La particularité de ce virus de l'hépatite B est la synthèse d'un ADN circulaire clos covalent (ADNccc) qui est la forme de persistance du virus dans la cellule. Cet ADN est maintenu à une copie par cellule en moyenne chez l'homme grâce à un recyclage des nucléocapsides dans le noyau. En effet, durant le cycle viral, les nucléocapsides sont soit redirigées dans le noyau pour former de l'ADNccc, soit enveloppées puis sécrétées pour former de nouveaux virions. Du fait de son maintien au sein de l'hépatocyte, la formation et la régulation de l'ADNccc restent des éléments clés du traitement antiviral. Il a été montré in vitro que l'accumulation de cet ADN était régulée par les protéines d'enveloppe. Lors de l'étude du taux d'ADNccc dans des biopsies de foie de patients coinfectés HIV-HBV chronique, il a été découvert un patient présentant 300 fois plus d'ADNccc intrahépatique que la moyenne de la cohorte. L'objectif de ma thèse a été de comprendre quel était le mécanisme conduisant à cette accumulation d'ADNccc in vivo. Cela nous a permis de mettre en évidence le rôle du gène core dans l'accumulation de l'ADNccc / The feature of hepatitis B virus is the synthesis of a covalently closed circular DNA (cccDNA) which is the persistence form of the virus in cell. cccDNA is maintained to 1 copy per human cell thanks to the recycling of capsids into the nucleus. Indeed, during the viral cycle, capsids are either transported into the nucleus to form cccDNA or enveloped and secreted to form new infectious virions. Because of its maintenance in the hepatocyte, cccDNA formation and regulation are still key elements of antiviral treatment. It has been shown that, in vitro, cccDNA accumulation was regulated by envelope proteins. Upon the study of cccDNA levels in liver biopsies of HIV-HBV co-infected patients, an individual with a cccDNA level 300 fold higher than the average of the cohort was identified. My thesis objective was to understand which is the mechanism leading to the cccDNA accumulation observed in vivo. This allowed us to highlight the role of core gene in cccDNA accumulation

Le virus de l’hépatite B (VHB) est un virus du foie qui cause 1 à 2 millions de morts chaque année. Approximativement 400 millions d’individus sont infectés chroniquement. Le VHB est un virus enveloppé et comprend un génome ADN de ~3.2 kbp au sein d’une capside icosaédrique. La capside est formée de 240 copies d’une protéine unique appelée Core ou protéine de la capside. Durant l’infection, la capside est importée dans le noyau pour libérer le génome viral. L’import est facilité au travers du complexe du pore nucléaire (NPC) en utilisant des récepteurs de transport nucléaire. Des biopsies réalisées sur des patients infectés par le VHB ont montrées que les capsides nucléaires sont issues de l’entrée nucléaire mais aussi de protéines Core nouvellement traduites.Ce travail analyse l’import nucléaire de la capside du VHB et la libération du génome viral. Nous avons montré que les imports des protéines Core et de la capside suivent des systèmes d’import différents. Il a été démontré à partir de tests d’import nucléaire basés sur des cellules perméabilisées par la digitonine que les capsides utilisent l’hétérodimère des importines α et β. Cette découverte est en accord avec de précédentes observations qui ont également démontrées l’exposition de NLS à la surface de la capside, sur lequel s’attache l’importine α. Des expériences de contrôle utilisant le GST-NLS ont permis de démontrer que la fixation du NLS sur l’importine nécessite une interaction avec l’importine  pour la stabilisation du complex de l’import. En analysant l’import nucléaire de la protéine Core non assemblée, nous avons pu observer un import basé uniquement sur l’interaction avec l’importine β, ce qui implique que la protéine Core présente un domaine IBB et non un NLS. Le transport a travers le NPC se termine par l’arrivée des capsides dans le panier nucléaire, qui est une structure en cage, du côté nucléaire. En accord avec la littérature, nous avons observé une liaison de l’importine β sur le domaine C-terminal de la Nup153. L’ajout de RanGTP, qui dissocie les complexes d’import, ne dissocie pas l’importine β de ce domaine, ce qui permet d’émettre l’hypothèse qu’un autre domaine de la Nup153 est impliqué. Contrairement aux autres cargos, la capside du VHB est stoppée dans le panier nucléaire par sont interaction avec la Nup153. Puisque le domaine de liaison de l’importine β chevauche celui de la capside, l’importine β doit se dissocier de la Nup153. L’interaction capside-Nup153 est supposée déstabiliser la capside et permettre la libération du génome viral dans le noyau et la diffusion des protéines Core en supériorité numérique par rapport à la Nup153.En conséquence, les capsides montrent une instabilité, comme nous l’avons démontré par chromatographie d’exclusion de taille, révélant non seulement la capside mais aussi ses intermédiaires d’association/dissociation. Ces expériences sont limitées aux capsides recombinantes car elles nécessitent une grande quantité d’échantillons. Dans le but de confirmer l’instabilité des autres capsides (matures et immatures), nous avons analysé l’accessibilité des acides nucléiques encapsidés pour la nucléase S7. Les résultats ont confirmé une dissociation in vitro partielle pour toutes les capsides, mais avec une cinétique lente, ce qui n’est pas cohérent avec la réaction in vivo. En analysant l’impact de la Nup153 sur cette accessibilité, nous observons qu’un facteur nucléaire supplémentaire, présent du moins dans les cellules hépatiques, accélère la cinétique de dissociation. / The hepatitis B virus (HBV) is a hepatotropic virus which causes 1 to 2 million of death every year. Approximately 400 million individuals are chronically infected. HBV is enveloped and comprises a DNA genome of ~3.2 kbp within an icosaedral capsid. The capsid is formed by 240 copies of one single protein species termed core or capsid protein. During the infection, the capsid is imported to the nucleus in order to release the viral genome. The import is facilitated through the nuclear pore complex (NPC) using nuclear transport receptors. Biopsies of HBV-infected patients show nuclear capsids, which are derived from nuclear entry of the capsid but also from nuclear import of progeny core proteins.This work investigates the nuclear import of the HBV capsid and the release of the viral genome. We showed that the imports of core protein and capsid follow different pathways. Capsids were shown to use the heterodimer of importin α and β for nuclear import as it was demonstrated by nuclear import essay, based on digitonin-permeabilised cells. This finding is consistent with earlier observations, which also demonstrated the exposure of NLS on the capsid surface, to which importin  attaches. Control experiments using GST-NLS demonstrated that binding of the NLS to importin  required interaction with importin  for stabilization of the import complex. Analysing the nuclear import of the unassembled core protein we observed an import based on interaction with only importin β implying that the core protein expose an importin -binding domain rather than an NLS.The transport through the NPC is terminated with the arrival of a cargo capsid in the nuclear basket, which is a cage like structure at the nuclear side of the NPC. Consistent with the literature we observed an attachment of importin  to the C terminal domain of Nup153. Addition of RanGTP, which dissociates import complexes, did not dissociate importin  from this domain, which led to the hypothesis that other Nup153 domains are involved. In contrast to other karyophilic cargos HBV capsids become arrested within the nuclear basket by capsid-Nup153 interaction. As the binding site of importin overlaps with the binding site of the capsid such importin -Nup153 interaction has to be dissociated. The subsequent capsid-Nup153 interaction was thought to destabilize the capsid allowing liberation of the viral genome into the nuclear and the diffusion of core proteins, supernumerous with regard to the Nup153 molecules, deeper into the nucleus. Accordingly, capsids show an imminent instability as we demonstrated by separation of capsids using size exclusion chromatography revealing not only capsids but assembly/disassembly intermediates. These experiments were limited to recombinant, E. coli-expressed due to the high amounts needed. To confirm the instability of other capsids e.g. genome-containing ones, we analyzed the accessibility of the capsid enclosed nucleic acids to the S7 nuclease. The results confirmed partial dissociation in vitro similar for all capsids but with a slow kinetic, which is not coherent with the in vivo reaction. Investigating the impact of Nup153 we observed that an additional nuclear factor, present in at least hepatoma cells accelerates the dissociation kinetic.

Le virus de l’hépatite B (VHB) utilise la machinerie transcriptionnelle nucléaire pour sa réplication. Le génome viral est transporté de la périphérie cellulaire à l’enveloppe nucléaire. Généralement, ce transport intracytoplasmique rétrograde est facilité par le réseau de Mt via l’utilisation du complexe moteur de la dynéine. Nous avons montré que le transport des capsides du VHB dépend des Mt, ce qui permet l’adressage des capsides aux complexes du pore nucléaire (NPC) ; lequel est requis pour l’étape de libération du génome de la capside dans le noyau.Dans cette étude, nous avons utilisé des capsides provenant de virus récupérés dans du surnageant de HepG2.2.15, qui contiennent le génome mature partiellement double brin (capsides matures), et des capsides exprimées chez E.coli. Ces dernières sont utilisées telles quelles, capsides E.coli contenant de l’ARN, ou bien sont utilisées pour préparer des capsides vides. Après microinjection dans des ovocytes de Xenopus laevis, nous avons observé que les capsides vides et les capsides matures sont transloquées aux NPC avec une cinétique similaire. Les capsides contenant de l’ARN ne sont pas identifiées aux NPCs ce qui implique que le transport des deux autres types de capsides est actif. Cela a été confirmé par la pré-injection d’anticorps anti tubuline qui neutralisent le transport assuré par les Mt.L’attachement spécifique des capsides matures et vides aux Mt a été confirmé en utilisant des Mt polymérisés in vitro, nous avons montré que cette interaction nécessitait des protéines cytosoliques. En utilisant des expériences de coïmmunoprécipitation et de cosédimentation nous avons identifié une chaîne légère de la dynéine (DynLL1 membre de la famille Lc8) comme partenaire des capsides. Dans les expériences de microinjection, la comicroinjection d’un excès de DynLL1 avec les capsides inhibe leur transport vers les NPCs, indiquant que DynLL1 est impliquée dans le transport actif des capsides.DynLL2 qui n’interagit pas avec les capsides diffère de DynLL1 de seulement six acides aminés. Par mutagénèse dirigée de DynLL1, nous avons montré l’implication de deux acides aminés dans l’interaction directe avec les capsides. Ces deux acides aminés sont présents à la surface du dimère de DynLL1 et absents dans le sillon résultant de la dimérisation de DynLL1, sillon impliqué dans l’interaction avec la DynIC. Nous avons partiellement reconstitué le complexe DynIC, DynLL1 et capsides vides qui doit en partie refléter la situation in vivo. / Hepatitis B virus (HBV) needs the nuclear transcription machinery for replication. The virus thus depends on the transport of its genome from the cell periphery to the nuclear envelope. In general this retrograde intracytoplasmic trafficking is facilitated along Mt (MT) using motor protein complexes of the dynein family. As we showed earlier HBV capsid transport also depends upon intact MT in order to allow their arrival at the nuclear pores, which in turn is required for genome liberation from the capsid.In the analysis we used virus-derived HBV capsids obtained from the supernatant of HepG2.2.15, which contain the mature partially double-stranded DNA genome (mature capsids) and capsids expressed in E. coli. The latter were applied in two forms: as unspecific E. coli RNA- containing capsids and as empty capsids. Upon microinjection into Xenopus laevis oocytes we observed that mature and empty capsids were translocated to the nuclear pores with a similar kinetic. RNA-containing capsids failed to arrive at the pores implying that transport of the two other capsid types was active. Active translocation was confirmed by pre-injecting anti tubulin antibodies which interfere with MT-mediated translocation.In vitro reconstitution assays confirmed the specific attachment of mature and empty capsids to MTs and showed the need of further cytosolic proteins. Using pull-down and co-sedimentation experiments we identified one dynein light chain (DYNLL1, member of the Lc8 family) as interaction partner of the capsids. Injecting an excess of recombinant DYNLL1 with empty capsids into Xenopus laevis oocytes inhibited capsid transport to the nuclear pores indicating that DYNLL1 was only functional interaction partner implied in active transport.DNYLL2 did not interact with the capsids although differing from DYNLL1 by just six amino acids. Site directed mutagenesis of DYNLL1 revealed that two amino acids were critical for a direct interaction with the capsids. Both localized at the exterior of the DYNLL1 dimer and not in the groove of DYNLL1, which interacts with the dynein intermediate chain. Accordingly we could reconstitute a complex consisting of empty capsids, DYNLL1 and dynein intermediate chain as it should be in the in vivo situation.

Hepatitis B virus (HBV) is a Hepadnaviridae virus infecting mammals. Its infection can result in an acute or chronic infection. Chronic infection can result in hepatocellular carcinoma and liver cirrhosis, potentially leading to death of the patient. HBV is a small 42 nm virus with a genome length of 3.2 kb encoding seven viral proteins. HBV Core protein (HBc) is a capsid forming protein which is pleiotropic in function. We have identified two ubiquitin ligases which could interact with this protein: F-box only protein 3 (FBXO3; E3 ubiquitin ligase) and Ubiquitin conjugating enzyme E2 O (UBE2O; E2/E3 ubiquitin ligase). By employing multiple methods we have confirmed these interactions. Co- immunoprecipitation and further western blot analysis unveiled multiple new insights into the ligases′ impact on HBc: FBXO3-mediated HBc polyubiquitination stimulation and UBE2O-mediated HBc monoubiquitination promotion. FBXO3's and UBE2O's role in HBV life cycle was investigated as well. By silencing the expression of FBXO3 and UBE2O respectively, we have observed changes in HBV replication levels: FBXO3 serves as an inhibitor of HBV replication, while UBE2O stimulates the course of HBV life cycle. Further investigation of these newly-discovered understandings may lead to a whole new HBV - host interplay...

Hepatitis B Virus (HBV) is a DNA virus and belongs to the genus Orthohepadnavirus of the Hepadnaviridae family which represents one of two animal viruses with a DNA genome which replicates by reverse transcription of a viral RNA intermediate. Nucleotide variation led to further sub-classification into 8 genotypes (A to H). The reverse transcription step within its life cycle is prone to the introduction of errors and recombination when dually infected. This leads to a viral quasispecies which forms during the course of infection with many minor population variants; such variants can however only be detected by means of ultra-deep sequencing. A recent study in the Department of Medical Virology (UP) by Mayaphi et al. identified a number of the specimens that partitioned away from the typical subgenotype A1 clades with high bootstrap values and longer branch lengths. Thus, the main objective of the current study was to characterize the full genome of all variants for the outliers observed in the aforementioned study, inclusive of potential recombination, dual infection and minor populations. Twenty samples were selected from a previous cohort for purposes of the present study. The viral DNA was extracted and amplified by PCR according to the methods described by Günther et al. with modified primer sets. Nineteen of the samples were successfully amplified and 15 of these were sequenced. Specimens were sequenced by NGS on the Illumina MiSeq™ sequencer and sequence data used to reconstruct the viral quasispecies of each specimen. Further analyses of the reconstructed variants included molecular characterization as well as phylogenetic analysis and screening for recombination and drug resistance mutations. Full genome coverage was obtained for twelve of the fifteen samples and full genome variants reconstructed, generating nearly 40 full genomes. Phylogenetic analysis showed that the majority of the samples are of genotype A, more specifically of subgenotype A1, differing by less than 4% from known sequences. The phylogenetic analysis revealed a similar clade of outliers, where four samples clustered together with significant bootstrap support (75%) and a fifth sample partitioned separate from, yet close to, this clade, away from the typical African A1 clade. This clade was assigned to genogroup III. Three samples were of the Asian A1 clade (genogroup I) with remaining specimens grouping within genotype D and E. The variants showed low diversity within each specimen with some differing at but a few positions across the genome while even the most diverse quasispecies differed by less than a percentage (32 positions). Several unique and atypical positional variations were observed amongst study samples of which some were present in but one of the variants for that sample. Twenty-six lead to shared amino acid changes. Some observed changes, such as A1762T/G1764A and G1896A, could explain the serological patterns such as HBeAg negativity while others, such as C2002T, were previously implicated in disease progression and severity. Sample N199 presented a longer branch length and revealed short regions within the genome that display evidence of recombination between HBV/A1 and HBV/A2. The results illustrate the utility of NGS technology in characterizing viral variants. / Dissertation (MSc)--University of Pretoria, 2014. / lk2014 / Medical Virology / MSc / Unrestricted

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and chronic hepatitis B virus (HBV) infection is the major risk factor of HCC. The virus encodes HBV X (HBx) protein that plays a critical role in the development of HCC. Studies have revealed numerous HBx-altered genes and signalling pathways that heavily contribute to tumourigenesis of non-tumour hepatocytes. However, the role of HBx in regulating other critical gene regulators such as microRNAs is poorly understood, which impedes the exploration of a complete HBx-associated carcinogenic network. Besides, critical microRNAs that drive the transformation of non-tumour hepatocytes are yet to be identified. Here, we overexpressed C-terminal truncated HBx protein in a non-tumour hepatocyte cell line MIHA, and measured a panel of cancer-associated miRNAs. We observed that oncogenic miR-21 was upregulated upon ectopic expression of this viral protein variant. HBx-miR-21 pathway was prevalent in HCC cells as inhibition of HBx in Hep3B and PLC/PRF/5 cells significantly suppressed miR-21 expression. Subsequently, we showed that the upregulation of miR-21 was mediated by HBx-induced interleukin-6 pathway followed by activation of STAT3 transcriptional factor. The high dependency of miR-21 expression to HBx protein suggested a unique viral oncogenic pathway that could aberrantly affect a network of gene expression. Importantly, miR-21 was essential in the HBx-induced transformation of non-tumour hepatocytes. Inhibition of miR-21 effectively attenuated anchorage-independent colony formation and subcutaneous tumour growth of MIHA cells. Our study suggested that overexpression of miR-21 was critical to promote early carcinogenesis of hepatocytes upon HBV infection.

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Hepatitis B virus (HBV) represents one of the hot topics of current basic and pharmaceutical research. Although an effective vaccine against HBV exists since 1982, the world prevalence of chronic infection is still alarming. The infection can lead to significant liver damage, often resulting in hepatocellular carcinoma. Chronic HBV infection cannot be cured due to the fact that the viral genome persists in the infected hepatocyte hidden from the host immune response as well as from the antiviral treatment. One of the novel approaches aiming for HBV cure suggests that this cccDNA pool could be destroyed using gene editing tools such as CRISPR/Cas9 system. In order to shift this gene editing system to possible medicinal application, CRISPR/Cas9 has to be specifically delivered into the target cell in order to minimize its putative off-target activity. This thesis focuses at first on the design and efficacy testing of new sgRNAs targeting HBV cccDNA and secondly, it describes modular lipid nanoparticles developed specially for delivery of the CRISPR/Cas9 system in the form of RNA. Keywords: hepatitis B virus, CRISPR/Cas9, gene editing, lipid nanoparticles, mRNA delivery, targeted delivery

Porcine epidemic diarrhea Virus (PEDV) is a virus effecting swine. It is the cause of disease that manifests with symptoms ranging from depression, to severe dehydration and death. Young piglets are particularly susceptible to the virus, which can reach mortality rates of 100%. Presence of the virus on a swine farm can therefore cause severe economic losses. Treatments currently exist for PEDV, but are mostly generated from the virus itself. There has recently been renewed interest in a vaccine that is made from a different source, which might help eliminate some of the side effects of those that currently exist on the market. This project outlines three experiments performed in animals. During the first experiment, a structural protein from the Hepatitis B virus was genetically altered to include important structural portions of PEDV. This new protein is generated in E. coli and purified. After purification, the protein assembles into a virus-like particle (VLP). VLPs are structural proteins of existing viruses that are expressed and assembled to mimic the virus. By doing so, the immune system recognizes the protein as a potential threat, and launches a response in the form of antibodies. Manipulations of the VLPs as describe herein allow the new vaccine to generate antibodies toward other diseases such as PEDV. Although all five of the vaccines used in the first experiment were able to generate appropriate antibodies, only two of them were effective at preventing PEDV from entering susceptible cells (virus neutralization). A second experiment, with three newly designed vaccines was therefore performed. This experiment, like the first, was successful in producing antibodies to several of the included PEDV protein sections, but none were able to neutralize the virus. These results led to a third experiment, during which further design improvements were made to the basic vaccine structure in an attempt to increase the neutralization capabilities of the vaccines. The results from the third experiment indicated that several changes to the vaccine increased the immune response to the structural portions of PEDV, providing a better overall vaccine candidate. This also led to the conclusion that one specific sequence from PEDV has a better ability to neutralize the virus than the other sections. / PHD