Bovine viral diarrhoea virus (BVDV) has emerged as one of the economically important pathogens in cattle populations with a worldwide distribution and causing a complex of disease syndromes. It is a single-stranded RNA virus of the genus Pestivirus in the family Flaviviridae. Two genotypes (1 and 2) of BVDV exist and can be distinguished on the basis of the 5' non-coding region (5' NCR) of the genome using real-time PCR. This technique is more sensitive, specific, less time consuming and has reduced risks of cross contamination of samples compared to a conventional PCR. Limited information exists on BVDV genetic subtypes in South Africa. The aim of this study was to determine the genotypes of BVDV currently circulating in South African feedlots. A total of 279 specimens (219 tissue samples, 59 trans-tracheal aspirates and one blood sample) were collected from dead and living cattle. Pooled homogenates from the same animals were prepared and total RNA was extracted from 200 μl of the homogenates using the RNeasy Mini Kit (Qiagen) as described by the manufacturer. A screening test was performed on the pooled samples and positive pools were investigated individually. The Cador BVDV Type 1/2 RT-PCR Kit (Qiagen, Hilden, Germany) was used for the real-time PCR assay. The PCR was performed on a Lightcycler® V2 (Roche Diagnostics, Mannheim, Germany) real-time PCR machine and the amplified products were detected via fluorescent dyes. The results were read at 530 and 640 nm for BVDV 1 and 2, respectively. Bovine viral diarrhoea virus was detected in a total of 103 samples that included 91 tissue samples, one blood sample and 11 trans-tracheal aspirates. Eighty five of the strains were genotype 1 strains and 18 were genotype 2. These results represent the first documented evidence for the presence of BVDV genotype 2 in South African cattle. / Dissertation (MSc)--University of Pretoria, 2010. / Veterinary Tropical Diseases / unrestricted

Submitted by Cássio da Cruz Nogueira (cassionogueirakk@gmail.com) on 2017-01-26T14:06:49Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_ReplicacaoViralPadrao.pdf: 2703656 bytes, checksum: ccbaf5da11f1dbae865d35717cc46fc9 (MD5) / Approved for entry into archive by Edisangela Bastos (edisangela@ufpa.br) on 2017-01-27T13:37:12Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_ReplicacaoViralPadrao.pdf: 2703656 bytes, checksum: ccbaf5da11f1dbae865d35717cc46fc9 (MD5) / Made available in DSpace on 2017-01-27T13:37:12Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_ReplicacaoViralPadrao.pdf: 2703656 bytes, checksum: ccbaf5da11f1dbae865d35717cc46fc9 (MD5) Previous issue date: 2015-07-13 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os arbovírus pertencentes ao gênero Flavivirus (Família Flaviviridae) são responsáveis por considerável morbi-mortalidade, podendo causar quadros graves de encefalite, febre hemorrágica, hepatite e doença febril em vertebrados, incluindo humanos. O flavivírus Rocio (VROC) é de grande importância para a saúde pública no Brasil, pois representa uma grave ameaça de ocorrência de súbitos surtos de encefalite. A imunopatologia das encefalites causadas por flavivírus ainda não está completamente esclarecida e muitos aspectos inerentes à modulação das respostas imunes do SNC carecem por ser desvendados. Deste modo, o objetivo deste trabalho foi analisar o padrão de expressão gênica de citocinas em cultura primária de células neurais submetidas à infecção pelo vírus Rocio. Culturas primárias mistas (neurônio/glia), obtidas a partir de cérebros de camundongos isogênicos neonatos da linhagem BALB/c, foram inoculadas com o VROC (MOI igual a 2) no sétimo dia de cultivo, a confirmação da infecção foi feita por imunocitoquímica (anti-VROC). Quantificou-se a replicação viral nas culturas primárias infectadas, em função do período infeccioso, pelo método da titulação viral. O RNA celular total foi extraído e utilizado para a detecção de citocinas através da técnica de RT-qPCR em tempo real. O estudo demonstrou que cultura primária de células neurais constitui um bom modelo experimental para estudo de infecções do SNC pelo flavivírus Rocio. O VROC infectou eficientemente a cultura primária de células neurais gerando alterações citopatogênicas a partir do 2º dia p.i., momento em que se detectou maior título viral. A cultura primária infectada com o VROC sobreviveu até 7 dias p.i. e a quantificação da carga viral revelou uma cinética de replicação viral compatível com a cinética de morte celular da cultura infectada pelo VROC. Durante os cinco primeiros dias p.i. da cultura primária, houve redução da expressão gênica de INF-α, INF-β, INF-γ e IL-1β, não houve alteração na expressão de TNF-α e houve aumento na expressão de TGF-β no 1º, 3º e 5º dia p.i. Os achados deste estudo sugerem que o VROC tem a capacidade de regular negativamente a expressão de citocinas moduladoras das respostas imunes antivirais e inflamatórias e que, neste modelo experimental, a imunorregulação exercida pelo TGF-β predomina sobre a modulação das respostas imunes antivirais e inflamatórias, sendo necessários maiores estudos para elucidar a imunopatologia da infecção do SNC pelo VROC. / Arboviruses belonging to the genus Flavivirus (Flaviviridae family) are responsible for considerable morbidity and mortality, may cause severe cases of encephalitis, hemorrhagic fever, hepatitis and febrile disease in vertebrates, including humans. Rocio flavivirus (ROCV) is very important for public health in Brazil, as it represents a serious threat of occurrence of sudden encephalitis outbreaks. The immunopathology of encephalitis caused by flavivirus is not yet fully understood and many aspects involved in modulation of immune responses in the CNS need to be unraveled. Thus, the aim of this study was to analyze the pattern of gene expression of cytokines in primary culture of neural cells when exposed to infection with Rocio. Mixed primary cultures (neuron/glia), obtained from the brains of BALB/C lineage isogenic newborns mice were inoculated with ROCV (MOI equal to 2) on the seventh day of culture and confirmation of infection was made by immunocytochemistry (anti-VROC). Viral replication was quantified in infected primary cultures, depending on the infectious period, by viral titer method. Total cellular RNA was extracted and used for detection of cytokines by real time RT-qPCR techniques. The study showed that primary cultures of neural cells is a good experimental model for the study of CNS infections by Rocio flavivirus. ROCV efficiently infected the primary cultured neural cells leading to cytopathic changes from the 2nd day a.i., when it detected the higher viral titer. The ROCV-infected primary culture survived up to 7 days a.i. and quantification of viral load showed a viral replication kinetics compatible with cell death kinetics of culture infected by ROCV. During the first five days a.i. of the primary culture, there was reduction of IFN-α gene expression, IFN-β, IFN-γ and IL-1β, there was no change in TNF-α expression and there was an increase in TGF-β expression in the 1st, 3rd and 5th day a.i.. The findings of this study suggest that ROCV has the ability to downregulate modulators cytokines of antiviral and inflammatory immune responses and, in this experimental model, immunoregulation exerted by TGF-β predominates over the modulation of inflammatory and antiviral immune responses, larger studies are needed to elucidate immunopathology of CNS infection by ROCV.

Mémoire en recherche subventionné par le Conseil de recherche en sciences naturelles et en génie du Canada (CRSNG) / Le génome du virus de l’hépatite C (VHC), membre des Flaviviridae, est constitué d’un ARN monocaténaire linéaire de polarité positive, et contient un seul cadre de lecture ouvert flanqué par deux régions non traduites désignées 5’UTR et 3’UTR. Ces régions contiennent des éléments structurés qui sont importants pour la régulation des processus de traduction et de réplication virale. Mon projet de recherche vise le 3’UTR. Celui-ci a une structure tripartite composée d’une région variable (VR), une région poly (U/UC) et une région X. Notre laboratoire a identifié une séquence VR qui forme une structure duplexe avec une séquence distale située dans le NS5B. Considérant que le gène NS5B code pour la polymérase virale, et que la 3’UTR est impliquée dans la réplication virale, nous postulons que ce duplex pourrait contrôler le niveau de synthèse de l'ARN du VHC. Afin de tester cette hypothèse, nous avons construit des mutants individuels des séquences VR et NS5B du VHC 1b afin d’empêcher la formation du duplex, ainsi qu’un mutant complémentaire aux deux sites permettant la reconstitution du duplex. L’ARN provenant de ces constructions a été synthétisé in vitro et transfecté dans les cellules Huh7.5. Au 9e jour de culture, l’ARN a été extrait des cultures, et la technique RT-qPCR a été ensuite utilisée afin de quantifier et comparer les niveaux d’ARN viral provenant des cultures transfectées avec les mutants versus celles transfectées avec le virus parental. Les résultats obtenus montrent une augmentation de 5.3X et 3.4X, respectivement, entre les niveaux d’ARN viral produits de cultures transfectées avec le virus muté dans les régions 3’UTR-VR et NS5B, comparé au virus parental. Cependant, l’ARN viral obtenu suite à la reconstitution des deux sites complémentaires montre une augmentation de 2.6X. Malgré que la différence entre les niveaux d’ARN des virus mutants ne soit pas statistiquement significative lorsqu’on les compare avec le niveau d’ARN généré par le virus parental, la tendance suggère que la fonction des séquences appariées serait de moduler à la baisse la synthèse de l’ARN viral. Il sera nécessaire de poursuivre davantage ce travail afin de mieux comprendre le rôle de la structure duplexe VR-NS5B sur la réplication du VHC. / The hepatitis C virus (HCV), a member of the Flaviviridae, contains a single (+) strand linear RNA genome which incorporates one long open reading frame flanked by two untranslated regions known as the 5’UTR and 3’UTR. These regions contain structures known to function in the regulation of HCV translation and replication. The 3’UTR is the focus of this research project. Its tripartite structure consists of a variable region (VR), a poly (U/UC) region and the X-tail. Our laboratory recently identified a VR sequence forming a duplex structure with a distal sequence located in the NS5B gene. Because NS5B encodes the viral polymerase, and seeing that the 3’UTR is involved in viral replication, we postulated that this duplex may function in controlling the level of HCV RNA replication. To test this hypothesis, we constructed HCV 1b mutants in the respective VR and NS5B annealing sequences to disrupt complementarity and prevent duplex formation. We also created a mutant with complementary mutations at both sites to reconstitute the duplex. RNA from these constructs was synthesized in vitro and transfected into Huh7.5 cells. Following a 9-day incubation period, RNA from all transfected cultures was harvested and HCV RNA was quantified by RT-qPCR. The data indicate an increase of 5.3X and 3.4X for HCV viral RNA harvested from cultures with disrupted 3’UTR-VR and NS5B, respectively, relative to wild-type HCV 1b, whereas the reconstituted HCV construct yielded a 2.6X increase in viral RNA. While these figures do not reach statistical significance, they suggest that the duplex structure modulates HCV replication downward. Further pursuit of this work is necessary to better elucidate the role of the VR-NS5B duplex structure on HCV replication.

Viruses are entities which are made of a few genes and are reliant on obligate parasitism to propagate. Due to the obligate connection to their hosts, virus evolution is constrained to the type of host. Viruses however do transmit to evolutionary distinct hosts; in these cases, the phylogenetic relationship of the hosts usually are close. In some instances, RNA-viruses have made host jumps between evolutionary distant hosts, such as the host jump from invertebrates to vertebrates, and fungi to arthropod. Partitiviruses are double stranded RNA viruses which mainly infect fungi and plants. The defining characteristic of these double stranded RNA viruses are the double layered capsids which are formed by a single open reading frame (ORF). The capsid proteins form icosahedral virus particles which are in the magnitude of 30-40 nm. Metagenomic studies have discovered partitiviruses originating from an insect in the Odanata family, a finding which contradicts the fungal host specificity of partitiviruses. The finding of the Hubei.PLV 11 thus implies the existence of a partitiviruses containing structural elements in their capsids which could be involved in the infection of arthropods. Thus, this virus could be used as a model for a structural comparison with its fungi infecting relatives with hopes to identify common viral structural factors necessary for the infection of arthropods. For this purpose, the Hubei.PLV ORF was cloned and then transfected into insect Spodoptera frugiperda (Sf-9) cells using a baculovirus expression system, “bac-to-bac” expression system. The FLAG-tagged capsid proteins were expressed by the Sf-9 cells to be approximately 60 kDa. After ultra-centrifugation in a sucrose gradient, some spontaneous assembly into the expected ~40 nm icosahedral virus-like particles were observed using low resolution scanning electron microscopy. The observed particles were also confirmed by a dynamic light scattering experiment (DLS) and a higher resolution cryo-EM microscope. Thus, the bac-to-bac expression system can be used to produce VLPs from this genus of viruses, and this metagenomically derived virus genome. However, for future success in defining a high-resolution model of this virus, it is recommended that the Sf-9 culture volume is sufficiently high for enough particle production which is necessary for a high-resolution map. The other virus, the Southern pygmy squid Flavilike virus (SpSFV) has been suggested to be the oldest relative of the land based flaviviruses. The SpSFV was found to be the most divergent of the flaviviruses, and to infect invertebrates. Solving for the structure of the SpSFV and comparing it to vertebrate infecting flaviviruses could therefore lead to the identification of factors necessary for the adaptation to vertebrates and thus the humoral immunity by flaviviruses. The soluble E-protein was expressed using the bac-to-bac expression system. The protein was indicated to be multiglycosylated and approximately 50 kDa which is in line with other strains in the genus. Affinity chromatography did not elute this protein, likely due to the His-tag not being spatially available. Cation exchange could elute some protein, but not much from the small ~30 mL culture. To conclude, VLP assembly was confirmed by the Hubei.PLV, thus, solving for the structure is a distinct possibility when a larger Sf-9 culture is used to produce the VLPs. For the SpSFV soluble E-protein, the protein is secreted into the supernatant of the Sf-9 cultures, making purification a possibility. For this, a large Sf-9 culture can be used to produce this protein and then purify it with a cat-ion exchange chromatography.

Dans le monde entier, les infections virales causent des problèmes de santé majeurs et récurrents, engendrant de sérieux problèmes socio-économiques. Notamment, les virus de la famille Flaviviridae qui représentent un fardeau considérable sur la santé mondiale et font partie des domaines prioritaires de la virologie médicale selon le rapport 2016 du ‘Global Virus Network’. Bien que le traitement actuel contre le virus de l’hépatite C (VHC) ait un taux de guérison dépassant 98%, d’autres comme le virus de la dengue (DENV) et le virus zika (ZIKV) n’ont pas encore de traitement spécifique autorisé. En prenant avantage de la grande expertise de notre laboratoire dans l’étude du VHC, nous avons utilisé des données d’une étude de biologie des systèmes visant à identifier l’interactome des différentes protéines virales. Les techniques utilisées ont combiné l’immunoprécipitation des protéines virales suivie de l’identification des protéines interacteurs humaines par spectrométrie de masse. Des études de génomique fonctionnelle par ARN interférent (ARNi) ont permis d’étudier l’effet de la diminution de l’expression des protéines identifiées sur la réplication du VHC. Cette étude a conduit à la découverte de l’interactant spécifique 17-bêta-hydroxystéroïde déshydrogénase de type 12 (HSD17B12 ou DHB12) de la protéine virale Core comme facteur cellulaire requis à la réplication du VHC. HSD17B12 est une enzyme cellulaire dont l’activité catalytique est requise pour l’élongation des acides gras à très longue chaîne (VLCFA) lors de la deuxième des quatre réactions du cycle d’élongation. Dans cette étude, nous avons déterminé que les cycles de réplication du VHC, ZIKV et DENV dépendent de l’expression et de l’activité métabolique du facteur cellulaire HSD17B12. Ainsi, nous avons étudié les effets de l’inhibition de l’expression génique par ARNi et de façon pharmacologique sur la réplication de plusieurs flavivirus dans une approche antivirale à large spectre. Nous avons démontré que le silençage de HSD17B12 diminue significativement la réplication virale, l’expression des protéines virales et la production de particules infectieuses de cellules Huh7.5 infectées par la souche JFH1 du VHC. L'analyse de la localisation cellulaire de HSD17B12 dans des ii cellules infectées suggère une colocalisation avec l'ARN double brin (ARNdb) aux sites de réplication virale, ainsi qu’avec la protéine Core (et les gouttelettes lipidiques) aux des sites d’assemblage du virus. Nous avons également observé que le silençage de HSD17B12 réduit considérablement le nombre et la taille des gouttelettes lipidiques. En accord avec ces données, la diminution de l’expression de HSD17B12 par ARNi réduit significativement l’acide oléique et les espèces lipidiques telles que triglycérides et phosphatidyl-éthanolamine dans l'extrait cellulaire total. Ces travaux suggèrent une contribution de la capacité métabolique de HSD17B12 lors de la réplication du VHC. De même, nous avons démontré que le silençage de HSD17B12 réduit significativement les particules infectieuses de cellules infectées par DENV et ZIKV. Ces études supportent le rôle de HSD17B12 dans l’efficacité des processus de la réplication de l'ARN viral et de l’assemblage de particules virales. De plus, l'inhibiteur spécifique de HSD17B12, INH-12, réduit la réplication du VHC à des concentrations pour lesquelles aucune cytotoxicité notable n'est observée. Le traitement avec 20 μM d'INH-12 réduit jusqu'à 1,000 fois les particules infectieuses produite par des cellules Huh-7.5 infectées par DENV et ZIKV lors de plusieurs cycles de réplication, et bloque complètement l'expression des protéines virales. En conclusion, ces travaux ont conduit à une meilleure compréhension du rôle de HSD17B12 lors de la synthèse de VLCFA et de lipides requise à la réplication du VHC, permettant d’explorer l’inhibition de HSD17B12 et de l’élongation d’acides gras à très longue chaîne comme nouvelle approche thérapeutique pour le traitement à large spectre des infections par les virus de la famille Flaviviridae. / Infections with viruses are major recurrent socio-economical and health problems worldwide. These include infections by viruses of the Flaviviridae family, which present a substantial global health burden and are among the priority areas of medical virology according to the Global Virus Network 2016 report. While the current treatment regimens for hepatitis C virus (HCV) infection have cure rates of more than 98%, other important members of Flaviviridae like dengue virus (DENV) and zika virus (ZIKV) have no specific licensed treatments. By taking advantage of the most-studied HCV, which our lab has developed a vast expertise in the last 20 years, we used proteomics data of an HCV interactome study, combining viral protein immunoprecipitation (IP) coupled to tandem mass spectrometry identification (IP-MS/MS) and functional genomics RNAi screening. The study uncovered the 17-beta-hydroxysteroid dehydrogenase type 12 (HSD17B12, also named DHB12), as a specific host interactor of core that promotes HCV replication. HSD17B12 catalytic activity is involved in the synthesis of very-long-chain fatty acids (VLCFA) upon the second step of the elongation cycle. In this study, taking HCV as a virus model, we elucidated the dependency of HCV, dengue virus (DENV) and zika virus (ZIKV) replication on expression and metabolic capacity of the host factor HSD17B12. We investigated the effects of the inhibition of gene expression by RNAi and of its pharmacological enzymatic inhibition on flavivirus replication in a broad-spectrum antiviral approach. We showed that silencing expression of HSD17B12 decreases viral replication, viral proteins and iv infectious particle production of the JFH1 strain of HCV in Huh7.5 cells. The cellular localization analysis of HSD17B12 showed a co-staining with double-stranded RNA (dsRNA) at viral replication sites and with core protein (and lipid droplets) at virus assembly sites. Furthermore, HSD17B12 gene silencing drastically reduced the number and size of lipid droplets. In association, the reduced expression of HSD17B12 by RNAi decreases oleic acid levels and lipids such as triglycerides (TG) and phosphatidylethanolamine (PE) in whole-cell extract. The data suggested the requirement of the metabolic capacity of HSD17B12 for HCV replication. Similarly, we provide evidence that HSD17B12 silencing significantly reduces DENV and ZIKV infectious particles. The studies support a role of HSD17B12 for effective viral RNA replication and particle assembly processes. Moreover, the specific HSD17B12 inhibitor, INH-12, reduces HCV replication at concentrations for which no appreciable cytotoxicity is observed. The treatment of DENV- and ZIKV-infected Huh- 7.5 cells with 20 μM of INH-12 dramatically reduces production of infectious particles by up to 3-log10 in infection assays, and completely block viral protein expression. In conclusion, these studies extends our understanding of the role of HSD17B12 in VLCFA synthesis required for the replication of HCV, allowing to explore the inhibition of HSD17B12 and elongation of VLCFA as a novel therapeutic approach for the treatment of a broad-spectrum of viruses of the Flaviviridae family.