Hepatitis C virus (HCV) causes severe illness in millions of people worldwide, but the epidemic strains responsible for most infections arose within the past hundred years and represent only a small part of total HCV diversity. In this thesis I combine laboratory and computational methods to study HCV in Africa. I aim to characterize its current genetic diversity and its historical transmission prior to the global HCV epidemic. In Chapter 2 I begin by screening samples from the Democratic Republic of the Congo (DRC) for HCV and the related human pegivirus. I find high HCV sequence diversity, including a putative new subtype, and find significantly higher HCV prevalence in those born before 1950. Chapter 3 continues this screening, and combines the sequences obtained with those from online databases. Using molcular clock methods I estimate that genotype 4 originated in central Africa around 1733, and that multiple lineages, including subtype 4a which dominates the HCV epidemic in Egypt, have moved to north Africa since ~1850. In Chapter 4 I analyse sequences sampled from an elderly population in Kinshasa to estimate HCV’s transmission history there during the 20th century. The results indicate a rapid increase in HCV transmission between 1950 and 1970 in multiple independent lineages. Possible causes of this increase are discussed. This study population also exhibits high HCV genetic diversity, including the second genotype 7 sample discovered to date. Finally, Chapter 5 uses a range of sequencing techniques, including RNAseq, to characterise two putative HCV recombinants from Cameroon. I confirm that both sequences are recombinants, and generate a full genome sequence for one. I also develop new tools to distinguish between dual infection and recombination in next-generation sequencing data, and discuss how recombination might affect HCV diversity and treatment.

Introduction and methods: Hepatocellular carcinoma (HCC) remains a difficult disease to study even after a decade of genomic analysis. Metabolic and cell-cycle perturbations are known, large changes in tumors that add little to our understanding of the development of tumors, but generate “noise” that obscures potentially important smaller scale expression changes in “driver genes”. Recently, some researchers have suggested that HCC shares pathways involving the master regulators of embryonic development. Here, we investigated the involvement and specificity of developmental genes in HCV-cirrhosis and HCV-HCC. We obtained microarray studies from 30 patients with HCV-cirrhosis and 49 patients with HCV-HCC and compared to 12 normal livers. Differential gene expression is specific to liver development genes: 86 of 202 (43%) genes specific to liver development had differential expression between normal and cirrhotic or HCC samples. Of 60 genes with paralogous function, which are specific to development of other organs and have known associations with other cancer types, none were expressed in either adult normal liver or tumor tissue. Developmental genes are widely differentially expressed in both cirrhosis and early HCC, but not late HCC: 69 liver development genes were differentially expressed in cirrhosis, and 58 of these (84%) were also dysregulated in early HCC. 19/58 (33%) had larger-magnitude changes in cirrhosis and 5 (9%) had larger-magnitude changes in early HCC. 16 (9%) genes were uniquely altered in early tumors, while only 2 genes were uniquely changed in late-stage (T3 and T4) HCC. Together, these results suggest that the involvement of the master regulators of liver development are active in the pre-cancerous cirrhotic liver and in cirrhotic livers with emerging tumors but play a limited role in the transition from early to late stage HCC. Common patterns of coordinated developmental gene expression include: (1) Dysregulation of BMP2 signaling in cirrhosis followed by overexpression of BMP inhibitors in HCC. BMP inhibitor GPC3 was overexpressed in nearly all tumors, while GREM1 was associated specifically with recurrence-free survival after ablation and transplant. (2) Cirrhosis tissues acquire a progenitor-like signature including high expression of Vimentin, EPCAM, and KRT19, and these markers remain over-expressed to a lesser extent in HCC. (3) Hepatocyte proliferation inhibitors (HPI) E-cadherin (CDH1), BMP2, and MST1 were highly expressed in cirrhosis and remained over-expressed in 16 HCC patients who were transplanted with excellent recurrence-free survival (94% survival after 2 years; mean recurrence-free survival = 5.6 yrs), while loss in early HCC was associated with early recurrence and (2 year). Loss of HPI overexpression was also correlated with overexpression of c-MET and loss of STAT3, LAMA2, FGFR2, CITED2, KIT, SMAD7, GATA6, ERBB2, and NOTCH2.

Infection with the hepatitis C virus (HCV) has a big impact on global health. It is estimated that approximately 3 % of the world’s population carry HCV, putting more than 200 million people at risk of developing severe liver disease, including chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. The HCV encoded viroporin p7 forms ion channels that are crucial for the assembly and secretion of infectious viruses, making it a potential drug target. Its hydrophobic nature makes p7 notoriously difficult to investigate in an untagged native form. A previously determined 16 Å electron microscopy single-particle reconstruction in detergent showed a hexameric, flower-shaped p7 protein. In conjunction with one hexameric and several monomeric p7 solution state NMR structures published, this constitutes the currently available structural information framework. An E. coli expression system is introduced, which is especially adapted to express isotopically labeled p7. For the first time, suitable solution-state NMR conditions at physiological pH and temperature were identified that gave rise to high quality spectra suitable to interrogate iminosugar drug interactions with untagged isotopically labeled J4 p7 (C27S) solubilised in detergent. A novel secondary structure topology was observed and preliminary iminosugar binding sites were determined. Further, a DIB (droplet interface bilayer) system to analyse p7 ion channel function was established, which is suitable to elucidate how inhibitors act on p7 genotypes and how different lipids influence the ion channel function of p7. The p7 oligomeric state was further investigated using native gel analysis, showing that isolates representing HCV genotypes 1 - 6 form oligomeric complexes. An ion channel defective dibasic mutant implicated in severely compromising viral fitness is also shown for the first time to form an oligomer, implicating that it is not an assembly problem that leads to the abrogated function.

Complex patterns of HCV infection are increasingly reported, particularly in highly exposed individuals, with multiple and variable subtype profiles seen in many chronic patients. This study aims to address some of the questions arising from this increasingly diverse and dynamic picture, both within hosts and at a population level. In Chapter 2 I find evidence for a highly dynamic infection profile in acute HCV, both in terms of viral load and the dominant subtype. I extrapolate these observations from individual patients to formulate a model of HCV transmission across a high-risk population in order to predict the impact of current and anticipated interventions in Chapters 3 and 4. I show that antiviral therapy and a putative vaccination can still have a significant impact on HCV prevalence at the population level, even when the latter offers only partial protection and in the epidemiological background of ongoing exposure. Thus, in an epidemic with more than one circulating strain it will be crucial for any individual or combination of interventions to target all variants present. In Chapter 5 I demonstrate that early viral load kinetics of patients initiating treatment are indicative of treatment outcome. Strain differences are also evident in the virologic response to treatment with hard-to-treat genotype 1 exhibiting a slower rate of viral load decline than genotypes 2 and 3.

Die Infektion mit dem Hepatitis C Virus (HCV) gilt als eine der Hauptursachen für chronische Hepatitiden und führt häufig zu Leberzirrhose und Leberkarzinom. Weltweit sind etwa 200 Millionen Menschen mit diesem Virus infiziert. Die aktuelle Behandlung der Hepatitis C mit Ribavirin und Interferon-alpha ist langwierig, beeinträchtigt durch Nebenwirkungen und führt nur bei einem Teil der Patienten zur Heilung. Aus diesem Grund ist die Entwicklung eines präventiv oder therapeutisch einsetzbaren Impfstoffes gegen HCV-Infektionen sehr wünschenswert. Das hoch attenuierte und in seiner Vermehrungsfähigkeit extrem eingeschränkte modifizierte Vakziniavirus Ankara (MVA) gehört zu den viel versprechendsten Kandidaten für die Entwicklung neuartiger rekombinanter Virusimpfstoffe. Im Rahmen dieser Arbeit sollten erste rekombinante MVA-HCV-Viren auf ihre Eignung als Impfstoffe untersucht werden. Als Zielantigene dienten wichtige virale Strukturproteine, darunter das unter den HCV-Genotypen hoch konservierte Nukleokapsidprotein Core, sowie das Nichtstrukturprotein NS3, welches als regulatorisches Virusprotein im HCV-Replikationszyklus eine wichtige Rolle spielt, untersucht werden. Hierfür wurden die rekombinanten MVA-Viren MVA-P7.5-HCV core (MVA-core) und MVA P7.5-HCV-1-830 (MVA-1-830) eingesetzt, welche für die HCV-Strukturproteine codierende Gensequenzen unter der Kontrolle des Vakziniavirus-spezifischen Promotors P7.5 exprimieren. Zusätzlich wurde ein weiteres rekombinantes Virus MVA-P7.5-HCV-NS3 (MVA-NS3) konstruiert, welches die Gensequenz für das HCV-Nichtstrukturprotein NS3 trägt. Alle Vektorviren erwiesen sich in in vitro Experimenten als genetisch stabil, erlaubten die Produktion der rekombinanten HCV-Antigene in infizierten Zielzellen und waren somit geeignet für in vivo Untersuchungen im Mausmodell. Da HCV-spezifischen CD8+-T-Zellantworten eine wichtige Rolle bei der Ausheilung einer Hepatitis C zugeschrieben wird, sollte insbesondere die Anregung dieser Immunantworten untersucht werden. Dabei zeigte sich, dass bereits eine einmalige Immunisierung mit MVA-core, MVA-1-830 oder MVA-NS3 ausreichend ist, um HCV-spezifische CD8+-T-Zellantworten zu induzieren. Diese CD8+-T-Lymphozyten konnten ex vivo in Epitop-spezifischer Weise zur Interferon-gamma-Synthese stimuliert werden, ließen sich Antigen-spezifisch in vitro expandieren und waren in der Lage, HCV-spezifische Zielzellen zu erkennen und zu lysieren. Zudem konnte eine Steigerung der Immunantworten durch Mehrfachapplikation der MVA-Vakzinen erzielt werden. Im Folgenden gelang es, die HCV-spezifischen CD8+-T-Zellantworten durch kombinierte Applikation der MVA-Vakzinen mit anderen rekombinanten Virusimpfstoffen wie Semliki-Forest-Viren oder Adenoviren, sowie mit Plasmid-DNA weiter zu verstärken. Solche Impfstrategien sind viel versprechend, da sich die gemeinsame Komponente der eingesetzten, unterschiedlichen Vektorvakzinen auf die rekombinanten Antigene beschränkt und eine starke Immunreaktion auf diese Antigene angeregt wird. Die in dieser Arbeit gewonnenen Erkenntnisse erlauben die Schlussfolgerung, dass rekombinante MVA-Vektoren, die HCV-spezifische Antigene produzieren, dafür geeignet sind, um nach Impfapplikation HCV-spezifische zelluläre Immunantworten zu induzieren. Die im Tiermodell erarbeiteten, optimierten Immunisierungsstrategien liefern eine erste Grundlage für weitere Immunisierungsexperimente in Primatenmodellen und zur Planung erster klinischer Studien im Menschen. / Infections with hepatitis C virus (HCV) are considered as one of the main causes for chronic hepatitis and often lead to liver cirrhosis and hepatocellular carcinoma. About 200 million people worldwide are chronically infected with this virus. The current antiviral therapy relying on ribavirin and interferon-alpha is time consuming, often impaired by side effects and leads to resolution of the disease in only a part of the patients. For this reason, the development of a prophylactic or therapeutic vaccine against HCV infections is very desirable. The highly attenuated and replication deficient modified vaccinia virus Ankara (MVA) is one of the most promising candidates for development of new generation virus vaccines. Purpose of this work was to evaluate first recombinant MVA HCV viruses for their suitability as vaccines against hepatitis C. HCV structural proteins, amongst them the highly conserved core protein, as well as the non-structural protein NS3, which plays a key regulatory role in the HCV replication cycle, served as target antigens for MVA vaccine development. First, we investigated recombinant MVA viruses MVA-P7.5-HCV-core (MVA-core) and MVA-P7.5-HCV-1-830 (MVA-1-830), which express the coding gene sequences for HCV structural proteins under control of the vaccinia virus specific promoter P7.5. Second, we constructed and characterized a recombinant virus MVA-P7.5-HCV-NS3 (MVA-NS3) that carries the gene sequence for the HCV non-structural protein NS3. As demonstrated by in vitro experiments, all vector viruses were genetically stable, permitted the production of recombinant HCV antigens in infected target cells and were thus suitable for in vivo experiments using mouse models. Since HCV specific CD8+ T cell responses are considered important in hepatitis C virus clearance, special emphasis was given to the analysis of induction of this kind of immune response. When tested in first vaccination experiments, already a single immunization with MVA-core, MVA-1-830 or MVA-NS3 was sufficient to induce HCV specific CD8+ T cell responses. These CD8+ T lymphocytes could be stimulated ex vivo in an epitope specific manner, resulting in interferon-gamma production, could be further expanded in vitro and were able to recognize and lyse HCV specific target cells. Additionally, multiple applications of the MVA vaccines resulted in an increase of these cellular immune responses. In a final series of experiments, the possibility to further amplify HCV specific CD8+ T cell responses could be demonstrated by using combined applications of MVA with other experimental gene transfer vaccines based on Semliki Forest virus, adenovirus or plasmid DNA. Overall, the results of this work clearly suggest that recombinant MVA vectors delivering HCV specific antigens, are suitable candidate vaccines for induction of HCV specific cellular immune responses upon immunization. Importantly, the definition of optimized immunization strategies offers a rational basis for further immunization studies in primate models and for the conception of first clinical studies in humans.

Infection with hepatitis C virus (HCV) can cause liver damage known as fibrosis, which often leads to liver disease and hepatocellular carcinoma. The impairment of circulating, bulk (non-specific and specific) CD8+ T cells within HCV-infection, characterized by an altered phenotype and the increased expression of pro-apoptotic genes, is observed when compared to uninfected controls. The relationship between bulk CD8+ T cell function and the extent of liver damage has not been demonstrated. In this study, widespread immune alterations were observed in untreated HCV infection with advanced liver fibrosis. Untreated HCV-infected individuals with advanced fibrosis possessed a significantly decreased proportion of naïve CD8+ T cells and an increased proportion of late effector memory CD8+ T cells compared to uninfected controls. Upon T cell receptor (TCR) stimulation, these individuals also had an increased intracellular IFN-γ expression for four CD8+ T cell subsets, a decreased CD107a expression for central memory CD8+ T cells, and a decreased perforin induction for naïve and central memory CD8+ T cells. These immune alterations did not reverse 24 weeks after viral cure. This study indicates there is a relationship between the differentiation and function of bulk CD8+ T cells and the extent of liver damage within HCV infection.

Hepatitis C virus (HCV) infection has become a global public health concern with over 130 million people chronically infected and over 350,000 deaths every year from HCV-related liver diseases. GB virus-B (GBV-B) infection in tamarins is a surrogate model for acute HCV infection. Whilst HCV infection commonly leads to chronicity, GBV-B is naturally cleared. To better understand this natural clearance, this project aimed to study the associated humoral immune response to GBV-B. Additionally, GBV-B-specific antibodies were produced with the aim of characterising the pathology of the virus. Previously, there was no available GBV-B neutralisation assay to identify antibodies in this animal model. Therefore, a GBV-B neutralisation assay, based on a method that is known to be successful for the closely-related HCV, was developed. This method involved producing pseudotyped retroviral particles (PV) expressing the GBV-B envelope that could infect a human hepatocarcinoma cell line. GBV-B PV production was confirmed by western blotting. Future studies can now test archived tamarin sera in this assay for the presence of neutralising antibodies. Neutralising antibodies found through this model could be epitope mapped, and incorporated into HCV vaccine design strategies. To study the pathology of GBV-B infection, GBV-B-specific antibodies were also produced using two techniques in parallel- classical hybridoma technology and ribosome display. Antibodies targeting the nucleocapsid core protein of GBV-B have been previously detected in tamarins and served as the target for production of GBV-B antibodies using both aforementioned technologies. GBV-B core-specific antibodies were successfully isolated using both technologies and can now be used in downstream techniques, such as immunohistochemistry, to characterise the pathology of GBV-B infection thereby further validating the use of the animal model.

Sofosbuvir is a uridine based nucleotide inhibitor of the hepatitis C viral (HCV) polymerase that is the backbone of many treatment regimens. In combination with drugs targeting other viral enzymes (including the poorly potent guanosine analogue ribavirin or highly potent inhibitors of viral NS5A or protease) most patients clear virus and resistance to sofosbuvir is rare, allowing effective retreatment with sofosbuvir. Patients with Genotype 3 HCV respond less well than other genotypes and response is reduced in those previously exposed to interferon. Here we show that patientderived virus from patients with Genotype 3 HCV who relapse to sofosbuvir-based therapies have a reduced sensitivity to SOF in an in-vitro phenotyping assay. Analysis of viral sequencing data revealed two distinct polymorphisms (A150V and K206E) in the HCV polymerase that are associated with treatment failure and in-vitro; they reduce sofosbuvir sensitivity against genotype 3 hepatitis C virions. However both polymorphisms modify the cellular response to type I interferon and in cells lacking response to interferon the impact on sofosbuvir sensitivity is minimal. The A150V polymorphism reduces the response to interferon 70 fold whereas the K206E substitution has minimal effects on interferon in isolation but in combination with A150V reduces the response 100 fold. Preliminary data indicates that the A150V polymorphism interferes with the late response to type I interferons enabling the virus to overcome the induction of interferon-stimulated genes. These data indicate a complex interaction between direct acting antiviral drugs and the innate antiviral response.

No description available.

L’infection par le virus de l’hépatite C (HCV) évolue dans la plupart des cas en hépatite chronique et peut conduire à une cirrhose ou un carcinome hépatocellulaire. Malgré les grandes avancées dans le traitement de l’hépatite C qui permettent d’inhiber ou même de bloquer l’évolution de cette infection vers la chronicité, l’absence de vaccin ainsi que sa répartition sur la surface du globe nous permet de classer cette pathologie en problème majeur de santé publique. La majorité des traitements actuels ciblent les protéines virales et leur fonction. Cependant un grand nombre de mécanismes du cycle viral de HCV reste à élucider.Comme pour la grande majorité des virus à ARN de polarité positive, la réplication de HCV a lieu dans des membranes cellulaires modifiées. Le remaniement de ces membranes est en lien étroit avec la voie de sécrétion précoce de la cellule. Il a été montré que GBF1, un facteur d’échange nucléotidique des protéines G de la famille Arf qui régulent la dynamique membranaire, est un facteur nécessaire à la réplication de HCV. L’inhibition de GBF1 par la bréfeldine A (BFA) inhibe la voie de sécrétion des protéines cellulaires néosynthétisées et inhibe aussi la réplication de HCV. Pour étudier le rôle de GBF1 pendant l’infection nous avons établi des lignées résistantes à la BFA. Deux de ces lignées étaient 100 fois plus résistantes que les lignées parentales à l’apoptose induite par la BFA, à l’inhibition de la sécrétion des protéines et à l’inhibition de l’infection par HCV. Ce phénotype était dû à une mutation ponctuelle dans le domaine catalytique sec7 de GBF1 de ces lignées. Un autre groupe de lignées était partiellement résistantes à l’inhibition de la sécrétion des protéines par la BFA tout en conservant un niveau d’infection proche de celui des lignées parentales dans les mêmes conditions. Ces résultats suggèrent que la fonction de GBF1 pendant l’infection HCV ne serait pas réduite à la régulation de la voie de sécrétion, évoquant ainsi un rôle additionnel de GBF1 nécessaire pour la réplication de HCV.Par ailleurs, nous avons pu montrer à l’aide des mutants de délétion de la protéine GBF1, que l’activité catalytique du domaine sec7 était nécessaire. Ceci suggère l’implication d’une protéine de la famille Arf dans l’activation de l’infection HCV via GBF1. L’implication de Arf dans l’infection HCV a été confirmée par la surexpression de dominants négatifs de la protéine Arf1 et par l’inhibition de l’activité de l’ArfGAP1 (régulateur des Arf) par l’inhibiteur spécifique QS11.Nous avons ensuite testé l’implication des différents Arf sensibles à l’inhibition par la BFA (Arf1, 3 ,4 et 5), dans l’infection HCV à l’aide de si-RNA. Il a été montré que ces protéines Arf possèdent des fonctions redondantes. Nos résultats confirment l’implication de Arf1 et indiquent que les 3 autres protéines sont aussi impliquées dans l’infection HCV. D’une manière intéressante, la déplétion combinée des Arf inhibe fortement l’infection HCV suggérant ainsi un rôle essentiel de certaines protéines Arf, probablement en activant des facteurs cellulaires nécessaires à l’étape de réplication. L’étude des facteurs cellulaires impliqués dans l’infection HCV permet de mieux comprendre l’étape de réplication et par conséquent le cycle viral de HCV. Par ailleurs, l’étude de ces facteurs pourrait permettre le développement éventuel de stratégies antivirales ciblant des facteurs de la cellule hépatique indépendamment du génotype viral, limitant ainsi le risque d’émergence de variants résistants au traitement. / The hepatitis C virus (HCV) infection progresses in most of the cases into a chronic hepatitis and can lead to cirrhosis or hepatocellular carcinoma. Despite the recent improvement of hepatitis C treatments, which inhibit or even block the progress of this infection into a chronic stage, a vaccine still not available and the worldwide distribution of the disease makes the hepatitis C a major public health problem. Most of the available treatments target viral proteins. However many mechanisms of the HCV life cycle remain unclear.As for many positive RNA viruses, HCV replication occurs in reorganized cellular membranes. These membrane rearrangements are closely linked to the early secretory pathway of the cell. It has been shown that GBF1, an exchange factor of small G proteins of the Arf family that regulates the membrane dynamics in the secretory pathway, is required for HCV replication. GBF1 inhibition by brefeldin A (BFA) inhibits the secretion of newly synthesized proteins and also inhibits HCV replication. To investigate the role of GBF1 in HCV infection, we isolated cell lines resistant to BFA. Two of these cell lines were 100 times more resistant than the parental cells to BFA-induced apoptosis, inhibition of proteins secretion and inhibition of HCV infection. This resistance was due to a point mutation in the catalytic sec7 domain of GBF1 of these cells. Another group of resistant cells was showing a partial resistance to the inhibition of proteins secretion while maintaining their sensitivity to the inhibition of HCV infection in the same conditions. These results suggest that GBF1 might fulfill another function, in addition to the regulation of the secretory pathway, during HCV replication. Using GBF1 deletion mutants we showed that the catalytic activity of the sec7 domain of GBF1 is required for HCV infection. This suggests that the function of GBF1 during HCV replication is mediated by Arf activation. The involvement of Arf was confirmed with the overexpression of restricted mutants of Arf1 and by the inhibition of ArfGAP1, another regulator of Arf function. We then tested the possible involvement of different Arfs (Arf1, 3, 4 and 5) in HCV infection. It has been reported that Arfs have redundant functions. The results confirm the involvement of Arf1 and indicate that all the other BFA-sensitive Arfs (Arf3, Arf4 and Arf5) are also involved in HCV infection. The combined knockdown of Arfs strongly inhibited HCV replication, showing that the Arf proteins are working together in HCV replication probably by activating several host factors required for the virus life cycle.The study of cellular factors required for HCV infection is crucial to better understand the interaction of the virus with the host cell and thus the whole HCV life cycle. This could help to develop new therapies targeting the host cell, regardless of viral genotypes and reducing the risk of emergence of new resistant forms.