Respiratorische Krankheitsbilder, an denen mehr als ein Pathogen ursächlich beteiligt ist, gewinnen in der Schweinepopulation zunehmend an Bedeutung. Diagnostische Methoden zum simultanen Nachweis mehrerer Erreger sind Bestandteil einer schnellen und effizienten Therapie und tragen zum ökonomischen Bestandsmanagement bei. Im Rahmen dieser Arbeit sollten Methoden für den Multiplex-Nachweis von Antikörpern und Nukleinsäuren viraler Erreger von respiratorischen Krankheitsgeschehen des Schweins entwickelt werden. Die Methode für den Multiplex-Nachweis von Antikörpern sollte auf Basis der xMAP® Flüssigchip-Technologie (Luminex Corporation, Austin, T, USA) an der LiquiChip®- Workstation (Qiagen, Hilden, D) etabliert werden. Da es sich um eine für den Antikörpernachweis im veterinärmedizinischen Bereich bislang nicht genutzte Methode handelte, erfolgte die Prüfung der Machbarkeit zunächst im Einfach-Format am Beispiel des Porzinen Circovirus Typ 2. Im Laufe der Arbeit wurde deutlich, daß die Kopplung des PCV2 ORF2-Proteins als Capture-Molekül sowie die Erstellung der Versuchsansätze mit akzeptablem Aufwand ohne Spezialtechniken durchführbar war. Aufgrund der Anordnung der Proben auf Platten im 96-well-Format und der vollautomatischen Messung war ein hoher Probendurchsatz möglich. Nach der Einführung von Waschschritten in die Versuchsansätze konnten hohe Fluoreszenzsignale erzeugt werden. Im Laufe der Optimierungsversuche wurde allerdings die fehlende Korrelation dieser Fluoreszenzsignale mit den Ergebnissen der Referenzmethode deutlich. Aufgrund der unbekannten Testeigenschaften sowie fehlender Kontrollmöglichkeiten wurden diese nicht sogleich als unspezifische bzw. falsch positive Signale erkannt. Erst durch die Testung von positiven und negativen Feldseren an verschiedensten Bead-Arten wurde ersichtlich, daß die Fluoreszenzen nicht ausschließlich durch die spezifische Bindung der PCV2-Antikörper an das Capture-Protein entstanden. Im Ausschlussverfahren konnte die Ursache eingegrenzt werden. Bestandteile aus dem Schweineserum führten vermutlich durch unspezifische Bindungen an die LiquiChip®-Beads zu einem Fluoreszenzereignis. Durch Vorinkubation der Beads in Pferdeserum und der Feldseren mit einem Block-Puffer wurde versucht, diese Serumbestandteile abzusättigen und so eine Bindung an die Beads zu verhindern. Die Inkubationsvarianten führten weder zu einer Minimierung der unspezifischen Bindung noch zu einer verbesserten Differenzierung PCV2-positiver und negativer Seren. Die in der vorliegenden Arbeit verwendeten Bead-Arten sind für den Nachweis von Antikörpern gegen das PCV2 ORF2-Protein nicht geeignet. Alternative Bead-Arten für einen vergleichbaren Versuchsansatz stehen derzeit nicht zur Verfügung. Ein weiteres Ziel der Arbeit bestand darin, eine bereits in der Diagnostik von Schweineviren etablierte Methode, die PCR, zu einer Multiplex-PCR zu erweitern. Als zu detektierende Parameter wurden die derzeit bedeutendsten viralen Erreger von respiratorischen Erkrankungen des Schweins, das PRRS-Virus (Typ 1 und Typ 2), das Porzine Influenzavirus mit den Subtypen H1N1, H3N2 und H1N2 und PCV2 gewählt. Es wurden die Primersequenzen von bereits etablierten Einfach-PCRs an die besonderen Ansprüche einer Multiplex-PCR angepasst und die Methode zunächst im Einzelansatz auf Funktionsfähigkeit überprüft. Im Anschluss wurden die Parameter zu einer Multiplex-PCR zusammengeführt, die Methode optimiert und auf Spezifität, Sensitivität und Verhalten in der Routinediagnostik überprüft. Aufgrund der im Gegensatz zur Einfach-PCR zum Teil herabgesetzten Sensitivität ist diese Methode für Ausschlussuntersuchungen weniger geeignet. Für die Untersuchung von Probenmaterial klinisch erkrankter Tiere ist sie jedoch gut geeignet und bietet die Möglichkeit einen schnellen Überblick über das Erregerspektrum zu erhalten. Es muss jedoch berücksichtigt werden, daß bestimmte Parameter, z.B. PCV2, die Sensitivität des Nachweises der anderen Parameter sehr deutlich herabsetzen kann. Dies ist insbesondere von Bedeutung, da PCV2-DNA in Probenmaterial von klinisch erkrankten Tieren in sehr hohen Mengen vorhanden ist und dadurch die weiteren Parameter noch zusätzlich beeinflusst werden können.

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Porcine reproductive and respiratory syndrome virus (PRRSV) is arguably the most economically devastating pathogen affecting the global swine industry. Since the emergence of the virus in the late 1980s, vaccination strategies aimed to control the virus have not been very effective. Current commercial vaccines are generally protective against homologous or closely-related strains but ineffective at conferring heterologous protection against genetically-diverse strains of the virus. Consequently, emergence of variant and sometime more pathogenic strains of PRRSV continues in global swine herds. As such, there is a need for better understanding of the molecular mechanisms involved in the replication of the virus. In order to better understand the molecular mechanisms of host responses to PRRSV replication, we first sought to evaluate the ability of the virus to induce stress granules (SGs) during PRRSV infection. SGs are intracellular, cytoplasmic aggregates of RNA-binding proteins (RBPs) and mRNA. Formation of SGs is observed upon cellular stress and ultimately function to arrest cellular translation to promote cellular survival until the stress has been remedied. Indeed, several viruses have been shown to modulate the SG pathways to facilitate viral replication and even suppress the host's immune response. However, it is currently unknown whether PRRSV modulates the SG response. First, we used confocal microscopy and fluorescent in situ hybridization (FISH) to determine the distribution of known SG marker proteins and cellular mRNAs. Our findings revealed that PRRSV induces a potent SG response at late time points post-infection, and that SGs were closely associated with viral replication complexes (VRCs). Subsequently, we demonstrated that SGs are dispensable for viral replication, as short hairpin RNA (shRNA)-mediated knockdown of critical SG components (G3BP1 and G3BP2) did not affect viral replication. Interestingly, we found that the PRRSV-induced SGs are formed in a PERK-dependent manner. PERK is an important sensor of ER stress and activator of the unfolded protein response (UPR). Further investigation into the PERK signaling pathway revealed that PRRSV induces a significant amount of ER stress upon the cell during viral infection, and that exogenous stress significantly impaired the ability of the virus to replicate in MARC145 cells. We also showed that PRRSV potently induces all three signaling branches of the UPR, including PERK. While PERK knockdown had no effect on cell viability or viral replication, it significantly upregulated the mRNA expression of interferon-β and interferon stimulated genes (ISGs). The results from our studies suggest a critical role for PERK in regulating the host innate immune response to PRRSV infection. Only with a better understanding of the underlying molecular mechanisms of PRRSV replication will we be able to rationally design more effective vaccines against the virus. / Doctor of Philosophy / Porcine reproductive and respiratory syndrome virus (PRRSV) causes an economically-devastating disease in the global swine industry. Annually, PRRSV is estimated to cause more than $600 million in economic losses to the swine industry in the United States alone. Current commercial vaccines against the virus are not effective against the diverse field strains largely due to the extreme heterogeneity of the virus. PRRSV is also able to potently suppress several aspects of the host's immune response and therefore establish a persistent infection. The underlying mechanisms of PRRSV-mediated immune suppression are not well understood. Therefore, in this dissertation we decided to investigate the molecular mechanisms of host responses to PRRSV infection. We first investigated the ability of the virus to induce stress granules (SGs). SGs are important intracellular regulatory components that modulate many aspects of the host's cellular processes, and have even been shown to play roles in regulating viral replication and controlling immune responses to viral infection. We demonstrate that PRRSV not only induces SGs, but that the PRRSV-induced SGs are closely associated with viral replication complexes (VRCs) within infected cells. The PRRSV-induced SGs were dispensable for viral replication. PRRSV-induced SGs were previously shown to form in a PERK dependent manner. Therefore, in the second part of this dissertation research, we decided to investigate the PERK signaling pathway during PRRSV infection. PERK is an important sensor of ER stress and activator of the unfolded protein response (UPR). Our results showed that PRRSV potently induces ER stress and all three signaling branches of the UPR, including PERK. Furthermore, we revealed that PERK may play an important role in regulating the type I interferon response to PRRSV infection. The results from our studies will aid in understanding the underlying molecular mechanism of PRRSV replication which will help rationally design the next generation of more effective vaccines against this devastating swine pathogen.

Doctor of Philosophy / Department of Diagnostic Medicine and Pathobiology / Raymond R. R. Rowland / Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most costly virus to the swine industry, worldwide. This study explored the application of deep sequencing techniques to understand better the virus-host interaction. On the virus side, PRRSV exists as a quasispecies. The first application of deep sequencing was to investigate amino acid substitutions in hypervariable regions during acute infection and after virus rebound. The appearance and disappearance of mutations, especially the generation of a new N-glycosylation site in GP5, indicated they are likely the result of immune selection. The second application of deep sequencing was to investigate the quasispecies makeup in pigs with severe combined immunodeficiency (SCID) that lack B and T cells. The results showed the same pattern of amino acid substitutions in SCID and normal littermates and no different mutations were identified between SCID and normal littermates. This suggests the mutations that appear during the early stages of infection are the product of the virus becoming adapted to replication in pigs. The third application of deep sequencing was to investigate the locations of recombination events between GFP-expressing PRRSV infectious clones. The results identified different cross-over occurred within three conserved regions between EGFP and GFPm genes. And finally, the fourth goal was applied to develop a set of sequencing tools for analyzing the host antibody repertoire. A simple method was developed to amplify swine VDJ repertoires. Shared and abundant VDJ sequences that are likely expressed by PRRSV-activated B cells were determined in pigs that had different neutralization activities. These sequences are potentially correlated with different antibody responses.

Doctor of Philosophy / Department of Anatomy and Physiology / Chris R. Ross / The immediate antiviral defense residing in the innate immune system of multicellular organisms critically determines the outcome of viral infection. This dissertation presents a study of the "effectors" and "receptors" of porcine innate immunity in infection caused by porcine reproductive and respiratory syndrome virus (PRRSV), which is the most devastating pathogen impacting the swine industry. In the first investigation, eleven novel porcine host defense peptides (HDPs), [Beta]-defensins (pBDs), were identified and characterized. All of these peptides have a consensus [Beta]-defensin motif and phylogenetically are similar to orthologs from other species. A differential expression pattern for these 11 newly identified genes was found. For example, pBD-2 and pBD-3 were expressed in bone marrow, lung, skin and other lymphoid tissues. pBD-2 and pBD-3 were further characterized for their gene structure, and antimicrobial activity of synthetic peptides. The second study was conducted to evaluate PRRSV-induced differential expression of porcine HDPs and direct antiviral activity of selected HDPs against PRRSV. In vitro incubation of PRRSV with synthetic pBD-3 or protegrin-4 (PG-4) significantly inhibited viral infectivity. Using nine protegrin-derived peptides, it was determined that cyclization of PG-4 increased anti-PRRSV activity and mutation of some residues in PG-4 diminished some of the activity. These findings suggest the potential role of porcine HDPs as a group of innate antiviral effectors. In the third and fourth investigations, porcine Toll-like receptor (TLR) 3 and TLR7 were identified and functionally expressed. Increased expression of TLR3 was observed in PRRSV-infected porcine lungs. Stimulation of porcine alovelar macrophages with poly (I:C), a synthetic TLR3 ligand, increased expression of interferon-[Beta] and suppressed PRRSV infectivity. Activation of porcine TLR3 overexpressed in a PRRSV-sensitive cell line, elicited antiviral responses to PRRSV infection. Partial silencing of TLR3 in PAMs resulted in increased PRRSV infection. In summary, these data provide molecular information on porcine TLR3 and TLR7, and their involvement in PRRSV pathogenesis, which may elicit new strategies to prevent this costly swine disease.

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Background: In this study, six enzyme-linked immunosorbent assays (ELISA), intended for routine porcine reproductive and respiratory syndrome virus (PRRSV) herd monitoring, are tested for their ability to detect PRRSV specific antibodies in the serum of pigs after vaccination with an inactivated PRRSV type 1 vaccine and subsequent infection with a highly pathogenic (HP) PRRSV field strain. For this reason, ten piglets (group V) from a PRRSV negative herd were vaccinated twice at the age of 2 and 4 weeks with an inactivated PRRSV vaccine. Ten additional piglets (group N) from the sameherd remained unvaccinated. Three weeks after second vaccination, each of the piglets received an intradermal application of an HP PRRSV field strain. Serum samples were taken before first vaccination as well as before and 3, 7, 10 and 14 days after HP PRRSV application. All serum samples were tested for PRRSV RNA by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) as well as for PRRSV antibodies with all six study ELISAs. Results: At the beginning of the study (before vaccination), all of the piglets were PRRSV antibody negative with all study ELISAs. They also tested negative for PRRSV RNA measured by RT-qPCR. From day 3 after HP PRRSV application until the end of the study, a viremia was detected by RT-qPCR in all of the piglets. On day 0 (day of HP PRRSV application), nine out of ten piglets of the pre-vaccinated group tested PRRSV antibody positive with one of the tested ELISAs, although with lower S/P values than after infection. On day 10 after HP PRRSV application, all study ELISAs except one had significantly higher S/P or OD values, respectively more positive samples, in group V than in group N. Conclusions: Only one of the tested ELISAs was able to detect reliably PRRSV antibodies in pigs vaccinated with an inactivated PRRSV vaccine. With most of the tested ELISAs, higher S/P values respectively more positive samples after PRRSV infection were seen in the pre-vaccinated group than in the non-vaccinated.

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are two of the most prevalent swine pathogens that have impacted the global swine industry for decades. Both are RNA viruses with increasing heterogeneity over the years, making a vaccine solution ever so challenging. Modified live-attenuated vaccines (MLVs) have been the most common approach, but the long-term safety regarding their potential for pathogenic reversion still needs to be addressed. Subunit based vaccines have been the focus of numerous development studies around the world with renewed interest in their promising prospects in both safety and efficacy. Our lab has developed a unique approach to use hepatitis B virus core capsid protein (HBcAg) as a vaccine delivery vehicle for either PRRSV or PEDV viral epitope antigens. Recombinantly produced HBcAg forms an icosahedral capsid virus-like particle (VLP) that has 240 repeats in a single assembled particle. By inserting different epitope antigens from these porcine pathogens into the particle, we can achieve repetitive antigen presentation to the host's immune system by taking advantage of the polymeric nature of VLP. The first animal study evaluated the efficacy of 4 VLP based vaccine candidates against PRRSV in mice. These 4 vaccines incorporated 2 B-cell epitopes (61QAAIEVYEPGRS72 and 89ELGFVVPPGLSS100) and 2 T-cell epitopes (117LAALICFVIRLAKNC131 and 149KGRLYRWRSPVIIEK163) from PRRSV structural proteins GP3 and GP5 respectively. Candidate GP3-4 was able to stimulate a significant viral neutralizing response in mouse sera against two PRRSV strains, one being heterologous, demonstrating its potential of cross-protection against PRRSV. The second animal study took an optimized VLP vaccine candidate against PEDV from previous development studies in mice, and assessed its efficacy through a comprehensive pregnant gilt vaccination and neonatal piglet challenge model. The vaccine candidate incorporated B-cell epitope 748YSNIGVCK755 from the PEDV spike protein. It was able to elicit significant viral neutralization antibody titer in gilt milk at 3 days post-farrowing (DPF), and provided nursing piglets with clinical relief in terms of morbidity, viral shedding, small intestinal lesions, and 10 days post-challenge (DPC) survival rate. / Doctor of Philosophy / Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are two pathogens that infect pigs, resulting in immense economic losses to the global pork production industry every year. Both viruses have large diversity with various strains due to mutations that have occurred over the years. This makes vaccine development that aims at combating the pathogens even more challenging. One common vaccine strategy has been immunizing animals with modified live viruses with decreased pathogenicity. Naturally, long term safety of this option has been a concern. A much safer vaccine approach that is purely protein based has attracted renewed interest around the world. Protein based vaccines lack genetic materials from the viruses and are not able to replicate inside the host. Our lab has developed a platform that uses protein-based particles (VLPs) originated from the hepatitis B virus (HBV), and incorporates short pieces of proteins from either PRRSV or PEDV to train host's immune system to recognize these pathogens, and hopefully to prevent future infection. For the first animal study, we tested 4 VLP vaccine candidates against PRRSV in mice and discovered that mouse serum from one candidate GP3-4 was able to prevent infection of 2 distinct PRRSV strains in petri dishes, paving the way for further development. For the second animal study, we took an optimized VLP vaccine candidate against PEDV from previous mouse studies, and evaluated its performance in pigs. We immunized pregnant mother pigs with the vaccine before they gave birth, then experimentally infected newborn piglets with the virus. Piglets from the vaccinated mothers showed improved clinical signs and faster recovery from the infection.

<p>Thyroid hormone is essential for regulating adult metabolism and proper fetal development. Under normal conditions, maternal and fetal thyroid hormones are subject to metabolism at the placenta and within fetal tissues through deiodination and sulfation to regulate fetal exposure to the bioactive hormone. Disruptions of the thyroid hormone system can result in non-thyroidal illness syndrome (NTIS), which is classified as the dysregulation of thyroid hormone homeostasis. The exact cause of the alterations in circulating thyroid hormone levels during NTIS is not well- known. In comparison, hypothyroidism results from the absence of thyroid hormone production and presents as low thyroid hormone levels.</p> <p>Porcine reproductive and respiratory syndrome virus (PRRSV) crosses the late gestation placenta and causes suppression of circulating maternal and fetal thyroid hormone. Chapter 2 investigates the potential role of thyroid hormone metabolism in this disruption. Pregnant gilts were challenged with PRRSV2 (n=22) or sham inoculated (n=5) at gestation day 85. Samples were collected on day 106, and viral load was assessed in fetal serum and thymus. From the entire fetal population, three distinct subsets of fetuses representing biological extremes were identified, including uninfected with no detectable viral load (UNIF), high viral load viable (HV-VIA), or high viral load with severe meconium staining (HV-MEC). In addition, control fetuses from sham inoculated gilts (CON) were used as a reference group. Samples of fetal liver, kidney, and the corresponding fetal placenta and maternal endometrium for n=10 fetuses per group were then used to evaluate gene expression. A total of 11 genes associated with thyroid hormone metabolism including deiodinases (DIO1,2,3), sulfotransferases (SULT1A3,1B1,1C2,1E1,2A1), sulfatase (STS), and solute carriers (SLC16A2,16A10) were quantified using absolute quantification qPCR. Evidence of fetal decompensation was observed within the high viral fetuses in the form of decreased DIO1 expression within the fetal liver and increased DIO3 expression in both components of the placenta. Circulating levels of T4 and inactive thyroid hormone metabolites, reverse-triiodothyronine (rT3) and two diiodothyronines (3,5-T2 and 3,3’-T2), were measured in fetal serum. While T4 was depressed, no change was observed in circulating rT3 levels, and neither T2 metabolite reached the lower detection limit. This may suggest that alterations in thyroid hormone metabolism generate a localized effect on hormone metabolites in the respective tissues.</p> <p>Alternatively, the low levels of available T3 and T4 limit the production of downstream metabolites to be found in serum.</p> <p>The cause-and-effect relationship between PRRSV infection, fetal thyroid disruption, and the effects on fetal thyroid hormone metabolism are unclear. Therefore, Chapter 3 developed a non-pathogenic model using methimazole (MMI) to induce hypothyroidism in the late gestation fetus and evaluate the impact on fetal development and thyroid hormone metabolism. Pregnant gilts were either treated with oral methimazole or equivalent sham from gestation day 85-106 (n=4/group), followed by classification of all fetuses as live, live but meconium stained, or dead. Fetuses exposed to MMI in-utero were notably hypothyroid with significantly suppressed serum T3 and T4 and histological evidence of goiter. Surprisingly, fetuses from MMI-treated dams were substantially larger but appeared to exhibit non-allometric growth with an increase in girth but not length. The liver, kidney, and the corresponding fetal placenta and maternal endometrium were collected from a subset of 16 fetuses per group to evaluate the relative expression of five genes associated with thyroid hormone metabolism, including three deiodinases and two solute carriers known to transport thyroid hormone. Compensatory transcription of DIO3 was observed in all tissues evaluated, suggesting increased vertical transfer of maternal thyroid hormone at the placenta and decreased breakdown of thyroid hormone within fetal organs.</p> <p>The evaluation of thyroid hormone metabolism within the fetus and within the placenta has allowed us to differentiate suppressed thyroid hormone levels of the pig fetus under pathogenic and non-pathogenic conditions. In the context of PRRSV infection, the observed decompensation of thyroid hormone metabolism would further exacerbate the hypothyroid state and is therefore consistent with NTIS. In contrast, fetuses with induced thyroid hormone suppression following maternal exposure to MMI showed compensatory thyroid hormone metabolism in the same tissues. This indicates true hypothyroidism and clearly demonstrates a fetal capacity to respond to such endocrine disruption.</p>