3. Electronic Theses and Dissertations (ETDs) - All submissions
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Item The Association of HLA Class II Genetic and Expression Level Variation with Response to the Hepatitis B Vaccine in South African Laboratory Workers(2017-12-01) Goldfein, Hadassa; de Assis Rosa, DebbieThe hepatitis B virus (HBV) vaccine has contributed greatly to decreasing the HBV epidemic. However, it remains unclear why 5-10% of individuals do not mount an adequate antibody response. Previous studies have shown that genetic variation influences HBV vaccine response. Since such studies are lacking in South African individuals, we examined the associations between HBV vaccine response and genetic variation in HLA-DPB1, additional candidate genes and HLA-DPB1 expression levels in a South African cohort. HLA-DPA1 and -DPB1 allele typing was performed using Luminex technology, twenty-four candidate SNPs were typed by MassArray Analysis and HLA-DPB1 mRNA expression levels were measured by qPCR. HLA-DPB1*01:01, *04:01:01G and *09:01 and SNPs and haplotypes in IL1B, IL4, IL12B, IFNG and the HLA region were significantly associated with HBV vaccine response. A trend of lower HLA-DPB1 expression associating with better anti-HBs response was observed, although this was not significant. Response to the HBV vaccine is multi-genic but HLA-DP plays an important role.Item Molecular characterization of hepatitis B virus (HBV) from mono-infected and HBV/human immunodeficiency virus (HIV) co-infected individuals in Sudan(2014-09-09) Yousif, MukhlidHepatitis B virus (HBV), the prototype member of the family Hepadnaviridae, is hepatotropic and replicates by reverse transcription. HBV is responsible for the chronic infection of more than 240 million people worldwide, of which 65 million reside in Africa. The nine HBV genotypes (A to I) identified to date, are geographically distributed and exhibit different clinical manifestations and treatment responses. The term occult HBV infection (OBI) refers to a HBV infection in which HBV surface antigen (HBsAg) cannot be detected by conventional serological assays as has been defined by the Taormina expert panel. . HBV and human immune deficiency virus (HIV) are both endemic in many parts of the world and share common transmission routes. Worldwide, 10% of those infected with HIV are also chronically infected with HBV. HIV co-infection has been shown to be a risk factor for the development of OBI in individuals infected with HBV. The aim of this study was to characterize, at the molecular level, HBV from mono-infected and HBV/HIV co-infected individuals in Sudan The objectives of this study were the systematic and comparative analysis of HBV genotype D sequences, available in the public databases; the molecular characterization of HBV from mono-infected Sudanese liver disease patients and from HBV/HIV co-infected Sudanese patients; and the development and testing of bioinformatics tools to explore HBV sequence data generated using ultradeep pyrosequencing (UDPS) and comparison of UDPS results with those obtained from cloning based sequencing (CBS). All available complete genomes of genotype D of HBV from the GenBank database were analyzed. The intra-group divergence of the subgenotypes ranged from 0.8% + 0.5 for subgenotype D6 to 3.0% + 0.3 for subgenotype D8. Phylogenetic analysis of genotype D showed separation into six distinct clusters (subgenotypes D1, D2, D3/D6, D4, D5 and D7/D8), with good bootstrap support. The mean intergroup divergence between subgenotype D3 and subgenotype D6 was 2.6%, falling below the accepted threshold of 4% required to define a subgenotype. This suggests that subgenotypes D3 and D6 are the same subgenotype because they also share signature amino acids. Furthermore, subgenotype D8 is a genotype D/E recombinant, which clusters with subgenotype D7. This analysis provided an update on the classification of the subgenotypes of genotype D of HBV. Although HBsAg seroprevalence in Sudan, a central-African country, is greater than 8%, the only sequencing data for HBV, available prior to our study, was from asymptomatic blood donors, where genotype E predominates, followed by genotype D and subgenotype A2. Ninety-nine HBV-positive liver disease patients were enrolled in our study, including: 15 with hepatocellular carcinoma (HCC), 42 with cirrhosis, 30 asymptomatic carriers, 7 with acute hepatitis and 5 with chronic hepatitis. The surface and basic core promoter/precore (BCP/PC) regions, and the complete genome of HBV were sequenced. Eighty-two percent of the samples from HBV mono-infected liver disease patients were genotyped. Fifty-nine percent were infected with genotype D (74% D1, 10% D2, 3% D3 and 13% D6), 30% with genotype E, 8.5% with genotype A and 2.5% with a genotype D/E recombinant. Patients infected with genotype E had a higher frequency of HBeAg-positivity (29.2%) and higher viral loads compared to patients infected with genotype D. BCP/PC region mutations, including the G1896A mutation, seen in 37% of the HBeAg-negative individuals, could account for the HBeAg-negativity. A total of 358 Sudanese HIV-positive patients were enrolled. HBsAg was detected in 11.7% of the participants, indicating chronic HBV infection. HBV DNA was detected in 26.8% of the participants: 11.7% were HBsAg positive (overt infection) and the remaining 15.1% were HBsAg-negative (OBI). Fifty serum samples from the HBV/HIV DNA-positive co-infected participants were selected for genomic analysis of HBV. Of these, the HBV genotype of 37 was determined. The genotype distribution of HBV isolates from the HBV/HIV co-infected participants did not differ significantly from those from the HBV mono-infected patients: genotype D (46%), E (21.6%), A (18.9%) and a D/E recombinant (13.5%). Compared to the HBV isolates from mono-infected liver disease patients, the frequency of the D/E recombinant and genotype A was higher in HBV/HIV co-infected patients, as was the intragroup divergence of genotype E. No difference in BCP/PC mutations affecting HBeAg expression at the transcriptional and translational levels between genotype D and E was observed. The following mutations could account for the HBsAg-negativity: sM133T, sE164G, sV168G and sS174N. No primary drug resistance mutations were found. Two online bioinformatics tools, the ―Deep Threshold Tool (DDT)‖ and the ―Rosetta Tool‖, were built to analyze data generated from UDPS and CBS of the BCP/PC region of four Sudanese serum samples, infected with either genotype D or E of HBV, from HBeAgpositive and HBeAg negative patients. A total of 10952 reads were generated by UDPS on the 454 GS Junior platform. The Threshold was calculated using DDT based on probability of error of 0.5%. In total, 39 unique mutations were identified by UDPS, of which 25 were nonsynonymous. The ratio of nucleotide substitutions between isolates from HBeAg-negative and HBeAg-positive patients was 3.5:1. From the sequences analyzed, compared to genotype E isolates, genotype D isolates showed greater variation in the X, BCP/PC/C regions. Only 18 of the 39 positions identified by UDPS were detected by CBS. Using the specific criteria, that have been suggested previously, to define genotypes/subgenotypes of HBV, we determined that genotype D has six and not eight subgenotypes. The importance of HBV genotypes in clinical consequences of infection and response to antiviral treatment has led us to characterize HBV genotypes circulating in Sudan. HBV mono-infected patients and HBV/HIV co-infected individuals, were mainly infected with genotype D or E. HBV mono-infected patients, infected with genotype E, had higher HBeAg-positivity and higher viral loads than those infected with genotype D. The ratio of genotype A to non- A, as well as the genotype E intra-group divergence were higher in HBV/HIV co-infected individuals compared to HBV mono-infected individuals. OBI was found in 15.1% HBV/HIV co-infected patients and its clinical relevance remains to be determined. In order to overcome the limitations of Sanger sequencing, which include its high cost and inability to detect minor populations in quasispecies, next generation sequencing techniques have been developed. It was demonstrated that correct analysis of UDPS data required appropriate curation of read data, in order to clean the data and eliminate artefacts and that the appropriate consensus (reference) sequence should be used in order to identify variants correctly. CBS detected fewer than 50% of the substitutions detected by UDPS. This new technology may allow the detection of minor variants between the different genotypes of HBV and provide biomarkers for the prediction of clinical manifestation of HBV and response to antiviral therapy.Item The unfolded protein response (UPR) in cultured cells expressing either wild-type or mutant hepatitis B e antigen (HBeAG) of the hepaptitis B virus(HBV)(2014-02-18) Bhoola, Nimisha HarshadraiHepatitis B virus (HBV) is hyperendemic to southern Africa, the Asia-Pacific region, and the Amazon Basin. HBV causes both acute, and chronic infection of the liver that result in a wide spectrum of liver diseases ranging from acute mild subclinical infection, and an asymptomatic carrier state (ASC) to severe clinical manifestations, including, severe acute and, chronic hepatitis, which can progress to cirrhosis, and the development of hepatocellular carcinoma (HCC). Several viral factors have been implicated in the activation, and inhibition of apoptosis. The development, and progression of this wide spectrum of liver diseases are associated with an unregulated increase or decrease in hepatocyte apoptosis as well as a loss of balance between cell proliferation, and apoptosis. In southern Africa, genotype A of HBV is the predominant genotype, with subgenotype A1 prevailing. Individuals infected with subgenotype A1 have several unique characteristics, including relatively lower levels of HBV DNA, and early seroconversion of hepatitis B e antigen (HBeAg) to antibodies against HBeAg during the course of HBV infection. Infection with this subgenotype is associated with rapid disease progression, and high frequency of HCC development. Moreover, patients infected with subgenotype A1 had increased levels of apoptosis when compared to the other subgenotypes. The G1862T mutation occurs most frequently in subgenotype A1. In the clinical setting, South African HCC patients infected with G1862T subgenotype A1 strains had higher levels of apoptosis while ASCs patients infected with G1862T subgenotype A1 strains had lower levels of apoptosis, when compared to those infected with wild-type. To date, G1862T has been functionally characterized in subgenotype A2, genotype B and in a genotype D HBV genome containing a subgenotype A1 precore (PreC) region. The objectives of our study were to construct 1.28 mer replication competent clones containing an endogenous HBV promoter for wild-type subgenotypes A1, A2, and D3 as well as mutant G1862T subgenotype A1, and to functionally characterize these strains in tissue culture. Transfection of Huh7 cells was used to follow the viral replication, expression of HBeAg, activation of the unfolded protein response (UPR), and subsequent apoptosis. The strategy used for the generation of these replication competent clones had several advantages. Very few PCR errors were introduced, and carry-over of enzymes, nonspecific products, and reaction reagents downstream was prevented. The clones contained endogenous HBV promoters, and enhancers, and were generated from a single complete genome of HBV. These replication competent clones may be used in future studies for the establishment of stable cell lines that constitutively express HBV proteins without the need for further manipulation. This strategy can be used for the generation of replication competent clones belonging to genotypes A to D, and G, and with a few minor modifications, for genotypes E, F, and H. Using the newly generated clones, their replication competence was demonstrated using transfection of Huh7 cells. Even in the absence of an exogenous promoter, these clones were able to support the expression of intracellular, and extracellular HBV DNA at levels of 108 to 109 genome copies/ml. HBcAg, HBeAg, and HBsAg were expressed for a period of five days, and the order of expression was similar to that seen during acute HBV infection. Comparison of transfection with a replication competent clone containing an exogenous HBV promoter demonstrated higher expression of HBV DNA, and proteins, as well as an earlier expression, and accumulation of HBeAg in the endoplasmic reticulum (ER) relative to the clone containing an endogenous HBV promoter. This initial increased accumulation of HBeAg in the ER did not affect the level of activation of the UPR, but led to an increased level of total cell death as a consequence of necrosis. When comparing the different subgenotypes following transfection into Huh7 cells, subgenotype D3 replicated at a lower level, as measured by HBsAg, and HBV DNA levels, with HBeAg passing through the secretory pathway earlier, when compared to cells transfected with genotype A. There was no difference in the intracellular, and extracellular HBsAg between cells transfected with either subgenotype A1 or A2. However, cells transfected with subgenotype A1 had higher levels of intracellular replicative intermediates, HBeAg, and HBcAg, and lower extracellular expression of HBeAg from days 1 to 3, when compared to cells transfected with subgenotype A2. The intracellular retention of the PreC/ core (C) precursor protein in cells transfected with subgenotype A1 was clearly demonstrated by its lower expression in the secretory pathway, and its higher co-localization in the nucleus, using indirect immunofluorescence. This intracellular retention led to greater ER stress, and an earlier, and prolonged activation of the UPR. This correlated well with the higher PERK, ATF6, and IRE1/XBP1 activity seen on days 3 than on day 5. These findings suggest that the prolonged activation of the UPR in cells transfected with subgenotype A1 led to increased apoptosis, and subsequent induction of liver damage, and may therefore, be a contributing factor to the higher hepatocarcinogenic potential of subgenotype A1. Our study demonstrated that G1862T reduced replication, and led to the initial temporal retardation of intracellular core-particle-associated HBV DNA. Although, G1862T did not affect HBsAg expression, it led to a decreased expression of HBcAg, and HBeAg. The decreased expression of extracellular HBeAg was probably as a result of decreased cleavage efficiency by the signal peptide, which consequently led to the retardation of the PreC/C precursor protein in the ER, and ER-Golgi intermediate compartment (ERGIC), and its decreased expression in the nucleus. This retardation, and accumulation led to the earlier activation of all three UPR pathways, but not to increased apoptosis. Therefore, it is evident that G1862T does not completely abolish HBeAg expression, but affects the rate of HBeAg maturation, and its expression through the secretory pathway. These findings suggest that in response to the accumulation of HBeAg in the ER, the UPR was activated resulting in the alteration of the capacity to overcome this stress, consequently leading to a new homeostasis of the ER being reached. The capacity of the ER is increased, with no further activation of the UPR and apoptosis, which facilitates maturation of HBeAg. In conclusion, our study for the first time demonstrated that there are a number of factors that influence the expression of proteins in HBV transfection studies including the type of transcriptional promoter, the different genotypes/subgenotypes of HBV, the use of protein expressing as opposed to replication competent clones, and the presence, and absence of mutations, such as the G1862T. Therefore, when comparing the outcomes of various experiments these factors should be taken into consideration, and the results interpreted with caution, because experiments may not be strictly speaking comparable. Importantly, replication competent clones were generated from strains circulating in southern Africa. The generation of these clones is an important step in further functional characterization of African strains of HBV, and their comparison to strains circulating other geographical regions of the world. These strains, in particular, subgenotype A1 can develop unique mutations, such as the G1862T, which we demonstrated can influence the expression of HBeAg, in a way that it can possibly account for the higher hepatocarcinogenic potential of subgenotype A1.