. Bindarit is a known inhibitor of CCL-2 and TNF- and has been found to prevent protein denaturation. Treatment with bindarit resulted in mice developing milder disease symptoms, reduced muscle damage and decreased inflammation of muscle and joint tissues. In particular, bindarit significantly reduced macrophage infiltration into skeletal muscle tissue. This thesis has contributed to the understanding of RRV pathogenesis. It has identified novel mechanisms of RRV-induced muscle and bone pathology and provided further evidence that associate pro-inflammatory host factors to RRV disease. This work has also demonstrated that bindarit should be considered as a candidate for treating RRV disease in humans.

Members of the alphavirus genus pose a serious or potential threat to public health in many areas of the world. Nearly all alphaviruses are maintained in nature by transmission cycles that involve alternating replication in a susceptible vertebrate and invertebrate host. The maintenance of this transmission cycle depends on the establishment of a life-long persistent infection in the invertebrate vector host. Although alphavirus replication has been extensively studied in vertebrate models, the strand-specific replication kinetics of alphaviruses during persistent infections of the invertebrate host have not been reported. We investigated the strand-specific replication of different alphavirus genotypes in invertebrate cells. By comparing different detection strategies and chemistries, we identified an optimal ssqPCR assay design for strand-specific quantification of viral RNAs in infected cells and tissues. We found that primer sets incorporating the use of a non-target tag sequence were able to avoid real-time PCR detection of amplicons that were falsely-primed during reverse-transcription. We also determined that DNA hydrolysis probes increased the sensitivity of ssqPCR assays when compared to a double-stranded DNA-specific dye, SYBR Green. Using this information, we determined the replication kinetics of two different genotypes of o'nyong nyong virus (ONNV) and chikungunya virus (CHIKV) in infected mosquito cells. We found that (-) strand viral RNAs persisted in invertebrate cells for up to 21 days after infection. We also found that significantly less (-) strand RNA was present in cells infected with opal variants of both ONNV and CHIKV than sense variants at several time points post infection, suggesting that the opal codon has a functional role in (-) strand RNA regulation. We also report the development of an ONNV replicon expression system. In total, the tools we developed for this report will facilitate future replication studies in the mosquito that may shed light on questions regarding the regulatory role of the opal codon and the persistence of (-) strand RNAs during long-term infections. The strand-specific replication kinetics of ONNV and CHIKV genotypes reported here will serve as a foundation for such investigations. / Master of Science in Life Sciences

Les alphavirus sont un groupe de virus enveloppés à ARN simple brin positif retrouvés sur la totalité du globe et responsables de nombreuses maladies humaines et animales. Durant la dernière décennie, une réémergence du virus du chikungunya (CHIKV) a été observée causant de nombreuses épidémies sur tous les continents. Malgré les nombreuses études, les mécanismes moléculaires de réplication du CHIKV et les interactions hôte-virus restent peu caractérisées. L’objectif de mon travail était de mieux comprendre et caractériser l’entrée du virus du chikungunya et les facteurs de l’hôte impliqués dans la réplication chez les mammifères. Plusieurs approches distinctes ont été utilisées dans ce projet. Dans un premier temps, nous avons mis en avant une diminution de l’infection du CHIKV après un traitement avec du fer sous forme de citrate d’ammonium ferrique et nous avons étudié le rôle potentiel dans l’entrée virale de NRAMP2 et TFRC, deux protéines impliquées dans le transport cellulaire du fer et connus comme récepteurs d’entrée de plusieurs virus. D’autre part, nous nous sommes intéressés à deux autres protéines, CD46 et TM9SF2, identifiés à travers un criblage par ARNi réalisé en collaboration, dans le but de déterminer si elles sont utilisées comme facteurs d’entrée par le virus du chikungunya. Dans un dernier axe, nous avons mis en place et réaliser un criblage perte de fonction sur le génome entier en utilisant la technologie CRISPR/Cas9 afin d’identifier des facteurs de l’hôte importants pour l’entrée du CHIKV, sa réplication ou la mort viro-induite. Bien qu’il soit apparu que l’approche utilisée pour le criblage devrait être optimisée, nous avons pu identifier des candidats potentiellement nécessaires pour l’infection par le CHIKV. Ces candidats sont testés individuellement afin de confirmer leur implication dans la biologie du virus / Alphaviruses are a group of enveloped, positive-sense RNA viruses which are distributed almost worldwide and are responsible for a considerable number of human and animal diseases. Among these viruses, the Chikungunya virus (CHIKV) has recently re-emerged and caused several outbreaks on all continents in the past decade. Despite many studies, molecular mechanisms of chikungunya virus replication and virus-host interactions remain poorly understood. The aim of my project was to better understand and characterize the CHIKV entry and the host factors involved during replication steps in mammals. Several different approaches have been used in this work. As a first step, we have demonstrated a decrease of CHIKV infection after iron treatment in form of ferric ammonium citrate and we have studied the potential role in viral entry of NRAMP2 and TFRC, two proteins involved in iron transport and known receptors for other viruses. On the other hand, we have also focused on two proteins, CD46 and TM9SF2, identified through an RNAi screen in collaboration, in order to determine if they are required as entry factors for chikungunya virus. In a last axis, we have set up and carried out a genome-wide loss of function screen with the CRISPR/Cas9 technology in order to identify host factors important for chikungunya virus entry, replication or virus-induced cell death. Although it appears that screen conditions should be optimized, we have identified potential candidates required for CHIKV infection and we are currently testing them

Chikungunya est un alphavirus transmis par les moustiques (Aedes) et qui provoque de la fièvre, des éruptions cutanées, des myalgies et des arthralgies. La maladie (CHIKVD) est transitoire, mais des formes sévères menant à des arthrites chroniques incapacitantes ont été signalées. Nous avons dans un premier temps étudié prospectivement les paramètres cliniques et immunologiques associés à la maladie chez des patients hospitalisés et identifiés comme étant ‘guéris’ ou 'chronique' à M12 après l'infection. Dans la deuxième partie, nous avons observé in vitro les mécanismes et le rôle de l'apoptose dans le processus infectieux permettant au virus de persister dans les sanctuaires tissulaires. En phase aiguë, une forte réponse immune dominée par une activation des cellules NK/dendritique/cellules T, la production d’anticorps spécifiques et une faible production de cytokines Th1 > Th2 a été observée mais sans aucune différence significative entre les deux groupes. Cependant, la virémie initiale s'est révélée beaucoup plus élevée dans le groupe chronique est nous avons pu identifier du matériel viral dans les macrophages du tissu synovial d'un patient chronique post-CHIKVD (M18). Dans la deuxième partie de l'étude, nous avons constaté que CHIKV est capable d'induire l'apoptose par la voie intrinsèque et extrinsèque et également par un mécanisme ‘bystander’. De plus, nous avons observé que le CHIKV présent dans des corps (blebs) apoptotiques était capable d'infecter les cellules voisines (Hela et macrophage MM6). Notre étude a permis de mettre en évidence pour la première fois que CHIKV contrôle et détourne à son profit les mécanismes de défense anti-infectieux. / Chikungunya is an Alphavirus transmitted by mosquitoes (Aedes) and which causes fever, rash, myalgia and arthralgia. The disease (CHIKVD) is transient but severe forms leading to chronic incapacitating arthritis have been reported. The study involved first a prospective cohort study of hospitalized patients from Reunion Island subsequently categorized into ‘recovered’ or ‘chronic arthralgia’ groups at M12 post infection. Clinical and immunological parameters were measured throughout the disease course. In part two, we addressed in vitro the role of apoptosis in the infection process and particularly to ascertain the mechanisms allowing the virus to persist in tissue sanctuaries. We observed that a rapid immune antiviral response was evidenced by the robust dendritic/NK//T cell activation and accompanied by a specific IgM/IgG response and a rather weak Th1/Th2 cytokine response in both groups. The viremia was much more pronounced in the chronic group and, critically, we found that CHIKV was persisting (M18) in perivascular synovial macrophages. Fibroblast hyperplasia, strong angiogenesis and acute cell deaths were observed in the injured synovial tissue. In the second part of the study, we found that CHIKV was able to trigger apoptosis through intrinsic and extrinsic pathways. Bystander apoptosis was also evidenced in neighboring cells in a caspase 8-dependent manner. Remarkably, CHIKV hiding into apoptotic blebs was able to infect neighboring cells and these events were inhibited specifically by inhibitors of caspases, blebbing and engulfment. We herein describe a novel mechanism by which CHIKV invades and escapes the host immune response and contribute to chronic arthralgia/arthritis.

Salmonid alphaviruses (SAV) are a group of viruses that have recently emerged as a serious threat to the salmonid aquaculture industry in Europe. Over recent years, diseases caused by SAV have severely hampered the Scottish, Irish and Norwegian Atlantic salmon industry, and are considered to be among the major economically important viral diseases affecting the industry at present. Amongst the six subtypes characterised so far, Salmonid alphavirus 1 (SAV1) causes severe pathology in the heart, pancreas and the skeletal muscle of Atlantic salmon leading to death and growth retardation in the affected fish. The biochemical characteristics of the virus and the sequential pathology of the diseases caused by SAV have been described; however the mechanisms responsible for causing the disease and the host defence mechanisms against the virus are poorly defined. This thesis therefore examined the pathogenesis of SAV infection at the cellular and molecular level in vivo in salmon and in vitro in salmonid cells, with a special emphasis on host immune defence mechanisms against the virus. SAV was first isolated from Chinook salmon embryo-214 (CHSE-214) cells in 1995 in Ireland. Several cell lines have since been used to grow the virus. In the present study, three established salmonid cell lines, Chum salmon heart -1 (CHH-1), CHSE-214 and Salmon head kidney -1 (SHK-1) were evaluated for their ability to support the isolation of SAV-1 from infected fish tissue, with CHH-1 cells giving the fastest cytopathic effect (CPE) during primary isolation. The CPE appeared as localised cell-rounding on CHH-1 and CHSE-214 cells, although in SHK-1 cells, the cells were seen to slough off the monolayer relatively later than with the other two cell lines during the infection. The host response to SAV infection was evaluated by experimentally infecting Atlantic salmon parr using a cell culture-adapted virus isolate. A quantitative reverse transcription polymerase chain reaction (qRT-PCR) was developed to examine the virus load in the fish, from which it was found that the highest viral RNA copy number was detected at 5 day post infection (d.p.i), of the 90 day experimental infection period. Characteristic pathological lesions were only seen in the pancreas and the heart but not in the skeletal muscles of the infected fish. A gene expression study using qRT-PCR revealed the rapid induction of interferon (INF) and INF-associated genes in the head kidney of the infected fish compared to the control fish. The Mx protein was found to be highly expressed in the heart and the mucous membranes of infected fish by immunohistochemistry. Interestingly, the pathological changes that were seen occurred some time after the peak expression of genes associated with the INF-1-pathway. When the host-virus interaction of Atlantic salmon infected with SAV was examined using a microarray, a potent first line defence response was observed, together with the signatures of early activation of the adaptive immune response during the initial stages of the infection. Genes associated with transcription, translation and lipid metabolism were significantly differentially expressed in virus infected fish compared to control fish. A large array of antiviral genes was significantly expressed, amongst which were some of the genes also described in mammalian alphavirus infections. Genes associated with apoptosis and anti-apoptosis were also seen to be differentially regulated showing the complexity of the host-virus interaction. Collectively, all of these findings suggest that a non-specific antiviral immune response takes place providing rapid immune protection during the early stages of SAV infection in salmon. In the study on morphogenesis of SAV in salmonid cells using electron microscopy (EM), a rapid internalization of virus into the cells and generation of replication complexes using the secretory pathway of the cell, similar to mammalian alphavirus replication was observed. The mature viruses were released through surface projections, acquiring envelopes from the host cell membrane. From the ultrastructural studies of the salmonid cells infected with SAV, a progressive chromatin marginalisation and condensation could be seen, leading to cellular fragmentation, forming membrane bound apoptotic bodies, characteristic of progressive apoptosis. The activation of caspase-3 in the cytoplasm and genomic DNA damage were also seen in the infected fish cells, indicating that apoptosis is the main cause of cell death during SAV infection. The results of this study have increased our knowledge and understanding of the cellular and molecular mechanisms involved in the pathogenesis of SAV infection, emphasising the importance of the first line defence mechanisms against SAV infection in salmon. This has given an interesting insight into the host mechanisms used to combat the virus during infection, and will undoubtedly be useful for designing new vaccines and management strategies for prevention and control of this important disease

Malnutrition, including both undernutrition and obesity, affects millions of people globally and is persistently on the rise. Obesity affects ~13% of adults globally and was identified as a risk factor for worse disease outcomes after the H1N1 influenza pandemic of 2009 and has since been shown to aggravate disease outcomes of respiratory viruses like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mosquito-borne viruses like West Nile Virus (WNV), chikungunya virus (CHIKV) and Mayaro virus (MAYV) and reduce the vaccine efficacy for influenza and SARS-CoV-2. Obesity is associated with a chronic state of inflammation and dysregulated immune response which has been proposed to be one of the mechanisms driving the severity of coronavirus disease 2019 (COVID-19). These altered signatures or biomarkers might be associated with disease outcome and prognosis. Therefore, animal models reflecting the clinical outcomes and natural immune responses observed in humans are crucial to identifying reliable biomarkers. Using mouse hepatitis virus 1 (MHV-1) as a model for SARS-CoV-2, we established obesity as a risk factor and identified biomarkers and pathways associated with worse disease outcomes. Obesity rates in low and middle-income countries (LMICs) are approaching levels found in high-income countries (HICs). Mosquito-borne viral diseases like dengue, chikungunya, and Zika pose a significant threat to LMICs and cause huge health and economic losses. Obesity was shown to worsen alphavirus pathogenesis, but interestingly, it also reduced their transmission by mosquitoes. Given the global prevalence of obesity and mosquito-borne viruses, it is critical to understand how obesity drives reduced alphavirus transmission. Using a natural transmission cycle between lean and obese mice and mosquitoes, we confirmed that obesity reduced the transmission potential of alphaviruses like CHIKV and MAYV and activated the Toll pathway in mosquito midguts. Various genes and other pathways were also altered in response to obese bloodmeal at various time-points post-bloodmeal; however, one gene, AAEL009965, was downregulated in the mosquito midguts 1-day-post-bloodmeal and its knockdown led to reduced infection rates and titers in mosquitoes. Through this thesis, we aimed to utilize obesity as a tool to identify biomarkers to predict coronavirus disease outcomes and design effective alphavirus transmission control strategies. / Doctor of Philosophy / Obesity, a global epidemic associated with chronic systemic inflammation, has emerged as an independent risk factor following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of obesity on COVID-19 severity, largely based on epidemiological data or research with non-natural hosts of SARS-CoV-2, necessitates the use of natural models of obesity to study the host's response to coronaviruses. Here we used mouse models of diet-induced obesity and infected them with a mouse coronavirus to account for the host's natural immune response against the virus. We showed that obesity exacerbates disease outcomes and identified various genes associated with disease severity in obese mice that correspond to the gene expression patterns in severe COVID-19 patients. These findings underscore the critical role of obesity in disease outcomes and pave the way for further research in this area. Obesity also worsens the disease outcome following infection with mosquito-borne alphaviruses like chikungunya (CHIKV) and Mayaro (MAYV), however, its impact on the vector's transmission potential is poorly understood. Using a natural transmission cycle between lean and obese mice and mosquitoes, we showed that obesity reduced alphavirus transmission by mosquitoes. We found altered expression of specific genes and pathways, in mosquito midguts exposed to alphavirus-infected obese bloodmeal compared to the lean ones and their knockdown led to altered infection rates in mosquitoes suggestive of their role in viral infection of mosquitoes. We also established insulin as a potential antiviral factor in obese bloodmeal. Therefore, these studies provide the basic framework for understanding the impact of obesity on viral transmission and pathogenesis by using relevant animal models. Furthermore, these studies utilize obesity as a tool to identify predictors of severe disease outcomes and identify genes that could be used as potential transmission control strategies for various mosquito-borne viruses.

Positive-strand RNA viruses associate with specific organelle membranes of host cells to establish viral replication complexes. The replication protein 1a of brome mosaic virus associates strongly with the nuclear endoplasmic reticulum (ER) membranes, invaginates membranes into the lumen, and recruits various host proteins to establish replication complexes termed spherules. 1a has a strong affinity towards the perinuclear ER membrane, however, the structural features in 1a that dictate its membrane associations and thereby membrane remodeling activities are unclear. This study examined the possible role of an amphipathic α-helix, helix B, in BMV 1a's membrane association. Deletion or single substitution of multiple amino acids of helix B abolished BMV 1a's localization to nuclear ER membranes. Additional reporter-based, gain-of-function assays showed that helix B is sufficient in targeting several soluble proteins to the nuclear ER membranes. Furthermore, we found that the helix B-mediated organelle targeting is a functionally conserved feature among positive-strand RNA viruses of the alphavirus-like superfamily that includes notable human viruses such as Hepatitis E virus and Rubella virus as well as plant viruses such as cucumber mosaic virus and cowpea chlorotic mottle virus. Our results demonstrate a critical role for helix B across members of the alphavirus-like superfamily in anchoring viral replication complexes to the organelle membranes. We anticipate our findings to be a starting point for the development of sophisticated models to use helix B as a novel target for the development of antivirals for positive-strand RNA viruses that belong to the alphavirus-like superfamily. / Doctor of Philosophy / Among the seven classes of viruses, the positive-strand RNA viruses dominate the domain of viral diseases of the world. Brome mosaic virus (BMV) is a positive-strand RNA virus that infects cereal crops such as wheat, barley, and rice. BMV has a simple genome organization and serves as a suitable model virus to study and characterize positive-strand RNA viruses. The replication of all positive-strand RNA viruses occurs at the organelle membranes of the host. Membrane association of the replication is one of the early steps and a crucial event in the life cycle of positive-strand RNA viruses. One of the proteins produced early on during BMV infection is the replication protein 1a, which is also the master regulator of viral replication; 1a recruits viral factors in addition to hijacking the necessary host factors at the membranous sites to initiate replication. Upon reaching the organelle membranes, 1a induces membrane rearrangements to form viral replication complexes that safeguard the recruited factors from the deleterious effects of the host cell. The structural determinants within 1a that are responsible for such membrane association are unknown. This study explored the potential roles of a short helical motif within the 1a protein for its ability to dictate such site-specific membrane associations. We show here that this helical region is necessary and sufficient for 1a's membrane-binding activity. We also discovered it to be a functionally conserved feature that is responsible for membrane associations in various viruses of the alphavirus-like superfamily that includes some of the notable human viruses such as Hepatitis E virus and Rubella virus in addition to plant viruses such as cucumber mosaic virus and cowpea chlorotic mottle virus.