Student Number : 9903144J - MSc (Med) dissertation - Faculty of Health Sciences / Since the introduction of vaccination against hepatitis B virus (HBV) infection in South Africa, at least one case of infection despite vaccination has occurred. The purpose of this study was to determine whether this infection was the result of mutations within the region of the surface (S) gene encoding the a determinant epitopes of the hepatitis B surface antigen, which permitted viral vaccine-escape. HBV DNA was extracted from the serum and liver tissue of the patient and amplified within the complete 3 215 bp genome and S gene, respectively. Following cloning, sequencing revealed a minor population displaying unique or uncommon S gene mutations that resulted in C138R, C139R, K141R, P142L, T143A, N146D, and T148A amino acid substitutions in the clones from the serum, and C139Y and D144N in the clones from the liver. Such isolates may represent South African HBV vaccine-escape mutants that caused chronic infection in the host prior to their reversion to wild-type.

An existing mathematical model of ordinary differential equations was studied to better understand the interactions between hepatitis C virus (HCV) and the immune system cells in the human body. Three possible qualitative scenarios were explored: dominant CTL response, dominant antibody response, and coexistence. Additionally, a sensitivity analysis was carried out to rank model parameters for each of these scenarios. Therapy was addressed as an optimal control problem. Numerical solutions of optimal controls were computed using a forward-backward sweep scheme for each scenario. Model parameters were estimated using ordinary least squares fitting from longitudinal data (serum HCV RNA measurements) given in reported literature.

Hepatitis B virus chronically infects 350-400 million people worldwide. It often leads to hepatocellular carcinoma, which causes >1 million deaths yearly. Current therapies prevent new viral genome formation but do not target pre-existing viral genomic DNA, thus curing only ~1/2 of patients. We targeted hepatitis B virus DNA for cleavage using zinc finger nucleases, which cleave as dimers. Co-transfection of our zinc finger nuclease pair with a target plasmid containing the hepatitis B virus genome resulted in specific cleavage. After three days in culture, 26% of the target remained linear, while ~10% was cleaved and mis-joined tail-to-tail. A portion of cleaved plasmids are repaired in cells, often with deletions and insertions. To track misrepair, we introduced an XbaI restriction site in the spacer between the zinc finger nuclease sites. Targeted cleavage and misrepair destroys the XbaI site. After three days in culture, ~6% of plasmids were XbaI resistant. 13 of 16 clones sequenced contained frameshift mutations that would lead to dramatic truncations of the viral core protein. These results demonstrate for the first time the feasibility of targeting episomal viral DNA genomes in cells using zinc finger nucleases. This strategy is broadly applicable toward inactivating other DNA viruses within cells. A major concern for the therapeutic use of zinc finger nucleases is off-target cleavage. To measure specificity, we employed in vitro assays and developed a bioinformatics method to find off-target cleavage sites in cultured cells. These sites can then be PCR amplified and tested using a mutation detection assay that we developed.

Background: The most recent estimate for the number of Australians living with chronic hepatitis B virus (HBV) infection is 150,000, with over one million ever having been infected. One in four people with chronic infection will die as a result. Worldwide, the burden of chronic HBV infection is great. As many as 400 million people are chronically infected, and the World Health Organisation estimates that as a result HBV infection is the tenth leading cause of death. / Aim: The aim of the research presented in this thesis is to improve the accuracy and relevance of our understanding of the epidemiology and control of HBV infection in Australia, through the development of new methodological approaches to the collection and analysis of relevant epidemiological data. / Methods: Three novel approaches were adopted. First, a serosurvey of a randomised, age-structured convenience sample of over 3200 specimens was performed spanning the period from 1995 to 2005 to estimate the prevalence of markers of infection with, and immunity to HBV. Secondly, a comparative analysis of the serosurvey results with national surveillance notifications since 1971 and migration records since 1945 was undertaken. Finally, a complex deterministic mathematical model of HBV infection in Australia was constructed simulating the entire population between 1951 and 2050. / Results: The serosurvey indicates that chronic infection with HBV is more common in the Victorian population than existing national serosurvey estimates suggest, and the coverage of immunisation programs (particularly of adolescents) is far from universal. Significant geographic, age, and gender disparities in the prevalence of chronic HBV infection were identified in the serosurvey, which appear in part to relate to historical migration patterns and which could be used to develop a targeted and effective public health response. The comparative analysis of the serosurvey results with notifications and migration data demonstrates coherence of these disparate sources of information, and suggest that knowledge of migration patterns can lead to robust predictions of future notifications. The novel regression model developed implies that at least 50,000 people with chronic HBV infection are undiagnosed. The mathematical model of HBV infection in the Australian population is unique in many respects, and has been validated against external data to provide reassurance regarding the accuracy of the simulated outcomes. Some of these outcomes include an estimated 160,000 Australians living with chronic HBV infection in 2009, increasing by several thousand people every year, and that less than 5 per cent of chronic infections entering the population are able to be addressed by domestic vaccination or other prevention programs. / Conclusion: The new insights into the epidemiology of HBV infection in Australia provided by the approaches described all suggest a large and increasing burden of chronic HBV infection. New approaches are needed to provide essential policy outcomes to assist and empower Australians living with chronic HBV infection. If this does not occur, the economic and human costs to our community are likely to become great.

<p>Since the discovery in 1989 of hepatitis C virus (HCV) as the infectious agent responsible for the vast majority of post-transfusion non-A non-B hepatitis, blood transfusions are no longer a source for HCV transmission in Sweden. Anti-HCV testing was implemented for all blood donations in 1992. Since then intravenous drug use (IDU) has become the major route of transmission in the western world. Six genotypes and more than 80 subtypes of HCV have now been identified world-wide. These genotypes and subtypes are determined by genetic divergences between the HCV strains. Subtypes 1a, 1b, 2b, 2c, and 3a have global spread, while the other subtypes have a more limited geographical distribution. Little was known on the prevalence of HCV among blood donors and on which genotypes and subtypes of HCV were circulating in Sweden before the testing of all blood donations was implemented. The prevalence of anti-HCV was therefore investigated in sera sent to the Swedish Institute for Infectious Disease Control (SMI) from 412 patients; 241 were sampled between 1970 and 1991 before the universal screening in 1992, while 171 were sampled between 1992 and 2002. The samples derived from 193 (47%) blood donors, (104 sampled before, and 89 after 1992), and from seven other groups of patients. Two groups had suspected known routes of infection, intravenous drug use (IDU) 33 patients and hemodialysis, 16 patients, while it was unknown for the other patients. Anti-HCV was detected in 120 (29%) samples. The highest frequency was found among IDUs, (91%). Before general screening was implemented, 2.8% of the blood donors were positive for hepatitis C, whereas 28% of those sampled after 1992 were anti-HCV positive. Those latter samples were sent to SMI due to anti-HCV reactivity in a primary test at the blood centre. HCV RNA could be detected by PCR in 56 (47%) of the anti-HCV positive samples, the subtype could be determined by sequencing in 45 (80%) of those. The subtypes found were 1a in 31 %, 1b in 18%, 2b in 22%, and 3a in 27%. One sample was of subtype 2c. There was a tendency of increase of genotype 2 and a decrease in subtype 1a with time. 1a was found in 38% of the samples collected before 1992, while it was only found in 19% of the samples from 1992 or later. On the other hand genotype 2 was found in 17% sera sampled before 1992 and in 37% of the samples collected 1992 or later. It is not known if this genotype has recently been introduced into Sweden. Further analysis on larger series of samples is needed to confirm these preliminary results.</p> / AcknowledgmentsI would like to express my gratitude to several people who have been supportive in different ways throughout this project.First of all, I want to thank my supervisor Helene Norder, for giving me the possibility to do my diploma thesis at the Department of Virology, Swedish Institute for Infectious Disease control (SMI) and for helping me during this study and for the many insightful conversations during the design and development stages of the application, and also for the many helpful comments and suggestions on the text of the thesis.I want to express my appreciation to my laboratory supervisor Regina Wallin, Camilla Jern and Josefine Ederth for helping me during the procedure for this study. Then, I want to thank my examiner Magnus Johansson from the Södertörns university collegefor his advice on writing this paper. Finally, I would like to thank my family and specially my mother Bahar Hamid for always supporting me during my whole life.Last, but not least, I would like to thank my friends Annika Andersson and Yourdons Yemane for being encouraging, understanding and always supportive.

Hepatitis C is a blood-borne disease affecting 130-170 million people worldwide. The causative agent, hepatitis C virus (HCV), infects the liver and is the major reason for chronic liver disease worldwide. The HCV NS3 protease, a key enzyme in the virus replication cycle, has been confirmed to be an important target for drug development. With the recent release of two HCV NS3 protease inhibitors onto the market and an arsenal of inhibitors in clinical trials, there are now hopes of finally combating the disease. However, the success of treatment relies heavily on the ability to overcome the emergence of drug-resistant forms of the protease. The main focus of this thesis was on designing and synthesizing novel inhibitors of the NS3 protease with a unique resistance profile. Efforts were also made to decrease the peptide character of the compounds, with the long-term goal of making them into more drug-like compounds. Special attention was devoted to developing inhibitors based on a phenylglycine in the P2 position, instead of the highly optimized and commonly used P2 proline. Around ninety acyclic and macrocyclic inhibitors have been synthesized and biochemically evaluated. P2 pyrimidinyloxy phenylglycine was successfully combined with an aromatic P1 moiety and alkenylic P1´ elongations, yielding a distinct class of HCV NS3 protease inhibitors. Macrocyclization was performed in several directions of the inhibitors via ring-closing metathesis. Only the macrocyclization between the P3-P1´ residues was successful in terms of inhibitory potency, which suggests that the elongated P1-P1´ residue is oriented towards the P3 side chain. The metathesis reaction was found to be significantly more dependent on the substrate than on the reaction conditions. It was also found that the P3 truncated inhibitors were able to retain good inhibitory potency, which initiated the synthesis and evaluation of a series of P2-P1´ inhibitors. The potential of the P3-P1´cyclized inhibitor and the smaller, acyclic P2-P1´ as new potential drug leads remains to be determined through pharmacokinetic profiling. Gratifyingly, all the inhibitors evaluated on A156T and D168V substituted enzyme variants were able to retain inhibitory potency towards these as compared to wild-type inhibition.

Hepatitis delta virus (HDV) is the smallest known human RNA pathogen. It requires the human hepatitis B virus (HBV) for virion production and transmission, and is hence closely associated with HBV in natural infections. HDV RNA encodes only two viral proteins - the small and the large delta antigens. Due to its limited coding capacity, HDV needs to exploit host factors to ensure its propagation. However, few human proteins are known to interact with the HDV RNA genome. The current study has identified several host proteins interacting with an HDV-derived RNA promoter by multiple approaches: mass spectrometry of a UV-crosslinked ribonucleoprotein complex, RNA affinity chromatography, and screening of a library of purified RNA-binding proteins. Co-immunoprecipitation, both in vitro and ex vivo, confirmed the interactions of eEF1A1, p54nrb, PSF, hnRNP-L, GAPDH and ASF/SF2 with both polarities of the HDV RNA genome. In vitro transcription assays suggested a possible involvement of eEF1A1, GAPDH and PSF in HDV replication. At least three of these proteins, eEF1A1, GAPDH and ASF/SF2, have also been shown to associate with potato spindle tuber viroid (PSTVd) RNA. Because HDV’s structure and mechanism of replication share many similarities with viroids, subviral helper-independent plant pathogens, I transfected human hepatocytes with RNA derived from PSTVd. Here, I show that PSTVd RNA can replicate in human hepatocytes. I further demonstrate that a mutant of HDV, lacking the delta antigen coding region (miniHDV), can also replicate in human cells. However, both PSTVd and miniHDV require the function of the small delta antigen for successful replication. Our discovery that HDV and PSTVd RNAs associate with similar RNA-processing pathways and translation machineries during their replication provides new insight into HDV biology and its evolution.

No description available.

The transmission and prevalence of Hepatitis C Virus (HCV) among those who use injection drugs is a major public health issue. Injection drug use has been identified as the main cause of transmission for HCV in Canada. Street youth are at risk for acquiring HCV due to injection drug use that is often a consequence of living in a street environment. Presently, research on prevalence trends, characteristics, and associated behaviors for injection drug use and HCV in street youth, is limited. <p>The purposes of this study were to determine prevalence of injection drug use and HCV in Saskatoon street youth, to identify demographic or other factors that may contribute to street youth using injection drugs, and to identify risk factors and other characteristics of street youth associated with HCV. This study utilized data from Phase III of the Enhanced STD Surveillance in Canadian Street Youth Study by Health Canada for those participants recruited from Saskatoon, Canada. Between February and July 2001, 186 Saskatoon street youth participants between the ages 14 and 24 years completed nurse-administered questionnaires and of these, 156 provided blood specimens. Analyses were conducted to compare population characteristics between street youth who have used injection drugs and those who had not. Similarly, population characteristics were analyzed among those street youth who were antibody-HCV positive and those that were antibody HCV negative.<p>In this study 32.3% of 186 participants had used injection drugs. Significant associations with injection drug use were found for older age (p = 0.01), having sexual partners that use injection drugs (p = 0.01), history of incarceration (p = 0.01), and history of living on the street (p = 0.02). Significant interactions were found for sex trade work by gender (p < 0.01) and by age (p = 0.03), and for living on the street by age (p = 0.02). A HCV prevalence rate of 9.3% of 156 participants was determined for Saskatoon street youth. Use of Ritalin by injection (p = 0.04) and history of living on the street (p = 0.05) were found to be significant risk factors associated with HCV. The interaction of living on the street by gender was also significantly associated with HCV (p = 0.05). <p>The relationship identified between HCV and injection drug use in Saskatoon street youth was a history of living on the street. This link between could serve as a valuable marker for use of injection drugs and developing HCV infection in street youth. Nurses are encouraged to seek out street youth social networks to provide health care and messages of health promotion and disease prevention. Strategies that are culturally, socially, and developmentally appropriate are needed to keep these youth off the streets in the first place.

The transmission and prevalence of Hepatitis C Virus (HCV) among those who use injection drugs is a major public health issue. Injection drug use has been identified as the main cause of transmission for HCV in Canada. Street youth are at risk for acquiring HCV due to injection drug use that is often a consequence of living in a street environment. Presently, research on prevalence trends, characteristics, and associated behaviors for injection drug use and HCV in street youth, is limited. <p>The purposes of this study were to determine prevalence of injection drug use and HCV in Saskatoon street youth, to identify demographic or other factors that may contribute to street youth using injection drugs, and to identify risk factors and other characteristics of street youth associated with HCV. This study utilized data from Phase III of the Enhanced STD Surveillance in Canadian Street Youth Study by Health Canada for those participants recruited from Saskatoon, Canada. Between February and July 2001, 186 Saskatoon street youth participants between the ages 14 and 24 years completed nurse-administered questionnaires and of these, 156 provided blood specimens. Analyses were conducted to compare population characteristics between street youth who have used injection drugs and those who had not. Similarly, population characteristics were analyzed among those street youth who were antibody-HCV positive and those that were antibody HCV negative.<p>In this study 32.3% of 186 participants had used injection drugs. Significant associations with injection drug use were found for older age (p = 0.01), having sexual partners that use injection drugs (p = 0.01), history of incarceration (p = 0.01), and history of living on the street (p = 0.02). Significant interactions were found for sex trade work by gender (p < 0.01) and by age (p = 0.03), and for living on the street by age (p = 0.02). A HCV prevalence rate of 9.3% of 156 participants was determined for Saskatoon street youth. Use of Ritalin by injection (p = 0.04) and history of living on the street (p = 0.05) were found to be significant risk factors associated with HCV. The interaction of living on the street by gender was also significantly associated with HCV (p = 0.05). <p>The relationship identified between HCV and injection drug use in Saskatoon street youth was a history of living on the street. This link between could serve as a valuable marker for use of injection drugs and developing HCV infection in street youth. Nurses are encouraged to seek out street youth social networks to provide health care and messages of health promotion and disease prevention. Strategies that are culturally, socially, and developmentally appropriate are needed to keep these youth off the streets in the first place.