Hepatitis C virus (HCV) is a leading cause of chronic liver disease. In the developed world, injection drug use (IDU) through sharing of infected needles and other paraphernalia remains the principal risk factor for HCV transmission. Effective but expensive treatment is now possible but there remains a pressing need for a vaccine. A proportion of people who inject drugs (PWIDs) remain uninfected despite HCV exposure from a long history of sharing needles and other paraphernalia. These cases are termed exposed but uninfected (EU) and test negative for both HCV antibodies and RNA and exhibit a phenotype of resistance to HCV infection. Improved understanding of the mechanisms that confer resistance in the EUs has the potential to aid development of an effective vaccine and novel therapeutic strategies. This thesis reports on the findings from 3 different strategies to identify characteristics of HCV resistance. I used urinary metabolomics, serum lipidomics and the study of adaptive and innate immune responses. Each of these methods has demonstrated clear differences between EU cases and healthy controls and/or spontaneous resolvers of HCV infection. Urinary metabolomics suggest a potential role of the gut microbiome, the serum lipidomics showed marked differences in lipid profiles in EU cases pointing towards a perturbed lipid/virus interaction, and the immune studies confirmed previous work identifying low level T cell responses in many EU cases but has also identified a marked upregulation of interferon alpha production to low dose viral RNA in EU cases utilising ELISA assay. In conclusion, this thesis reports data that identifies a number of new findings that provide insight into mechanisms of resistance to HCV infection. My findings suggest that the complex interplay between the virus and lipids together with an upregulated innate immune response may together help determine the outcome following HCV exposure. In summary, studies performed in this thesis have demonstrated that there are different pathways that define the EU phenotype. Despite being a heterogenous subgroup of PWIDs, the EUs are clearly distinct from a healthy control population.

Lors d’une infection chronique, le virus de l'hépatite C (HCV) circule sous forme de lipoviroparticule (LVP) : particules hybrides associant des composants viraux (ARN, les protéines structurelles) et des composants cellulaires (apolipoprotéines, cholestérol). Au cours de ma thèse, nous nous sommes intéressés à identifier la plateforme d'assemblage du HCV, et le rôle du rassemblement des protéines virales par NS2 dans sa formation. Nous avons montré que des interactions de natures différentes sur la membrane du RE sont impliquées dans cette association protéique. Nos résultats suggèrent que des interactions complexes (directes ou via des « membranes résistantes aux détergents » (DRM)) entre les protéines complexées par NS2, peuvent immédiatement précéder la formation LVP. Nous avons également démontré que l’hétérodimère E1E2, les apolipoprotéines B et E (ApoB, ApoE) s’associent en un complexe de protéines dans le réticulum endoplasmique (RE) lorsqu'elles sont exprimées ensembles. Ce complexe se forme au début de l'assemblage du HCV, quelle que soit l'expression des autres protéines virales, et est conservée sur les LVP sécrétées. Basé sur ces données, nous avons proposé un mécanisme expliquant l’initiation de la morphogenèse des LVP. Ensuite, nous avons évalué l'importance de l'association E1E2/ApoE pour le cycle de vie du virus. Nous avons initié une étude pour identifier les acides aminés E1E2 impliqués dans l'interaction avec les apolipoprotéines. Avec ces données, nous souhaitons proposer une meilleure compréhension des mécanismes de la morphogenèse du HCV. / In chronic infection, the hepatitis C virus (HCV) circulates as lipoviral particles (LVP): hybrid particles associating viral (RNA, structural proteins) and cellular components (apolipoproteins, cholesterol). During my PhD, we were interested in identifying the HCV assembly platform, and the role of the association of the viral proteins by NS2 during its formation. We showed that different natures of interactions on the ER membrane are involved in this proteic association. Our results suggest that a complex interplay between proteins of the complex formed by NS2, directly or through “detergent resistant membranes” (DRMs) may be immediately followed by LVPs formation. We also demonstrated that E1E2 heterodimer, apolipoproteins B and E (ApoB, ApoE) associate as a protein complex in the endoplasmic reticulum (ER) when expressed together. This complex is formed early in HCV assembly, regardless the expression of other viral proteins, and is conserved on the secreted LVPs. Based on these data, we proposed a mechanism explaining LVP morphogenesis initiation. Then we assessed the importance of E1E2/ApoE association for viral life cycle. We initiate a study to identify the E1E2 amino acids involved in the interaction with apolipoproteins. With these data, we wished to provide a better understanding of the mechanisms of the HCV morphogenesis.