Tez (Tıpta Uzmanlık) - Süleyman Demirel Üniversitesi, Tıp Fakültesi, Tıbbi Mikrobiyoloji Anabilim Dalı, 2007. / Bibliyografya var.

Thesis (M.D.)--University of Hong Kong, 1996. / Includes bibliographical references (leaf 102-116).

Thesis (M.Sc.)--Memorial University of Newfoundland, Faculty of Medicine, 2000. / Typescript. Bibliography: leaves 219-243.

Thesis (M.Med.Sc.)--University of Hong Kong, 2004. / Also available in print.

Thesis (M.D.)--University of Hong Kong, 1996. / Includes bibliographical references (leaf 102-116). Also available in print.

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.

Le virus de l'hépatite C (VHC) est une menace majeure avec plus de 130 millions de personnes infectées chaque année. Il constitue la principale cause de cancer du foie. Le VHC est un virus transmis par le sang soit au cours de consommation de drogue par voie intraveineuse soit lors de transfusions sanguines. Il s'adapte à l'environnement de l'hôte grâce à un taux de mutation élevé qui amoindrit l’efficacité des traitements. Le virus se multiplie rapidement dans l'hôte et crée ainsi une population de virus génétiquement hétérogènes, appelée quasi-espèces, qui peut ainsi répondre aux pressions sélectives liées au traitement. Les traitement antiviraux existants sont des tri-thérapies contenant des peg-interféron, de la ribavirine et des inhibiteurs de la protéine (PI). Les inhibiteurs comme la telaprevir ou la bocéprévir ciblent la région NS3 du génome en bloquant le mécanisme de réplication. Cependant, en raison de la nature dynamique des quasi-espèces, les séquences cibles sont variables et les inhibiteurs conçus pour se lier à une région génomique particulière sont rendus inefficaces.Nous analysons ces populations virales en utilisant les techniques modernes de séquençage et le pyroséquencage profond qui permet l’analyse à grande échelle des données génétiques. La technique “Amplicon Sequencing” permet de cibler des régions particulières du génome viral, comme les régions NS3 ou NS5B qui participent au mécanisme de réplication et qui sont des cibles pour les thérapies antivirales. Par rapport au séquençage Sanger, notre pipeline NGS permet d’appréhender l’hétérogénéité de la population virale au sein d’un hôte. Pour analyser les données NGS, nous avons implémenté un pipeline d’analyse bioinformatique qui a été automatisé avec eHive.Nous étudions des échantillons de VHC de 40 patients traités par trithérapie. Deux sources de cellules virales sont utilisées pour le séquençage: les cellules du plasma et les cellules mononuclées du sang périphérique. L'objectif est de vérifier si une analyse des mutations de la région génomique NS3 peut aider à prédire le résultat du traitement. Nous constatons que des mutations de résistance aux antiviraux se trouvent à la fois chez les individus qui ont répondu et qui n’ont pas répondu au traitement. Nous avons donc recherché d'autres signatures génétiques de l'échec du traitement. Nous constatons que l'hétérogénéité génétique est plus faible chez les individus qui répondent de manière favorable au traitement. Notre conclusion est que l'hétérogénéité virale est un facteur indépendant pour prédire la réponse à un traitement, en plus de la présence de mutations spécifiques dans les régions ciblées par le traitement.Les techniques NGS permettent également d’étudier l'évolution virale au sein d'un seul hôte. En utilisant de multiples temps d'échantillonnage, nous pouvons mesurer les caractéristiques de l'évolution de la population virale. Pour trois patients avec des échantillons viraux couvrant une période de 13 ans, nous avons utilisé la technique “Amplicon Sequencing“ pour les régions NS3 et NS5B. Des infections mixtes comprenant de multiples génotypes sont retrouvées chez deux patients. Nous avons montré qu’il existe de la structure de populations et des lignées divergentes de VHC au sein de chaque patient. Au cours du traitement, l'hétérogénéité génétique et la taille efficace de la population dans la région NS5B augmente fortement après le début du traitement. Ces résultats mettent en évidence un processus de sélection diversifiante suite au traitement qui augmente l'hétérogénéité génétique virale. Nous mettons ainsi en évidence un processus dit de balayage sélectif doux qui est observé pour la première fois chez des patients infectées par des génotypes multiples du virus VHC.Notre analyse NGS montre que l'hétérogénéité génétique du VHC est liée à l'échec ou à la réussite du traitement et que son évolution permet de mieux comprendre la façon dont les virus s'adaptent au traitement. / Hepatitis C virus (HCV) is a major threat to global health, with over 130 million annual infections. HCV is a blood borne virus transmitted primarily via intravenous drug use or hospital transfusions. It infects the liver cells and is the leading cause of liver cancer. It adapts to the host environment with a high mutation rate and can make efficient treatment very difficult. Due to poor replication proofreading, the virus multiplies rapidly in the host and creates a population of viruses which is genetically heterogeneous enough to escape selective pressures. This HCV population called quasispecies is found within and between infected hosts. Current antiviral treatment consists of a triple therapy of peg-Interferon, ribavirin and protein inhibitors (PI). PIs such as telaprevir, boceprevir target the NS3 region of the genome, blocking the replication mechanism. However due to the highly dynamic nature of the quasispecies, the target sequences are variable and PIs designed to bind to a particular genomic region are therefore rendered ineffective.We analyse viral populations of HCV using Next generation Sequencing (NGS) technologies and ultradeep pyrosequencing, which allow for rapid and large scale analysis of genetic data. Amplicon sequencing allows for targeting particular regions of the viral genome, such as the NS3 or NS5B which form a part of the replication mechanism and hence are targets for antiviral therapy. Compared to Sanger sequencing, our NGS pipeline ascertains viral population heterogeneity within a host. We implemented the bioinformatics workflow manually and in eHive as an automated pipeline.We study HCV samples from 40 patients treated with triple therapy. Two sources of the virus, plasma and peripheral blood mononuclear cells are used for sequencing. The main aim is to check if a baseline analysis of the NS3 genomic region can help to predict the outcome of the treatment. We find that antiviral resistance mutations are found in both responders and non-responders to the treatment. Since no correlation exists between observed mutations and failure of tri-therapy, we look for other genetic signatures of treatment failure. We find that genetic heterogeneity, calculated using Shannon’s entropy, is lower in responders. We conclude that the viral heterogeneity can be used as an independent factor to predict response to treatment, more than presence of specific mutations at baseline.NGS also enables large-scale studies of viral evolution within a single host. Using multiple sampling time points, we gain insights about viral evolutionary characteristics of HCV and responses to selective pressures during infection. For three patients with viral samples covering a period of 13 years, we perform amplicon sequencing on the NS3 and NS5B regions. Mixed infections comprising of multiple genotypes are found in two patients. We find considerable population structure and diverging HCV lineages within each patient. Over the course of treatment, genetic heterogeneity and effective population size in the NS5B regions increases sharply after treatment initiation compared to baseline. These results provide evidence of diversifying selection occurring post-treatment, acting on standing genetic variation resulting in high genetic heterogeneity. These are characteristics of a soft selective sweep, which is observed for the first time in chronic HCV patients infected with multiple genotypes.Our NGS analysis show that genetic heterogeneity in HCV is related to treatment failure and that its evolution provides insights about how viruses adapt to treatment.

BACKGROUND: Rapid advances in the treatment of the hepatitis C virus (HCV) have been witnessed in clinical practice over the last five years. Pharmacological developments have ended the reliance on the drug interferon-α as a component of successful therapy, heralding the dawn of a new era in the fight against the disease. How this new era is being understood and experienced by those individuals living with the virus is currently unknown. METHODS: A purposive sample of 20 individuals participated in face-to-face semi-structured interviews exploring their experience of living with HCV. Eight of these participants were interviewed again following a period of interferon-free treatment. All interviews were conducted between June 2015 and March 2016. The interviews were transcribed verbatim and explored using thematic analysis, underpinned by social phenomenological theory. RESULTS: Analysis of the corpus of data resulted in three overarching themes entitled ‘positioning HCV', ‘beyond a physical burden' and ‘reconstructing uncertainty'. These themes offer original insight into how this new era of therapy is being realised by those living with the virus. The experience of interferon-free treatment was also explored through the narratives of those individuals who participated in a further post-treatment interview. Three further themes entitled ‘expectations and realisations', ‘an honour and a pleasure' and ‘treatment needs' encapsulate their experience. DISCUSSION: The findings from this study recontextualise the lived experience of HCV within a new era of treatment. In doing so, they expose social and emotional spheres of illness, and a perception of illness chronicity, which remain untouched by the treatment revolution. Further, this work emphasises how treatment inequalities fundamentally underpin multiple aspects of the daily lived experience, and are integral to how those living with HCV articulate the disease. The implications of this work challenge current HCV policy and clinical practice.

Objetivos: Estimar a prevalência de anticorpos contra hepatite A (anti-HAV) em grupo de crianças e adolescentes de laboratório público e privado em Porto Alegre e comparar com estudo realizado na década anterior. Métodos: Entre 2007 e 2008 foi realizado estudo transversal onde foram incluídas, consecutivamente, 465 amostras de soros de crianças e adolescentes entre 1 e 19 anos de idade para determinar a prevalência de anticorpos anti-HAV total. As amostras foram fornecidas por laboratório público (Grupo 1), que atende somente Sistema Único de Saúde, e por laboratório privado (Grupo 2), representando os estratos socioeconômicos mais baixo e mais alto, respectivamente. O teste foi realizado em único laboratório (eletroquimioluminescência - Roche Diagnostics). Resultados > 20 UI/L foram considerados positivos. Resultados: A soroprevalência de anti-HAV no grupo 1 foi de 37,6% e o percentual de positividade aumentou conforme a idade, variando de 19,4% entre 1-4 anos a 54,1% entre 15- 19 anos. No grupo 2, a frequência de anti-HAV foi de 46,1% e foi inversamente relacionada à idade, caindo de cerca de 50,0% nas faixas etárias menores para 29,1% aos 15-19 anos. Houve diminuição significativa na prevalência do anti-HAV nas crianças de 5-9 anos do grupo 1 (P=0,03), quando comparadas com estudo realizado na década de 1990. Conclusões: Os resultados sugerem queda na endemicidade da hepatite A em Porto Alegre na última década e indicam maior suscetibilidade à doença em crianças e adolescentes, principalmente no estrato socioeconômico mais baixo. / Objectives: To estimate the prevalence of anti-hepatitis A virus (anti-HAV) antibodies in serum samples from children and adolescents obtained at two clinical pathology laboratories (one public, one private) in the city of Porto Alegre, state of Rio Grande do Sul, Brazil, and compare findings to those of a study carried out in the 1990s. Methods: In this cross-sectional study conducted between 2007 and 2008, 465 serum samples obtained from children and adolescents (1-19 years) were consecutively tested to determine the prevalence of total anti-HAV antibodies. Samples were provided by a public laboratory (Group 1) that serves the Unified Health System exclusively, meant to represent the lowest socioeconomic strata, and by a private laboratory (Group 2), meant to represent the higher socioeconomic classes. Tests were performed at a single laboratory using commercially available electrochemiluminescence kits. Antibody levels ≥ 20 UI/L were considered positive. Results: The seroprevalence of anti-HAV in Group 1 was 37.6%. The percentage of anti- HAV reactivity increased with age, ranging from 19.4% in the 1-to-4-year group to 54.1% in the 15-to-19-year group. In Group 2, the overall frequency of anti-HAV positivity was 46.1% and was inversely correlated with age, declining from roughly 50% in the youngest age groups to 29.1% in the 15-to-19 group. Comparison of sample findings to those reported in a 1990s study showed a significant reduction in anti-HAV prevalence among 5-to-9-year-olds in Group 1 (p = 0.03). Conclusions: The results suggest that the endemicity of hepatitis A in Porto Alegre has been declining over the past decade, and that children and adolescents, particularly those in the lowest socioeconomic strata, are more susceptible to the disease.

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