Master of Science / Department of Anatomy and Physiology / Jishu Shi / The development of reverse genetics systems for the manipulation of viral and bacterial genomes has provided platforms for identifying virulence genes, studying pathogenesis and developing vaccines. Replication-competent vaccines (e.g., modified live virus (MLV) vaccines and replicating viral/bacterial vectors) are considered the most efficacious approach for vaccine development. We constructed replication-competent candidate vaccines for two viral diseases in pigs via reverse genetics. The first vaccine we designed is to protect against highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). HP-PRRSV can cause high mortality in pigs of all ages. Vaccines to protect pigs from HP-PRRSV are not commercially available in the US. According to previous studies, the non-structural protein (NSP) coding region of HP-PRRSV is closely related to the high mortality rate and the structural protein (SP) coding region contributes to the induction of broadly protective neutralizing antibodies. We created a chimeric PRRSV, of which the SP coding region was derived from HP-PRRSV and NSP coding region was derived from a low-pathogenic strain. This chimeric PRRSV caused similar CPE in cells as parental viruses, but had slower growth kinetics. We hypothesize that this chimeric virus will have a low pathogenicity and could serve as a candidate vaccine that can provide protection against HP-PRRV. The second vaccine vector is a modified Listeria innocua (L.inn), a non-pathogenic strain of Listeria. Genetically related Listeria monocytogenes (L.m) is a well-known intracellular pathogen that encodes specialized virulent determinants facilitating its intracellular growth and spread. Our goal is to make L.inn a vaccine vector that can deliver classical swine fever (CSF) viral antigen into intracellular environments by complementation of L.inn with selected L.m virulence genes necessary for intracellular survival and induction of a robust immune response. In this study, we constructed a shuttle vector pHT-E2 that can express CSFV antigen E2 in L.inn. We cloned the plcA-prfA operon of L.m virulence gene cluster (vgc) into pHT-E2, which enhanced the expression of E2 in L.inn. In future studies, we plan to clone additional L.m virulence genes into the shuttle vector to increase immunogenicity of this recombinant L.inn and test its ability to protect pigs from CSFV.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Raymond R. R. Rowland / Interferons (IFNs) comprise a group of antiviral cytokines; however, their expression at the porcine maternal-fetal interface and in fetal tissues has not previously been investigated. The purpose of this study was to analyze the expression of type I IFNs and their receptors in maternal and fetal tissues from sows infected with PRRSV. The approach was to use real-time RT-PCR to identify the expression of different subtypes of type I IFN genes. The results show that the constitutive gene expression of some subtypes including IFN-[alpha] and IFN-[alpha][omega] were detected in fetal lymphoid nodes (IFN-[alpha][omega]), placenta (several IFN-[alpha] subtypes and IFN-[omega]5) and particularly, thymus (multiple IFN-[alpha], IFN-[delta] and IFN-[omega]5). The results demonstrate that porcine type I IFNs are differentially expressed at the maternal-fetal interface and in fetal tissues in response to PRRSV infection.

Master of Science in Biomedical Sciences / Department of Anatomy and Physiology / Yongming Sang / Animal metabolic and immune systems integrate and inter-regulate to exert effective immune responses to distinct pathogens. The signaling pathway mediated by mechanistic target of rapamycin (mTOR) is critical in cellular metabolism and implicated in host antiviral responses. Recent studies highlight the significance of the mTOR signaling pathway in the interferon (IFN) response. Type I IFNs mediate host defense, particularly, against viral infections, and have myriad roles in antiviral innate and adaptive immunity. In addition to their well-known antiviral properties, type I IFNs also affect host metabolism. However, little is known about how animal type I IFN signaling coordinates immunometabolic reactions during antiviral defense. Therefore, understanding the interaction of mTOR signaling and the type I IFN system becomes increasingly important in potentiating antiviral immunity. Tissue macrophages (MФs) are a primary IFN producer during viral infection, and their polarization to different activation statuses is critical for regulation of immune and metabolic homeostasis. Using porcine reproductive and respiratory syndrome virus (PRRSV) as a model, we found that genes in the mTOR signaling pathway were regulated differently in PRRSV-infected porcine alveolar MФs at different activation statuses. Therefore we hypothesize that: 1) the mTOR signaling pathway involves host anti-PRRSV regulation; 2) mTOR signaling interacts with IFN signaling to modulate the antiviral response; and 3) different type I IFN subtypes (such as IFN-α1 and IFN-β) regulate mTOR signaling differently. We show that modulation of mTOR signaling regulated PRRSV infection in MARC-145 cells and porcine primary cells, in part, through regulating production and signaling of type I IFNs. In addition, expression and phosphorylation of two key components in the mTOR signaling pathway, AKT and p70 S6 kinase, were regulated by type I IFNs and PRRSV infection. Taken together, we determined that the mTOR signaling pathway, a key pathway in regulation of cell metabolism, also mediates the type I IFN response, a key immune response in PRRSV infection. Our findings reveal that the mTOR signaling pathway potentially has a bi-directional loop with the type I IFN system and implies that some components in the mTOR signaling pathway can serve as targets for augmentation of antiviral immunity and therapeutic designs.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically significant viral diseases facing the global swine industry. Viraemia profiles of PRRS virus challenged pigs reflect the severity and progression of infection within the host and provide crucial information for subsequent control measures. In this thesis we analyse the largest longitudinal PRRS viraemia dataset from an in-vivo experiment, and corresponding immune measures in the form of cytokine data and neutralising antibodies. In the PRRS Host Genetic Consortium (PHGC) trials, pigs were challenged with one of two PRRSV isolates (NVSL and KS06, respectively). In Chapter 2 we derive a statistical description of the temporal changes in viraemia and determine the influence of diverse factors (e.g. PRRSV strain, pig genetic background, resistance genotype, etc.) on viraemia profiles. The well-established methodology of linear mixed modelling with a repeated measures model and fitting a linearized Wood’s function, a gamma-type function, is applied to the viraemia dataset. The virus isolate had a significant impact on the viraemia profiles which was captured by statistically significant differences in model parameters via both statistical methods. The more virulent NVSL isolate had higher early viraemia predictions and a faster rate of decline than KS06. In line with previous studies the WUR “resistance” genotype, associated with lower AUC viraemia found in previous studies, also resulted in lower viraemia predictions in the statistical models. The typical time trends of the viraemia profiles were a rise to a peak followed by a period of decline with dynamics and magnitude influenced by the virus isolate. Both uni and bimodal viraemia profiles were observed. The Wood’s model appeared a suitable candidate model for the data associated with uni-modal profiles and captured the time trends concisely in only three model parameters which also had a biological relevance. Overall the best fitting Wood’s model (y=atbe-ct) was when there was a random effect in Wood’s parameters b and c. Bimodal profiles significantly reduced the model fit, particularly in the later phase of infection resulting in large model residuals. However bimodal profiles did not impact upon the significance of the differences between the LSM repeated measures estimates nor the LSM linearized Wood’s model parameter estimates. The longitudinal viraemia measures from the PRRSV challenge experiment revealed substantial differences in the viraemia profiles between hosts infected with the same PRRSV challenge dose, pointing to considerable variation in the host response to PRRSV infections. In Chapter 3 we provide a suitable mathematical description of all viraemia profiles with biologically meaningful parameters for quantitative analysis of profile characteristics. The Wood’s function and a biphasic extended Wood’s function were fit to the individual profiles using Bayesian inference with a likelihood framework in Chapter 3. Using maximum likelihood inference and numerous fit criteria, we established that the broad spectrum of viraemia trends could be adequately represented by either uni-or biphasic Wood’s functions. Three viraemic categories emerged: cleared (uni-modal and below detection within 42 days post infection(dpi)), persistent (transient experimental persistence over 42 dpi) and rebound (biphasic within 42 dpi). The convenient biological interpretation of the model parameters estimates, allowed us not only to quantify inter-host variation, but also to establish common viraemia curve characteristics and their predictability. The convenient biological interpretation of the model parameters estimates, allowed us not only to quantify inter-host variation, but also to establish common viraemia curve characteristics and their predictability, which were utilized in subsequent quantitative genetic analyses to identify genomic regions associated with these new resistance traits. The Bayesian approach for curve fitting in Chapter 3 led to better model fits than the classical linear mixed models approach of Chapter 2. Furthermore in Chapter 4 we explored the association between the observed PRRS viraemia profile characteristics and the corresponding measures of the immune response in the form of: neutralising antibody (nAb) cross protection data and longitudinal cytokine profiles. Statistical analysis of the profile characteristics revealed that persistent profiles were distinguishable already within the first 21 dpi, whereas it is not possible to predict the onset of viraemia rebound. Analysis of the neutralizing antibody (nAb) data indicated that there was a ubiquitous strong response to the homologous PRRSV challenge, but high variability in the range of cross-protection of the nAbs. Persistent pigs were found to have a significantly higher nAb cross-protectivity than pigs that either cleared viraemia or experienced rebound within 42 dpi. We determined the typical features and time trends of each cytokine profile, examined the associations between cytokines, and characterised the cytokine response. A stronger association was found in the direction of cytokines driving the ensuing viraemia characteristics as opposed to vice versa. It was found that viraemia class differences were best captured in the anti-viral cytokine IFNA and also the chemokine CCL2, furthermore these key cytokines were the most strongly associated with viraemia measures. The breadth of the cytokine responsiveness was associated with viral profile class and genetic background but not the WUR genotype. The statistical categorization of pigs from each PHGC trial through model fitting provides a critical basis for the generation of new desirable host phenotypes, and of potential use in the genetic selection of pigs with favourable infection traits. Our study provides novel insights into the nature and degree of variation of hosts’ responses to infection as well as new informative traits for subsequent genetic and modelling studies.

No description available.

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease that has devastated the global swine industry since the mid 1980s. Although modified live vaccines (MLVs) are typically used for the prevention of clinical disease, they are not always fully effective. Additionally, acute PRRS outbreaks, characterized by more severe clinical signs, have appeared in herds that were previously vaccinated. In this dissertation, we further analyzed the pathogenesis of PRRSV through genetic characterization, assay development, and quasispecies evaluation using the PRRSV ORF5 gene while also attempting to develop an improved PRRS vaccine. To explore the possible mechanism for the emergence of acute PRRS, the open reading frame 5 (ORF5) gene encoding the major envelope protein (GP5) of acute PRRSV isolates was characterized. Sequence and phylogenetic analyses revealed that seven of the acute PRRS virus (PRRSV) isolates were related to other N. American PRRSV isolates while one isolate, 98-37120-2, was very closely related to and may have been derived from the MLV, RespPRRS. We also developed a heteroduplex mobility assay (HMA) for quickly identifying PRRSV field isolates with significant nucleotide sequence identities (â d98%) with the MLVs based on the amplification, denaturation, and reannealing of the ORF5 gene of the field isolates with those of MLV reference strains. All of the field isolates that were highly related to RespPRRS (â T2% nucleotide sequence divergence) were identified by the HMA to form homoduplexes with the reference RespPRRS MLV. We also developed a unique strategy for infecting pigs with PRRSV, known as in vivo transfection, by bypassing the traditional in vitro cell culture step required for in vivo studies. We demonstrated that inoculation of RNA transcripts of a PRRSV infectious cDNA clone directly into the lymph nodes and tonsils of pigs produces active PRRSV infection. Using this method, we also examined the quasispecies populations of PRRSV. Finally, we evaluated the ability of Salmonella choleraesuis to express the PRRSV GP5, and tested its immunogenicity in mice. Based on our data, there was no indication of Salmonella replication in the mice or any evidence of antibody production against S. choleraesuis or PRRSV GP5. / Ph. D.

Porcine reproductive and respiratory syndrome (PRRS) is the most significant infectious disease currently affecting the swine industry worldwide. Several inactivated and modified live vaccines (MLV) have been developed to curb PRRSV infections. The unsatisfactory efficacy and safety of these vaccines, drives for the development of new generation PRRS universal vaccines. Virus like particles (VLPs) based vaccines are gaining increasing acceptance compared to subunit vaccines, as they present the antigens in more veritable conformation and are even readily recognized by the immune system. Hepatitis B virus (HBV) core antigen (HBcAg) is very well studied and has been successfully used as a carrier for more than 100 other viral sequences. In this study, hybrid HBcAg VLPs are generated by fusion of the conserved protective epitopes of PRRSV and expressed in E. coli. An optimized purification protocol that overcomes issues from ultracentrifugation is developed to obtain hybrid HBcAg VLP protein from the inclusion bodies. This hybrid HBcAg VLP protein self assembled to 23nm VLPs that were shown to block virus infection of susceptible cells when tested on MARC 145 cells. Therefore, the safety of non-infectious and non-replicable VLPs and production through low-cost E. coli fermentation may make this vaccine competitive against current vaccines on both efficacy and cost. / Master of Science

Porcine reproductive and respiratory syndrome virus (PRRSV) is the cause of a pandemic that has been devastating the U.S. and global swine industry for more than twenty years. PRRSV vaccine development is challenging due to virus heterogeneity. Evidence indicates that the major envelope protein, GP5, is the primary target for a subunit vaccine. In native virions GP5 primarily exists as a disulfide linked complex with the membrane protein, M, which also possesses immunogenic properties. Recent studies report that the GP5/M complex is a more significant vaccine candidate. Currently, no bulk purification methods have been reported for PRRSV proteins. The objective of this research was to develop a purification process for GP5 or GP5/M from native virions. PRRS virions were isolated and concentrated through sucrose cushion ultracentrifugation and target envelope proteins were solubilized with Triton X-100 detergent for further processing. GP5/M was not consistently identified in samples and was therefore abandoned. GP5 was identified by Western blot throughout processing with a αORF5 antibody. Cation exchange chromatography (CEX) was utilized for partial fractionation of GP5, although the viral nucleocapsid protein, N, was a major impurity in CEX elution fractions. As a second chromatographic step, hydrophobic interaction chromatography (HIC) further purified GP5 by means of a two-stage elution scheme. Pure GP5 was eluted from the HIC resin in the second HIC elution stage by Triton X-100 displacement; however the protein is present as a homodimeric/tetrameric aggregate. This process will be useful in PRRSV vaccine development and the purified GP5 product could be used as much needed positive controls in animal studies. / Master of Science

Background: The monitoring of infectious diseases like the porcine reproductive and respiratory syndrome (PRRS) using pen-wise oral fluid samples becomes more and more established. The collection of individual oral fluid, which would be useful in the monitoring of PRRSV negative boar studs, is rather difficult. The aim of the study was to test two methods for individual oral fluid collection from pigs and to evaluate the specificity of a commercial ELISA for detection of PRRSV antibodies in these sample matrices. For this reason, 334 serum samples from PRRSV negative pigs (group 1) and 71 serum samples from PRRSV positive pigs (group 2) were tested for PRRSV antibodies with a commercial ELISA. Individual oral fluid was collected with a cotton gauze swab from 311 pigs from group 1 and 39 pigs from group 2. Furthermore, 312 oral fluid samples from group 1 and 67 oral fluid samples from group 2 were taken with a self-drying foam swab (GenoTube). The recollected oral fluid was then analysed twice with a commercial ELISA for detection of PRRSV antibodies in oral fluid.

No description available.