Master of Science / Department of Diagnostic Medicine/Pathobiology / Natalia Cernicchiaro / Japanese encephalitis virus (JEV) is a virus of the Flavivirus genus that may result in encephalitis in vertebrate hosts. This vector-borne zoonosis occurs in Eastern and Southeastern Asia and an intentional or inadvertent introduction into the United States (US) would lead to important public health and economic consequences. The objective of this study was to gather, appraise, and synthesize primary research literature to identify and quantify vector and host competence for JEV, using a systematic review-metaanalysis (SR-MA) approach. After defining the research question, we performed a search in selected electronic databases. The title and abstract of the identified articles were screened for relevance using a defined set of exclusion and inclusion criteria, and relevant articles were subjected to a risk of bias assessment followed by data extraction. Random-effects subgroup meta-analysis models were fitted by species (mosquito or vertebrate host species) to estimate pooled summary measures as well as to compute the variance between studies. Meta-regression models were fitted to assess the association between different predictors and the outcomes of interest and to identify sources of heterogeneity among studies. Data were extracted from 171 peer-reviewed articles. Most studies were observational (59.06%) and reported vector competence (60.2%). The outcome measures reported pertained to transmission efficiency, host preference, and vector susceptibility to infection within vector competence; and susceptibility to infection within host competence. All outcome measures (JEV proportion of infection in vectors and hosts from observational studies; and JEV infection, dissemination, and transmission rates in vectors from experimental studies) had high heterogeneity. Mosquito species, diagnostic method, country, and capture method represented important sources of heterogeneity associated with the proportion of JEV infection in vectors; host species and region were considered sources of heterogeneity associated with the proportion of JEV infection in hosts; and diagnostic and mosquito capture methods were deemed important contributors of heterogeneity for the minimum infection rate (MIR) outcome. Mosquito species and administration route represented the main sources of heterogeneity associated with JEV infection rate in vectors. Quantitative estimates resulting from this SR-MA will be inputted into risk assessment models to evaluate risks associated with the introduction of JEV in the US.

Japanese encephalitis virus (JEV) causes viral encephalitis in new born and young adults that is prevalent in different parts of India and other parts of South East Asia with an estimated 6000 deaths per year. JEV is a single stranded RNA virus that belongs to the Flavivirusgenus of the family Flaviviridae. It is a neurotropic virus which infects the central nervous system (CNS). The virus follows a zoonotic life-cycle involving mosquitoes and vertebrates, chiefly pigs and ardeid birds, as amplifying hosts. Humans are dead end hosts. After entry into the host following a mosquito bite, JEV infection leads to acute peripheral leukocytosis in the brain and damage to Blood Brain Barrier (BBB). The exact role of the endothelial cells during CNS infection is still unclear. However, disruption of this endothelial barrier has been shown to be an important step in entry of the virus into the brain. Humoral and cell mediated immune responses during JEV infection have been intensively investigated. Previous studies from our lab have shown the activation of cytotoxic T-cells (CTLs) upon JEV infection. MHC molecules play pivotal role in eliciting both adaptive (T-cells) and innate (NK cells) immune response against viral invasion. Many viruses such as HIV, MCMV, HCMV, AdV and EBV have been found to decrease MHC expression upon infection. On the contrary, flaviviruses like West Nile Virus (WNV) have been found to increase MHC-I and MHC-II expression. More recently, data from our lab has shown that JEV infection can lead to upregulation of mouse non-classical MHC class Ib molecules like Qb1, Qa1 and T-10 along with classical MHC molecules. Non-classical MHC molecules are important components of the innate and adaptive immune systems. Non-classical MHC molecules differ from their classical MHC class I counterparts by their limited polymorphism, restricted tissue distribution and lower levels of cell surface expression. Human classical MHC class I molecules are HLA-A, -B and –C while non-classical MHC Class Ib molecules are HLA-E, -G and –F. HLA-E, the human homologue of the mouse non-classical MHC molecule, Qa-1b has been shown to be the ligand for the inhibitory NK, NKG2A/CD94 and may bridge innate and adaptive immune responses. In this thesis, we have studied the expression of human classical class I molecules HLA-A, -B, -C and the non-classical HLA molecule, HLA-E in immortalized human brain microvascular endothelial cells (HBMEC), human endothelial like cell line ECV304 (ECV), human glioblastoma cell line U87MG and human foreskin fibroblast cells (HFF). We observed an upregulation of classical HLA molecules and HLA-E mRNA in endothelial and fibroblast cells upon JEV infection. This mRNA increase also resulted in upregulation of cell surface classical HLA molecules and HLA-E in HFF cells but not in both the human endothelial cell lines, ECV and HBMECs. Release of soluble classical HLA molecules upon cytokine treatment has been a long known phenomenon. Recently HLA-E has also been shown to be released as a 37 kDa protein from endothelial cells upon cytokine treatments. Our study suggests that JEV mediated upregulation of classical HLA and HLA-E upregulation leads to release of both Classical HLA molecules and HLA-E as soluble forms in the human endothelial cell lines, ECV and HBMEC. This shedding of sHLA-E from human endothelial cells was found to be mediated by matrix metalloproteinase (MMP) proteolytic activity. MMP-9, a protease implicated in release of sHLA molecules was also found to be upregulated upon JEV infection only in endothelial cell lines but not in HFF cells. Our study provides evidence that the JEV mediated solubilisation of HLA-E could be mediated by MMP-9. Further, we have tried to understand the role of the MAPK pathway and NF-κB pathway in the process of HLA-E solubilisation by using specific inhibitors of these pathways during JEV infection of ECV cells. Our data suggests that release of sHLA-E is dependent on p38 and JNK pathways while ERK 1/2 and NF-κB pathway only had a minor role to play in this process. Treatment of endothelial cells with TNF-α, IL-1β and IFN-γ is known to result in release of sHLA-E. In addition to TNF-α and IFNtreatment, we observed that activating agents like poly (I:C), LPS and PMA also resulted in the shedding of sHLA-E from ECV as well as U87MG but not from HFF cells. Treatment of endothelial cells with IFN-β, a type-I interferon also led to release of sHLA-E. IFN-γ, a type II interferon and TNF-α are known to show additive increase in solubilisation of HLA-E. We studied the interaction between type I interferon, IFN-β and TNF-α with regard to shedding of sHLA- E. Both IFNand TNF, when present together caused an additive increase in the shedding of sHLA-E. These two cytokines were also found to potentiate the HLA-E and MMP-9 mRNA expression. Hence, our data suggest that these two cytokines could be working conjunctly to release HLA-E, when these two cytokines are present together as in the case of virus infection of endothelial cells. HLA-E is known to be a ligand for NKG2A/CD94 inhibitory receptors present on NK and a subset of T cells. Previous reports have suggested that NKG2A/CD94 mediated signaling events could inhibit ERK 1/2 phosphorylation leading to inhibition of NK cell activation. IL-2 mediated ERK 1/2 phosphorylation is known to play a very important role in maintenance and activation of NK cells. We studied the effects of sHLA-E that was released, either by JEV infection or IFN-γ treatment on IL-2 mediated ERK 1/2 phosphorylation in two NK cell lines, Nishi and NKL. The soluble HLA-E that was released upon JEV infection was functionally active since it inhibited IL-2 and PMA induced phosphorylation of ERK 1/2 in NKL and Nishi cells. Virus infected or IFN-γ treated ECV cell culture supernatants containing sHLA-E was also found to partially inhibit IL-2 mediated induction of CD25 molecules on NKL cells. CD25 is a component of the high affinity IL-2 receptor and hence could play an important role in proliferation and activation of NK cells. sHLA-E was also found to inhibit IL-2 induced [3H]-thymidine incorporation suggesting that, similar to cell surface expressed HLA-E, sHLA-E could also inhibit the proliferation and activation of NK cells. In summary, we found that establishment of JEV infection and production of cytokines like IFN-β, TNF-α, IL-6 along with MMP-9 in human endothelial cells. These cytokines may also indirectly lead to the reported damage and leukocyte infiltration across infected and uninfected vicinal endothelial cells. The increased surface expression of HLA-E in fibroblast and release of sHLA and sHLA-E molecules from endothelial cells may have an important immunoregulatory role. HLA-E is an inhibitory ligand for NKG2A/CD94 positive CD8+ T and NK cells. Hence our finding that sHLA-E can inhibit NK cell proliferation suggests an immune evasive strategy by JEV.

Chapter 1: Role of JEV NS1 in protective immunity and in immunopathology. Previous studies from our laboratory revealed T cell immunodominance of non structural proteins NS3 and NS1 during natural JEV infections in humans where as the structural protein E, which is a good target for neutralizing antibody response is a poor inducer of T cells. Flavivirus NS1 is also known to induce humoral immune response. Several studies in different flaviviruses have indicated a role for NS1-specific immune responses in protection against flaviviruses. Paradoxically, studies also pointed to the contribution of NS1 in pathology and immune modulation. We screened serum samples from 72 convalescent JE patients for the presence of anti-NS1 antibodies by ELISA and radioimmunoprecipitation and found NS1 reactivity in 45 samples. These antibodies to NS1 are capable of inducing complement mediated cytolysis of cells expressing NS1 on the surface. Additionally, we demonstrated twenty two fold reduction in the infectious virus produced at 48h in SW-13 cells in the presence of human complement and NS1 antiserum compared to control serum, suggesting that complement mediated cytolytic activity of anti NS1 antibody helps the host in controlling the virus propagation. Chapter 2: Comparison of immune responses to JEV structural proteins Capsid and Envelope in human volunteers vaccinated with inactivated JE vaccine and naturally exposed to live JEV. We compared the CMI responses to structural proteins E and C in human volunteers vaccinated with commercially available killed JE vaccine and in humans naturally exposed to live JEV. The results revealed that structural proteins E and C are inherently poor inducers of T cells even in killed vaccine preparation, where there is no competition from immunodominant non structural proteins. Therefore inclusion of nonstructural proteins NS1 and NS3 along with neutralizing antibody inducing envelope should improve memory and efficacy of a JE vaccine. Chapter 3: Construction and testing in the mouse model of experimental recombinant poxvirus vaccines expressing prM, E, NS1, and NS3 of JEV. Guided by the information on immune responses to JEV in the JE endemic human cohort and volunteers vaccinated with killed JE vaccine, we designed experimental vaccines as recombinant vaccinia viruses expressing NS1, NS3, prM, and E proteins of JEV (vNS1NS3prME) or NS1, NS3, prM, and C-terminally truncated E (vNS1NS3prMΔE) and studied the immune responses elicited by these vaccines in mice. Our data showed that a recombinant vaccinia virus expressing prM, ΔE, NS1, and NS3 of JEV is superior to killed JE vaccine in eliciting long lived neutralizing antibodies as well as NS1 and NS3-specific cytotoxic T lymphocytes (CTL) in addition to NS1-specific cytolytic antibodies, resulting in long lasting and enhanced protection from lethal JEV infection in mice. Our results thus identified all B and T cell antigens whose inclusion in a live-vectored vaccine would provide a vaccine with far superior efficacy over the inactivated JE vaccine.

This document describes an evaluation of acute (meningitis)-encephalitis syndrome (AES/AMES) surveillance established in India, Bangladesh and China. The key objectives of the project included 1) building on existing networks for syndromic surveillance and laboratory confirmation, 2) establishing laboratory-based surveillance for vaccine-preventable causes of encephalitis and meningitis, 3) enhancing capacity to use data to guide disease control and prevention programs, and 4) improving capacity to recognize new or emerging diseases. The syndromes encompass several diseases, including Japanese encephalitis (JE), pneumococcal meningitis, Haemophilus influenzae type b (Hib), and meningococcal meningitis. The purpose of the evaluation is to assess the extent to which the key objectives were met in the three project countries, compare and contrast the experiences among the countries, document the strengths and weaknesses, and make recommendations. The indicators used in the evaluation include feasibility of integration, availability of country protocols, appropriate training, data quality, sensitivity, specificity, positive predictive value, negative predictive value, representativeness, timeliness, integration with AFP surveillance, simplicity and efficiency, acceptability, usefulness, flexibility, stability, and sustainability. The criteria and standards are based on WHO recommendations. Data sources include AES/AMES epidemiologic and laboratory data sets, trip reports, country reports, field observations, and published bulletins. All countries made substantial progress in a relatively short period of time using the infrastructure and technical tools of existing surveillance and laboratory networks for acute flaccid paralysis. After one year, India and Bangladesh collects and maintains high quality epidemiologic data, exceeds targets for timeliness of reporting, and has quality-assured capacity for laboratory confirmation of Japanese encephalitis (JE) virus infection. India now has regional laboratory capacity for reference testing on virology and bacteriology. After two years of operations, China has population-based surveillance data for JE that meets targets for timeliness. Several levels have well-established capacity for laboratory confirmation of JE virus infection. The national level has the technical ability to provide proficiency testing for virology and to provide reference testing for bacteriology. In all countries, challenges in building capacity for basic bacteriology, quality control and quality assurance for all laboratory testing, and management of laboratory data.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Dana Vanlandingham / Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus maintained among swine and avian species. In infected pigs, replication of JEV leads to the onset of viremia and the development of neurological and reproductive disease in young and naïve pregnant animals. The high-titer viremia levels associated with JEV infection in pigs, whilst important to the enzootic transmission cycle responsible for viral maintenance, also have human health implications within the zoonotic cycle. Sensitive and specific veterinary diagnostic methods capable of readily detecting JEV infection are critical components of JEV surveillance programs in the Asian Pacific region. In this study, reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) assays were evaluated for use in veterinary diagnosis of JEV. Our hypotheses for this research project were that RT-qPCR assays with fewer oligonucleotide mismatches between the primers and probes of the assays and JEV genomes will be more sensitive for the diagnosis of JEV infection and that oral shedding of JEV in swine would allow for detection of viral RNA using oral fluids. The sensitivity and specificity of three RT-qPCR assays for the detection of JEV were determined using tissue culture fluids of five representative JEV strains belonging to four endemic genotypes. The first assay (assay #1), targeting the highly conserved NS5 gene and 3UTR regions, provided optimum detection for the current predominant genotype, GI-b. All three assays were highly specific for JEV when tested against other selected flaviviruses in the JEV serocomplex. A rope-based collection method allowed for the simplified collection of oral fluids from three-week-old piglets challenged with endemic JEV strain JE-91. These fluids were then evaluated using RT-qPCR assays for the presence of viral RNA. The results suggest that the shedding of JEV in oral fluids can be readily detected and that non-invasive oral fluid collection can serve as a novel sampling method for the diagnosis and surveillance of JEV in swine.

Japanese encephalitis virus (JEV), a mosquito-borne flavivirus is the causative agent of Japanese encephalitis (JE). The disease affects mostly children and around 30000– 50000 cases of JE and up to 15000 deaths are reported annually. No anti-viral drugs have been discovered against JE so far, but advances in our knowledge of the molecular biology of flaviviruses is propelling flaviviral drug research at an expeditious pace. Since JEV has a small genome which encodes for only ten proteins, there is dearth of potential drug targets. Researchers are now focusing on cellular interactomes, a complex and dynamic molecular biosystem which identifies host proteins which interact with either viral proteins or viral genomes, leading to the generation of an astronomical number of potential drug targets involving common cellular pathways that are required for the life cycle of different viruses. Such studies can pave way for the development of ‘broad-spectrum’, ‘silver-bullet’ anti-viral drugs for the treatment of multiple viral diseases. The cellular interactomes can be studied by Genomics tools such as microarray. Systematic profiling of genes involved in virus infection by RNAi, transcriptome sequencing, microRNA profiling and yeast two-hybrid system has allowed us to assess global gene expression changes providing an unprecedented view on the host-side of the virus–host interactions. Advent of these tools has led to identification of plethora anti-viral genes. For example, over expression of IFN-stimulated gene15 (ISG15) results in inhibition of JEV leading to significant reduction of viral titers. Chemokine profiling of JEV-infected cells by microarray can provide possible therapeutic modalities that can mitigate the morbidity associated with JEV infection. Functional classification of interferon-stimulated genes (ISG) identified using innovative methods have been the stepping stone for identification of many anti-viral genes, among them are few Broadly acting effectors like IRF1, C6orf150, HPSE, RIG-I, MDA5 and IFITM3 and some more targeted antiviral specific like DDX60, IFI44L, IFI6, IFITM2, MAP3K14, MOV10, NAMPT, OASL, RTP4, TREX1 and UNC84B. In this study, we have identified a B16F10 murine melanoma cell line that is resistant to JEV infection. DNA microarray analysis of JEV-susceptible and resistant B16F10 cell lines gave us interesting insights into JEV-induced host gene expression changes. Real time PCR validation of microarray data indicates that a number of virus and interferon inducible genes are expressed constitutively at high levels in this JEV-resistant cell line. Further, several of the mouse genes induced by JEV in B16F10 cell line were also upregulated in JEV-infected mouse brain. To understand the significance of these host gene expression changes, we attempted to generate stable murine cell lines constitutively expressing select JEV-inducible genes and study the JEV infection pattern in these cell lines. One of the JEV-inducible genes encoding thymidylate kinase (Tyki), a mitochondrial protein involved in the sysnthesis of nucleoside diphosphates, when overexpressed in NIH3T3 cells confers resistance to JEV infection as evident from reduced JEV-induced cytopathic effects and significant reduction in viral titer. Since TYKI has two distinct domains: the N-terminal domain with unknown function and the C-terminal domain with the nucleoside monophosphate kinase function, suggest that TYKI may be a bifunctional protein with other biological functions in addition to its UMP-CMP kinase activity. In order to examine whether N-terminal domain is responsible for antiviral activity of the protein, a stable cell line constitutively expressing N-terminal domain of gene was made, but the overexpression of N-terminal domain didn't confer any antiviral immunity. Thus signifying importance of kinase activity in confering antiviral immunity. Our studies indicate for the first time that Tyki may have a role in host resistance to JEV and understanding the mechanism of action Tyki may pave way for novel anti-JEV therapy. Stable cell lines constitutively expressing other JEV-inducible genes (Atf3, Gimap3, Rtp4, Glipr2, Tmem140 and Garg49) couldn't be generated. Therefore, to study the effect of overexpression of these genes on JEV infection, expression vectors encoding these genes were transfected individually to human 293T cells by nucleofection, then infected with JEV and viral titres were examined by plaque assay. Nucleofection was opted as a method of choice since it is the only non-viral method, which transfects DNA directly enter the nucleus. In contrast, other commonly used non-viral transfection methods rely on cell division for the transfer of DNA into the nucleus. Nucleofection of vectors encoding different JEV-inducible genes followed by JEV infection and assay of viral titer led to identification of one more anti-viral gene and three pro-viral genes. Garg49, an interferon and JEV inducible mitochondrial gene was identified as antiviral gene. Further studies led to the identification of GARG49 as a mitochondrial protein. Three genes, Atf3, encoding a cAMP responsive element binding protein family transcription factor, Glipr2, encoding a Glioma related pathogenesis protein and Gimap3, encoding an outer mitochondrial membrane GTPase were identified as pro viral genes. Overexpression of Tmem140, encoding a transmembrane protein and Rtp4, encoding a golgi chaperone did not significantly affect JEV titer. Conclusions: . A JEV-resistant B16F10 murine melanoma cell line was identified and several JEV-inducible genes were found to be expressed constitutively at high levels in this cell line. .We demonstrate for the first time that Tyki/Ump-Cmpk2 encoding a mitochondrial nucleoside monophosphate kinase has an anti-JEV function and the C-terminal domain is essential for anti-viral activity. .Garg49/Ifit3 encodes an interferon and JEV-inducible mitochondrial protein and it has an anti-JEV function. . Activating transcription factor 3 (ATF3), GTPase, IMAP family member 3 (GIMAP3) and GLI pathogenesis-related 2 (GLIPR2) are pro-viral proteins which facilitate virus multiplication resulting in enhanced JEV titer.

L’encéphalite Japonaise (EJ) est une maladie zoonotique virale et c’est la principale cause d'encéphalite humaine en Asie et le Pacifique. Elle est due à un Flavivirus, transmis de l’animal à l'Homme par des moustiques, elle peut se transmettre entre porcs par contact direct. Malgré une baisse significative des cas d’EJ dans de nombreux pays suite à la mise en place de programmes de vaccination, l’EJ continue à sévir d’une manière importante en Asie. Notre objectif dans cette thèse est de (i) construire un modèle mathématique de la dynamique de transmission du virus de l’EJ (VEJ), (ii) paramétrer ce modèle pour déterminer l’importance de la transmission directe entre porcs en milieu naturel (iii) et déterminer des stratégies de contrôle. Nous avons développé un modèle de propagation du VEJ. Ensuite, nous avons adapté ce modèle pour avoir deux modèles intégrant la transmission vectorielle seulement ou une combinaison de la transmission vectorielle et directe. Nos résultats montrent que la transmission directe entre porcs pourrait contribuer à la dynamique de transmission du VEJ dans le contexte Cambodgien, toutefois elle ne pourrait pas permettre toute seule une épidémie. Enfin, nous avons considéré la lutte anti-vectorielle, la vaccination des truies et la gestion d’élevages en bandes pour déterminer des stratégies de contrôle pour éradiquer le VEJ au sein des troupeaux de porcs, baisser les avortements des truies, évaluer les risques pour les humains vivant à proximité des fermes et des abattoirs ainsi que le coût-efficacité de la vaccination. Nos résultats confirment que la lutte anti-vectorielle est le meilleur moyen pour contrôler le VEJ. La vaccination des truies gestantes fait diminuer les avortements comme attendu. Paradoxalement, si le contrôle vectoriel est moyen l’efficacité de la vaccination pourrait être compromise. La gestion d’élevages en bandes a un faible impact sur l'incidence et les avortements, par conséquent sur le contrôle de l’EJ. Combiner la vaccination des truies et la lutte anti-vectorielle pourrait être une alternative et/ou une mesure supplémentaire à la vaccination humaine pour réduire à la fois l'incidence de l'EJ chez l'Homme et l'impact économique de l'infection du au VEJ dans les élevages des porcs. / Japanese encephalitis (JE) is a viral zoonotic disease and it is the leading cause of human encephalitis in Asia and the Pacific. Japanese encephalitis virus (JEV) is a Flavivirus of the family of Flaviviridae transmitted from animals to human by mosquitoes, direct transmission between pigs can occur via direct contact. Despite a significant decline in JE cases in many countries as a result of vaccination programs, JE continues to have a significant impact in Asia. Our objective in this thesis is to (i) built a mathematical model of the transmission dynamics of JEV, (ii) parameterize this model to determine the importance of direct transmission between pigs under field conditions (iii) and determine control strategies. We developed a propagation model of JEV. Next, we adapted this model to have two models incorporating vector-borne transmission alone or a combination of vector-borne and direct transmission. Our findings suggest that direct transmission between pigs does contribute to transmission dynamics of JEV in Cambodia; although, alone direct transmission cannot sustain an outbreak. Finally, we considered vector control, sow vaccination, and herd management to determine control strategies to eradicate JEV in pig herds, reduce sow abortions, assess the risk for human beings living in the vicinity of pig herds and near pig slaughterhouse, and the cost-effectiveness of vaccination. Our results confirm that vector control is the best way to control JEV. Vaccination of pregnant sows reduces abortions as expected. Paradoxically, if the vector control is medium the effectiveness of the vaccination could be compromised. Herd management has a low impact on incidence and abortions, therefore on JE control. Combining sow vaccination and vector control could be an alternative and/or an additional measure to human vaccination to reduce both JE incidence in humans and the economic impact of JE infection on pig breeding.

One of the key events in a virus-infected host cell is the activation and repression of a large number of host genes. In recent years, such differentially expressed host genes have been identified for several viruses, bacteria and parasites. Such studies indicate that reprogramming of host transcriptome during infection by a pathogen is a major component of host response and many of the reprogrammed genes may promote or prevent pathogen infection or may contribute to pathogen-induced pathological changes. Host gene expression changes have been studied for a number of viruses in cell lines. However, in case of neurotropic viruses which infect nonrenewable populations of central nervous system (CNS), changes in the host gene expression need to be studied in the intact host rather than cells grown in culture. Since such studies are reported only for a few neurotropic viruses, an attempt has been made in this thesis to identify and characterize genes that are differentially expressed in the mouse brain during infection by Japanese encephalitis virus (JEV) and rabies virus. Using subtraction hybridization technique, subtraction cDNA libraries were generated representing mRNAs that are induced or repressed in the mouse brain during JEV infection. Sequence analysis of the 350 isolated clones resulted in the identification of 73 unique genes. Out of these, 66 were of forward library clones (upregulated genes) and 7 of reverse library clones (downregulated genes). The forward library clones was clustered in different functional groups such as, proteins involved in immune response and interferon-inducible proteins, GTPase and GTP binding proteins, transcriptional regulators, enzymes, ribosomal proteins, neuronal proteins, carrier proteins, DNA-binding proteins, miscellaneous and proteins of unknown function. The differential expression of all these genes was further validated by northern blot analysis of brain RNA isolated from normal and JEV-infected mice, which indicate that out of 66 forward library clones 33 were genuinely upregulated in JEV-infected mouse brain, whereas all 7 reverse library clones were repressed in JEV infection. Since vaccination is known to prevent virus replication in the brain, host gene expression changes in mice immunized with BIKEN JE vaccine was also examined. There was a good correlation between inhibition of JEV replication and reduced expression of JEV-inducible CNS genes in the vaccinated mice. To check whether JEV-induced CNS genes identified in this study are specific to JEV or can be induced by any other neurotropic virus, expression patterns of 15 randomly chosen genes were checked in RV infected mouse brain. Results indicated that all the chosen genes are modulated in the same way during RV infection as well. Comparison of JEV-induced gene expression changes with those induced by other neurotropic viruses indicated that 83% of the JEV-inducible mouse CNS genes are also induced by Sindbis virus, a neurotropic virus of the family alphaviridae, indicating that despite diverse life cycles, these two viruses may activate common host signaling pathways. This study also led to the identification of 9 unique JEV-inducible genes (LRG-21, VHSV induced gene1, Tpt1, SLC25A3, Olfm1, Ina/NF-66, Dst/Bpag1, Mdm2 and Gbp5) which are not reported to be activated by any other neurotropic virus. Since it is beyond the scope of this study to characterize all the JEV-induced and repressed genes, two genes were chosen for a detailed analysis. These are: JEV-inducible gene encoding GARG-39 protein which is a member of the glucocorticoid attenuated response gene family and an unannotated, JEV-repressible gene designated in this study as clone # 137. The gene encoding GARG-39 identified as a JEV-inducible gene in this study was originally discovered as lipopolysaccharide- and interferon-inducible gene in macrophages. This protein contains tetratricopeptide repeat (TPR) motifs that are known to be involved in protein-protein interactions. However, the function of this protein remains unknown till date. Therefore the gene was cloned and over-expressed in E. coli and antibodies were raised against the recombinant protein. Western blot analysis revealed that GARG-39 protein is detectable only in JEV-infected but not in the normal mouse brain. Surprisingly, immunoflourescence studies carried out in NIH3T3 cells revealed that GARG-39 is localized in the cytosol of normal cells and it colocalizes with α-tubulin in the mitotic spindle in a small fraction of cells which are in the mitotic stage. Further, in an in vitro assay, GARG-39 was found to interact with taxol-stabilized tubulin polymers. Since microtubules are known to play an important role in virus assembly, it is possible that GARG-39 may have a role in virus assembly and maturation. Alternatively, microtubule-associated proteins are implicated in several neurodegenerative disorders including Parkinson’s, Alzheimer’s and mental retardation and therefore, a role for GARG-39 in virus-induced neuropathogenesis cannot be ruled out. In addition, the expression of GARG-39 in normal dividing cells in the culture indicates a role for this protein in mitosis. In a normal mouse brain, mitotically active cells are very low in number and hence GARG-39 expression (both at the RNA and protein levels) is below the detection limits. JEV infection may trigger mitotic activity in brain leading to increased expression of GARG-39. One of the cDNA clones identified in this study, designated as clone # 137, hybridized to a ~2.6 kb transcript which was found to be down regulated in the mouse brain by JEV as well as rabies virus. A series of investigations led to the conclusion that clone #137 corresponds to the 3′ end of a ~2.6 kb transcript encoding mouse calcium calmodulin kinase inhibitor II α (mCaMKIINα). Interestingly, only the α isoform but not the β isoform of mCaMKIINα mRNA is down regulated in the mouse brain during JEV infection. Since the physiological function of mCaMKIINα is not known, the gene encoding 8 kDa mouse mCaMKIINα open reading frame was cloned into an E. coli expression vector and antibodies were raised against the purified recombinant protein. Surprisingly, antibodies raised against the ~8 kDa recombinant mouse CaMKIINα reacted with a ∼37 kDa mouse brain protein. This protein designated as CaMKIINα-immunoreactive protein (CaMKIINα-IRP) is also down regulated during JEV infection and is localized in the post synaptic density (PSD) of normal mouse brain. In addition, distinct changes are also observed in the subcellular localization and phosphorylation of CaMKIIα leading to an increase in cytosolic CaMKII activity in JEV-infected mouse brain. The differential regulation of CaMKIIα and CaMKIINα during JEV infection suggests a possible role for CaMKII signaling pathway in JEV infection and/or JEV-induced neuropathogenesis in the CNS. Conclusions: • A number of host genes whose expression is modulated in the mouse brain during JEV and/or rabies virus infection have been identified. • One of the JEV-inducible genes encoding the GARG-39 protein was shown to be a microtubule-associated protein with a possible role in mitosis. • One of the JEV-repressible genes was found to encode the mouse CaMKIINα mRNA. • A novel JEV-repressible ∼37 kDa protein immunoreactive to antibodies raised against the recombinant CaMKIINα was identified in the post synaptic density of the mouse brain.

Japanese encephalitis virus (JEV) is the causative agent of Japanese encephalitis (JE), the leading cause of vaccine-preventable neurological disease. JEV is a flavivirus that is primarily transmitted through the bite of infected mosquitoes, similar to dengue virus (DENV), St. Louis encephalitis virus (SLEV), West Nile virus (WNV), and Zika virus (ZIKV). The two viral characteristics that dictate virulence are (1) neuroinvasiveness, the ability of the virus to invade the central nervous system(CNS), and (2) neurovirulence, the capacity of the virus to kill resident cells in the CNS. The clinically proven live-attenuated JEV vaccine, SA14-14-2, lacks both pathogenic characteristics unlike its virulent parental virus, SA14. Previous work has revealed the viral E gene as the main determinant of these two pathogenic properties, though the molecular mechanisms behind their attenuation remain unclear. The E gene encodes for the viral envelope glycoprotein that is involved in viral entry into susceptible host cells. The E protein of SA14-14-2 differs from SA14 by nine amino acids. To investigate the role of these mutations in JEV virulence, we created a series of SA14E mutants using infectious cDNA technology. Here, we report the independent function of domains I (DI) and II (DII) of the viral E protein in JEV neurotropism. We reveal that an individual mutation in DI, E138K,and synergism between two mutations in DII, E244G and K279M,are independently sufficient for the attenuation of JEV neuroinvasion. Also, we report that multiple E mutations are required for full attenuation of JEV neurovirulence. Overall, our findings show the direct relationship between genetic factors and JEV neuroinvasion. These results provide a solid foundational base for the logical development of other, currently non-existing, live-attenuated neurotropic flavivirus vaccines and antivirals.

Japanese encephalitis virus (JEV) is one of the major causes of encephalitis in Asia. JEV causes serious inflammation of the brain, which may lead to permanent brain damage and has a high mortality rate. Almost 3 billion people live in JE endemic areas and JEV causes an estimated 20,000 cases of disease and 6000 deaths per year. JEV is a positive stranded RNA virus belonging to the Flavivirus genus of the family Flaviviridae. The genome of JEV is about 11 kb long and codes for a polyprotein which is cleaved by both host and viral encoded proteases to form 3 structural and 7 non-structural proteins. JEV transmission occurs through a zoonotic cycle involving mosquitoes and vertebrate amplifying hosts, chiefly pigs and ardeid birds. Humans are infected when bitten by an infected mosquito and are dead end hosts. The role of humoral and cell mediated immune responses during JEV infection have been studied by several groups. While the humoral responses play a central role in protection against JEV, the cell mediated immune responses contributing to this end are not fully understood. The MHC molecules have been known to play predominant roles in host responses to viral infections and the consequences of virus infection on the expression of MHC molecules are varied. The expression of MHC-I molecules is known to decrease upon infection with many viruses such as HIV, MCMV, HCMV, Adv, and EBV. In contrast, infection with flavivirus such as West Nile Virus (WNV) has been shown to increase the cell surface expression of both MHC-I and MHC-II molecules. It has been reported previously that WNV infection increases the cell surface expression of adhesion molecules such as ICAM-1, VCAM-1 as well as E-Selectin and these changes were mediated directly by WNV and not by soluble cytokines. In contrast to classical MHC-I molecules, the nonclassical MHC-I molecules do not belong to a single group of structurally and functionally homologous proteins and normally have lower cell surface expression. Earlier studies have shown that the expression of nonclassical MHC-I molecules were induced during infection with JHM strain of mouse hepatitis virus (MHV). However, the functional significance of this induction is unclear. Expression of nonclassical MHC-I molecules upon flaviviral infection is not very well understood. In this thesis, evidence is presented that JEV infection induces the expression of both classical and nonclassical MHC-I molecules on primary mouse brain astrocytes, mouse embryonic fibroblasts (MEFs) and H6 (hepatoma cell). The levels of adhesion molecules as well as molecules involved in antigen processing and presentation were also analyzed and our results clearly demonstrate that JEV infection induces their expression on astrocytes, MEFs and H6. The role of NF-κB and type-I IFNs in the induction of classical and nonclassical MHC-I molecules as well as molecules involved in antigen processing and presentation were also analyzed and our results demonstrated that type-I IFN mediated signaling is responsible for the induction of these molecules during JEV infection. Chapter 1 discusses the innate and adaptive immune system, the role of classical and nonclassical MHC molecules in the initiation of immune response and diverse strategies adapted by different viruses to evade the immune response. It also includes a detailed discussion about the IFN and NF-κB signaling pathways and their modulation by viral infection. Finally, the genome organization, epidemiology, transmission cycle, pathogenesis and pathology, clinical features, humoral as well as cell mediated immune response to JEV infection and the current vaccine status to JEV infection are briefly discussed. Chapter 2 describes the general materials and methods used in this study. It includes the details of the reagents and cell lines used in the experiments. It also discusses the various techniques such as RT-PCR, FACS analysis, EMSA and ELISA. Chapter 3 focusses on the validation of different knockout MEFs used in the study as well as confirming the purity of primary astrocyte cultures established from pub brains. The susceptibility of various cells to JEV infection has also been investigated. Our results confirmed the authenticity of all the cells and the purity of primary astrocyte cultures used in the study. Our results also indicated that all the cells used in the study are susceptible to JEV infection. Chapter 4 discusses the expression of MHC and related genes involved in immune response upon JEV infection of primary mouse brain astrocytes, MEFs and H6. Chapter 4 demonstrates for the first time that JEV infection induces the expression of nonclassical MHC-I or class Ib molecules namely Qa-1, Qb1 and T10 in addition to the induction of classical MHC-I molecules. In contrast to WNV, there was no increase in the cell surface expression of MHC-II molecules upon JEV infection of primary mouse brain astrocytes. JEV infection also induces the expression of adhesion molecules as well as molecules involved in antigen processing and presentation namely Tap1, Tap2, Tapasin, Lmp2, Lmp7 and Lmp10. Chapter 5 demonstrates that JEV infection induces NF-κB activation in astrocytes and MEFs. Studies using MEFs deficient in classical and alternate pathways of NF-κB activation indicate that JEV activates the classical pathway of NF-κB activation and is dependent on canonical lKKβ/IKK2 activity. JEV infection of astrocytes, MEFs and H6 induces the production of type-I IFNs. To determine the mechanism of type-I IFN induction during JEV infection, MEFs deficient in NF-κB signaling and IFN signaling were used. Results indicate that type-I IFN production in MEFs occurs by both NF-κB dependent and independent mechanisms. In contrast, the production of IFN-α was completely abrogated in IFNAR-\- MEFs whereas IFN-β production was greatly reduced. Production of type-I IFNs in IFNGR-\- MEFs is also reduced upon JEV infection but the reason for this is unclear. Chapter 6 demonstrates that JEV induced expression of classical MHC-I molecules occurs by type-I IFN mediated signaling. This result is in contrast to WNV infection, in which both NF-κB and type-I IFNs are involved in the induction of classical MHC-I molecules. Type-I IFNs were also shown to be involved in the induction of nonclassical MHC molecules namely, Qa-1 and Qb1 during JEV infection. In contrast, the expression of T10, another nonclassical MHC molecule occurs independent of type-I IFN signaling. The expression of molecules involved in antigen processing and presentation namely, Tap1, Tap2, Lmp2 and Lmp7 was type-I IFN-mediated, whereas the expression of Tapasin and Lmp10 was mediated by both type-I IFN dependent and independent mechanisms. The expression of VCAM-1 was dependent on NF-κB mediated signaling. Chapter 7 precisely describes the underlying mechanism of induction of MHC and various other related molecules and their significance during JEV infection. In addition, it also includes a working model for the induction of these molecules during JEV infection. In summary, this is the first study in which the mechanism of JEV mediated induction of classical as well as nonclassical MHC molecules has been studied in detail. This study clearly demonstrated that type-I IFNs are involved in the induction of classical and nonclassical MHC-I molecules during JEV infection. The functional significance of this JEV mediated induction of classical MHC-I molecules is unclear, but it has been proposed that this is to escape from the action of NK cells. The absence of MHC-II induction during JEV infection could be important because it may lead to the initiation of an immune response which is different from that induced during other viral infections which induce the expression of MHC-II molecules. In contrast to classical MHC-I molecules, the functional and biological significance of nonclassical MHC-I molecules are poorly studied. Nonclassical MHC-I molecules play an important role in bridging adaptive and innate immune response. So the nonclassical MHC molecules induced during JEV infection may play an important role in the initiation of immune response during JEV infection. The role these nonclassical MHC-I molecules in antigen presentation during JEV infection is not known. These nonclassical antigens are also recognized by NK and γδT cells, thus the expression of nonclassical MHC-I molecules during JEV infection might also confer a protective role.