Mainz, Univ., Diss., 2001.

The purpose of this study was to identify mutations in the basic core promoter and enhancer II region a* the hepatitis B virus (HBV) that might result in the hepatitis B virus e antigen (HBeAg)-negative phenotype and contribute to hepatocarcinogenesis in black African carriers of the virus. The basic core promoter/enhancer II overlaps the X gene. HBV DNAfrom serum of 47 asymptomatic carriers and 50 patients with hepatocellular carcinoma and from 29 tumorous and 10 nontumorous liver tissues was amplified and sequenced directly. That part of the enhancer II region not overlapping the basic core promoter was reasonably well conserved in all samples. Missense mutations at positions 1809 and 1812 were found in 80% of all sequences and may represent wiidtype sequence in southern African isolates. Nucleotide and amino acid divergences were higher in the basic core promoter of hepatocellular carcinoma patients than of asymptomatic carriers (p<0.0001). This applied particularly to the paired 1762 adenine to thymine (1762T) and 1764 guanine to adenine (1764*) missense mutations, the prevalence of which was 66% in patients with hepatocellular carcinoma compared with 11% in asymptomatic carriers (p<0.0001). There was no association between the presence of 1762T1764A and the rate of HBeAg negativity, although these mutations suppressed HBeAg titres in HBeAg-positive patients. Suppression of HBeAg expression as well as alteration of amino acid sequence of the X protein may be contributing factors in the development of hepatocarcinogenesis.

A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Medicine Johannesburg, 2017 / Hepatitis B is a global health problem that kills about 600 000 people annually. It is an infectious disease caused by the Hepatitis B Virus (HBV), which infects the liver and leads to liver inflammation and secondary complications such as cirrhosis and Hepatocellular Carcinoma (HCC). The available therapies are only partially effective and are associated with adverse side effects and viral drug resistance. RNA interference (RNAi) pathway is a gene silencing pathway found in diverse living systems including mammals. Harnessing of this pathway to inhibit HBV replication has shown a lot of promise, with highly effective anti-HBV RNAi activator sequences designed. However, the lack of safe and efficient delivery and expression systems for these sequences is one of the obstacles that need to be overcome before RNAi effectors can reach clinical application. For easy assessment of transduction efficiency, Helper Dependent Adenoviral vectors (HDAd) expressing β-galactosidase (encoded by lac Z gene) are commonly used to deliver anti-viral RNAi activators. However, this reporter protein has been blamed for induction of innate immune response and concomitant clearance of the HDAds by the host. For the first time, this study explored the use of lac Z-deficient HDAds to deliver anti-HBV RNAi activators expressed under the control of a liver-specific phosphoenolpyruvate carboxykinase (PEPCK) promoter. HDAd expressing Firefly luciferase resulted in a significant luminescence detected in cell culture lysates and a sustained bioluminescence in mice. HDAds expressing anti-HBV sequences transduced the liver efficiently and did not induce a pronounced inflammatory response or liver toxicity in mice. However, this did not translate into maximal anti-HBV sequence expression and HBV replication inhibition in vitro and in vivo. This suggests that the PEPCK promoter is inadequate for RNAi activator expression. This study highlights the importance of careful RNAi activator regulatory elements selection and presents the therapeutic potential and utility of HDAd vectors for hepatotropic delivery of antiviral sequences with markedly attenuated immune response stimulation and toxicity. For improved anti-HBV RNAi activator expression and HBV knockdown, a different liver specific promoter mouse transthyretin receptor (MTTR) promoter is currently being investigated in our lab. / MT2017

Zhu, Lin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 103-118). / Abstracts in English and Chinese. / Contents --- p.I / List of Abbreviations --- p.IV / List of Tables and Figures --- p.V / Chapter Chapter One: --- Introduction --- p.1 / Chapter 1.1 --- Viral Hepatitis --- p.2 / Chapter 1.2 --- Global Epidemiology of HBV --- p.3 / Chapter 1.3 --- Modes of Transmission --- p.4 / Chapter 1.4 --- Diagnostic Tests --- p.5 / Chapter 1.4.1 --- HBeAg and Anti-HBe --- p.7 / Chapter 1.4.2 --- Serum Enzymes --- p.8 / Chapter 1.4.3 --- HBV DNA Assays --- p.9 / Chapter 1.4.3.1 --- HBV DNA Assays --- p.9 / Chapter 1.4.3.2 --- Clinical Applications of DNA Assays --- p.10 / Chapter 1.4.4 --- Histology --- p.13 / Chapter 1.5 --- Natural Course of Chronic Hepatitis infection --- p.18 / Chapter 1.5.1 --- Phases of chronic hepatitis B --- p.18 / Chapter 1.5.2 --- HBeAg-negative chronic hepatitis B --- p.21 / Chapter 1.6 --- Molecular biology of HBV --- p.23 / Chapter 1.6.1 --- Overview --- p.23 / Chapter 1.6.2 --- Genomic structure and organization --- p.24 / Chapter 1.6.2.1 --- Surface ORF --- p.24 / Chapter 1.6.2.2 --- Precore/Core ORF --- p.25 / Chapter 1.6.2.3 --- Polymerase ORF --- p.25 / Chapter 1.6.2.4 --- X ORF --- p.26 / Chapter 1.7 --- Genetic Variation of HBV --- p.31 / Chapter 1.7.1 --- HBV genotypes --- p.31 / Chapter 1.7.2 --- Predominant genotypes and their subgroups in Asia --- p.33 / Chapter 1.7.3 --- HBV mutations --- p.36 / Chapter 1.7.3.1 --- Precore mutations --- p.37 / Chapter 1.7.3.2 --- Core promoter mutations --- p.38 / Chapter 1.7.3.3 --- Other Mutations associated with clinical outcome --- p.40 / Chapter Chapter Two: --- Methodology --- p.44 / Chapter 2.1 --- Aims and Hypothesis --- p.45 / Chapter 2.1.1 --- Aims --- p.46 / Chapter 2.1.2 --- Hypothesis --- p.47 / Chapter 2.2 --- Patient Recruitment --- p.48 / Chapter 2.3 --- Laboratory Assays --- p.49 / Chapter 2.3.1 --- Preparation of serum HBV DNA --- p.49 / Chapter 2.3.2 --- Quantification of serum HBV DNA --- p.51 / Chapter 2.4 --- Full-genome Amplification of HBV DNA --- p.53 / Chapter 2.5 --- Full-genome Sequencing of HBV DNA --- p.55 / Chapter 2.6 --- Assembly of HBV Full-genome Sequence --- p.58 / Chapter 2.7 --- Phylogenetic Analysis --- p.59 / Chapter 2.7.1 --- Construction of phylogenetic tree --- p.59 / Chapter 2.7.2 --- Genotype and subgenotype determination --- p.60 / Chapter 2.8 --- HBV Mutations --- p.62 / Chapter 2.9 --- Info-gain program --- p.64 / Chapter 2.10 --- Statistical Analysis --- p.65 / Chapter Chapter Three: --- Results --- p.67 / Chapter 3.1 --- Patient Information --- p.68 / Chapter 3.2 --- Phylogenetic Analysis --- p.69 / Chapter 3.3 --- HBV genotypes/subgenotypes --- p.76 / Chapter 3.4 --- “Hot-spo´tح HBV Mutants --- p.79 / Chapter 3.5 --- HBV Mutation Associated with Liver Fibrosis --- p.82 / Chapter 3.5.1 --- Mutant selection --- p.82 / Chapter 3.5.2 --- Clinical significance of novel mutants --- p.84 / Chapter Chapter Four: --- Discussion --- p.88 / Chapter 4.1 --- Full-genome Sequencing Strategy --- p.89 / Chapter 4.2 --- HBV genotypes/subgenotypes Distribution and Disease Activity --- p.90 / Chapter 4.2.1 --- HBV genotypes/subgenotypes distribution --- p.90 / Chapter 4.2.2 --- Clinical significance of genotypes/subgenotypes --- p.91 / Chapter 4.3 --- HBV Hotspot Mutants and Disease Activity --- p.93 / Chapter 4.4 --- HBV Novel Mutants --- p.96 / Chapter 4.5 --- Limitation of the Study and Future Work --- p.97 / Chapter 4.5.1 --- Limitation --- p.97 / Chapter 4.5.2 --- Future Direction --- p.98 / Chapter Chapter Five: --- Conclusions --- p.99 / References --- p.102

Dissertation (PhD)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: Since the advent of recombinant DNA technology in the 1970s, various microbial hosts have been employed for the efficient high-level heterologous production of a variety of proteins, ranging from enzymes and reagents to therapeutics and vaccines. More recent microbial hosts to be employed for these purposes are filamentous fungi, and particularly the genus Aspergillus. Aspergilli have been associated with industrial processes for many years and are used in the production of antibiotics, enzymes, citric acid and Oriental foods and beverages, and thus strains such as Aspergillus niger and Aspergillus oryzae have been afforded GRAS (Generally Regarded 8s ~afe) status. They also secrete copious amounts of homologous and heterologous proteins and are able to perform post-translational modifications effectively. Various proteins of pharmaceutical interest have been successfully expressed in Aspergillus, but the potential of these fungi to produce heterologous viral proteins has not been explored extensively. In this study, we evaluated the potential of the filamentous fungi A. niger and Aspergillus awamori as alternative hosts for the heterologous production of hepatitis B viral proteins. Hepatitis B is a serious, potentially lethal liver disease that affects 2000 million people world-wide and has a high endemicity in Southern Africa. Currently there is no effective treatment for viral hepatitis and thus a mass vaccination strategy is the only solution to curb the spread of the disease. This kind of vaccination strategy requires a cheap, safe and effective vaccine and these objectives have been achieved in the development of recombinant subunit vaccines from yeasts such as Saccharomyces cerevisiae, Hansenula polymorpha and Pichia pastoris that are commercially available. The hepatitis B virus envelope consists of a membrane fraction and three proteins, namely the major (S) protein (encoded by the S gene), the middle (M) protein (encoded by the preS2S gene) and the large (L) protein (encoded by the preS1preS2S gene). When produced in the above-mentioned yeasts, the S protein was shown to spontaneously assemble into pseudoviral particles devoid of viral DNA, which were then purified and used as vaccine. In the present study the Sand preS1preS2S genes from a local isolate of hepatitis B subtype adw2 were placed under transcriptional control of the constitutive Aspergillus nidulans glyceraldehyde-3-phosphate dehydrogenase (gpdA) promoter and the inducible A. niger glucoamylase (glaA) promoter. The respective viral genes were also fused to the region encoding the catalytic domain of the highly expressed and secreted A. niger glucoamylase, which served as a carrier moiety to possibly facilitate viral protein secretion. The various gene constructs were subsequently transformed to laboratory strains of A. niger and A. awamori and numerous transformants were obtained. One A. niger transformant carrying the S gene under control of the gpdA promoter contained approximately 7 integrated copies of the expression cassette and produced hepatitis B pseudoviral particles intracellularly at levels of 0.4 mg/I culture. These levels are approximately ten-fold higher than those initially obtained from the yeast S.cerevisiae, which showed yields of 0.01 to 0.025 mg/I. None of the other transformants could be shown to produce recombinant S or L protein and no secretion of viral protein could be demonstrated. This could be attributed to numerous factors, including vector copy number, site of integration or proteolytic activity. The most important insight emerging from this work regarding secretion of heterologous viral protein was that the addition of a carrier protein hampered, rather than enhanced secretion of the viral envelope protein, due to the inherent properties of viral protein assembly. This work also serves as a "proof of principle", showing that Aspergillus is indeed a viable alternative host for the production of hepatitis B pseudoviral particles, and could be investigated further for its potential as host for the heterologous expression of other viral proteins. / AFRIKAANSE OPSOMMING: Sedert die ontwikkeling van rekombinante DNA tegnologie in die sewentigerjare is verskeie mikroorganismes reeds gebruik vir die doeltreffende produksie van 'n verskeidenheid proteïne teen hoë vlakke; onder andere ensieme, reagense, terapeutiese middels en vaksiene. Onlangs is filamentagtige swamme, veral van die genus Aspergillus, ontwikkel vir heteroloë proteïenproduksie. Aspergilli word al vir baie jare in nywerheidsprosesse gebruik, onder andere in die vervaardiging van antibiotika, ensieme, sitroensuur en sekere Oosterse voedsel- en drankprodukte. As gevolg van hierdie jarelange gebruik van rasse soos Aspergillus niger en Aspergillus oryzae, word hulle algemeen aanvaar as veilig vir menslike gebruik. Hierdie swamme besit veral die vermoë om hoë vlakke van homoloë en heteroloë proteïene uit te skei en die na-translasiemodifisering van proteïene korrek uit te voer. Verskeie proteïene van farmaseutiese belang is al suksesvol in Aspergillus uitgedruk, maar die potensiaal van hierdie swamme om virale proteïene te vervaardig is nog nie deeglik ondersoek nie. Hierdie studie ondersoek die geskiktheid van die filamentagtige swamme A. niger en Aspergillus awamori om as alternatiewe gashere vir die heteroloë produksie van hepatitis B proteïene te dien. Hepatitis B is 'n ernstige en selfs dodelike lewersiekte. Omtrent 2000 miljoen mense wêreld-wyd is met die virus geïnfekteer en dit is veral endemies in Suiderlike Afrika. Daar is tans geen doeltreffende behandeling vir virale hepatitis en dus is wêreld-wye inentingsprogramme die enigste oplossing om die verspreiding van die siekte te bekamp. Hierdie inentingsstrategie vereis die beskikbaarheid van 'n bekostigbare, veilige en doeltreffende vaksien. Die rekombinante subeenheidvaksiene wat ontwikkel is deur van gashere soos Saccharomyces cerevisiae, Hansenula polymorpha en Pichia pastoris gebruik te maak, voldoen aan hierdie vereistes en is kommersieel beskikbaar. Die omhulsel van die hepatitis B virus bestaan uit 'n membraangedeelte en drie proteïene, naamlik die hoofproteïen (S) (gekodeer deur die S-geen), die middelproteïen (M) (gekodeer deur die preS2S-geen) en die grootproteïen (L) (gekodeer deur die preS1preS2S-geen). Wanneer die S-proteïen in bo-genoemde giste uitgedruk word, vorm dit spontaan pseudovirale partikels wat nie virale DNA bevat nie. Hierdie partikels word dan gesuiwer en as vaksien gebruik. In hierdie studie is die S- en preS1preS2S-gene, vanaf 'n plaaslike isolaat van hepatitis B subtipe adw2, onder transkripsionele beheer van die konstitutiewe Aspergillus nidulans gliseraldehied-3-fosfaat-dehidrogenasepromoter (gpdA) en die induseerbare A. niger glukoamilasepromoter (glaA) geplaas. Die onderskeie virale gene is ook aan die koderende gedeelte vir die katalitiese domein van A. niger glukoamilase gelas om fusieproteïene te vorm. Glukoamilase word teen hoë vlakke deur Aspergillus vervaardig en uitgeskei en kan dus moontlik dien as draerproteïen om sekresie van die proteïne te bevorder. Transformasie van die geenkonstrukte na laboratoriumrasse van A. niger en A. awamori het verskeie transformante gelewer. Een A. niger transformant bevattende die S-geen onder transkripsionele beheer van die gpdA promoter het minstens sewe kopieë van die uitdrukkingskaset in sy genoom geïntegreer en het hepatitis B pseudovirale partikels intrasellulêr teen vlakke van 0.4 mg/I swamkultuur vervaardig. Hierdie vlakke is omtrent tienvoudig hoër as die vlakke van 0.01 - 0.025 mg/I wat S.cerevisiae oorspronklik opgelewer het. Nie een van die ander transformante het rekombinante S of L proteïene vervaardig nie en sekresie van virale proteïen kon nie getoon word nie. Hierdie verskynsel mag te wyte wees aan verskeie faktore insluitende vektor-kopiegetal, setel van integrasie en proteolitiese aktiwiteit. Die belangrikste insig uit hierdie studie aangaande sekresie van heteroloë virale proteïene is dat die koppeling van die virale omhulsel-proteïen aan 'n draerproteïen sekresie benadeel het, eerder as om dit te bevorder. Hierdie verskynsel is te wyte aan die inherente geneigdheid van virale omhulselproteïene om 'n kompleks te vorm. Die studie dien ook as "bewys van beginsel" dat Aspergillus wel 'n werkbare alternatiewe gasheer vir die produksie van hepatitis B pseudovirale partikels is, en dat dit verder ondersoek sou kon word as potensiële gasheer vir die heteroloë uitdrukking van ander virale proteïene.

published_or_final_version / Surgery / Master / Master of Philosophy

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy Johannesburg, 2002 / Hepatitis B virus (HBV) infection is endemic to several populous regions and is often complicated by cirrhosis and hepatocellular carcinoma (HCC). Present treatment of chronic HBV infection is usually ineffective and novel therapeutic approaches are an important medical objective. The X open reading frame (ORF) of HBV, HBx, is a conserved sequence that overlaps with the polymerase ORF and viral c/'s-elements, and is present within all viral transcripts. In addition, the HBx ORF encodes a 17 kDa transactivator protein, HBx, which is required for the establishment of viral infection and has been implicated in HBV-associated hepatocarcinogenesis. The HBx sequence thus represents a compelling target for applying nucleic acid hybridisation-based therapeutic agents for the inhibition of HBV gene expression and replication. / IT2018

Thesis ( M Med (Virological Pathology))--University of Limpopo, 2010. / Introduction: Hepatitis B virus (HBV) is a serious problem worldwide causing various liver diseases such as chronic hepatitis and hepatocellular carcinoma (HCC). The pathogenesis of HBV related HCC is not well established. Hepatitis B X protein (HBx) plays an important role in the pathogenesis of HCC. HBx coded by HBV X gene enhances several cellular pathways in hepatocytes which may lead to HCC. The genetic variability of other HBV genomic regions plays a significant role in diagnosis, vaccine development and drug resistance. However, the genetic variability of HBV X gene is not well understood. In addition the dual basal core promoter mutations found within the X gene have been implicated in the inhibition of hepatitis B e antigen (HBeAg) expression. Studies focusing on HBV X gene are scarce in South Africa. Consequently HBV X gene variability may reveal interesting mutations and substitutions that are important in chronic liver diseases or HCC. This study aimed at characterising HBV X gene at a molecular level isolated from patients with different serological profiles. Methods: This was an exploratory study which used 20 stored sera (-70°C) collected from adult patients at Dr George Mukhari hospital, Pretoria. The samples were already tested for HBsAg, anti-HBs, anti-HBc and HBeAg serological markers (Elecsys, Roche Diagnostics, Penzburg, Germany). HBV DNA extraction was performed from serum using High Pure Viral Nucleic Acid Assay (Roche Diagnostics, Penzburg, Germany). Nested PCR assay was used for the amplification of 465 nucleotide HBV X gene. Sequencing of PCR positive samples was done using spectruMedix SCE2410 genetic analysis system. Six samples selected, were cloned into the pGEM®-T Easy vector system (Promega, Madison, USA). Three clones of each sample were selected and their plasmids purified using Pure Yield™ Plasmid Miniprep System (Promega, Madison, USA). The plasmid DNA was recovered using optimised nested PCR assay and sequenced. A total of 38 sequences were generated from the study and compared with reference strains retrieved from GenBank. Phylogenetic analysis based on HBV X gene sequences was done using MEGA 4 software to determine different genotype clusters. vi Results: HBV X gene was successfully detected and amplified in 20 study samples. The sequenced HBV X gene products revealed mutations and insertions. Particularly a six nucleotide insertion, GCATGG between nucleotides 1611 and 1618 which was detected in five samples. In addition, the six cloned samples confirmed the six nucleotide insertion and other mutations associated with inhibition of hepatitis B e antigen (HBeAg) detected in the study. The substitutions within HBx were detected in the N (1-50 amino acids) and C (51-154) terminals by comparing our sequences with archival sequences from GenBank. Important substitutions found within the N and C terminals were S31A, P38S, A42P, F73L, H94Y, P101S, K118T, D119N, I127T/N, K130M and V131I. These substitutions are associated with various biological functions and pathogenesis. Other substitutions with unknown functions detected in the study include A2G, A3G, A4G, C6W, P42S and V116L. Further mutations of T1753M, A1762T and G1764A associated with inhibition of HBeAg expression were detected in most samples and only one sample had C1766T mutation. Phylogenetic analysis resulted in A, C and D HBV genotypes. Five samples and 11 clones clustered with genotype D, two samples and four clones clustered with genotype C and finally 13 samples and 3 clones clustered with genotype A. Conclusion: HBV X gene was successfully characterised using various molecular methods. HBx substitutions detected are involved in various pathogenic effects and may present a risk of HCC for patients infected with HBV. Genotype D samples displayed most mutations/substitutions and this can be regarded as an important genotype with high risk of HCC. The detection of a six nucleotide insertion (GCATGG) in 5 samples may emerge as a new variant of genotype D. Furthermore triple mutations of T1753M/A1762T/G1764A within basal core promoter region were detected mostly in HBeAg negative samples. However further analysis of HBV X gene variability is needed.

Thesis (Ph. D.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

The Hepatitis B virus (HBV) chronically infects 350 million individuals worldwide, leading to mortality by end-stage liver disease, liver cirrhosis, and hepatocellular carcinoma. The vaccine to prevent HBV infection is highly effective but is not extensively available in endemic areas, resulting in high infection rates. Nucleoside analogue treatment of HBV has allowed for higher rates of viral clearance in infected individuals, but most patients must remain on therapy long term and viral resistance to the drugs is growing. The HBV viral genome is an episome in the nucleus of infected hepatocytes. It is called covalently closed circular (ccc) DNA and is highly stable, has a long half-life, and is the template for all viral transcription and progeny production. Nucleoside analogues do not directly target cccDNA, therefore many patients experience rebound when antiviral therapy is stopped. I have designed novel DNA binding proteins called zinc finger proteins (ZFPs) to specifically bind to the cccDNA in infected cells and inhibit viral transcription. Seven ZFPs targeting the model duck HBV (DHBV) and ten ZFPs targeting HBV were developed. Kinetic analyses of the purified ZFPs were performed, characterizing their specificity and binding properties. Using the DHBV tissue culture model system, I have demonstrated that the DHBV-specific ZFPs can specifically inhibit transcription from the viral template, resulting in reduced viral RNA, protein products and progeny virions. The DHBV-specific ZFPs were tested in primary duck hepatocytes (PDH) and in vivo in the Pekin duck model. ZFPs failed to express in PDH transduced by baculovirus vectors when DHBV was present in the cells. In vivo gene delivery of the ZFPs was carried out by portal vein injection of chitosan-based nanospheres. Unfortunately, non-specific reductions in viral levels masked any direct effect by the ZFPs. Testing of the HBV-specific ZFPs in tissue culture was hindered by a lack of transfectable cell culture model. A number of different transfection methods were tested to express the HBV-specific ZFPs, all without success. Further work is being carried out using baculovirus vectors to deliver the HBV-specific ZFPs to HBV-harbouring cell lines and HBV-infected scid-Alb/uPA chimeric mice with human liver cells. / Virology