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Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Despite the decreased rate of HBV horizontal transmission in South Africa (SA) due to the HB vaccine, the risk of perinatal transmission remains of concern, especially in HIV/HBV co-infected women. Loss of HBV immune control, resulting in higher HBV replication and thus increasing the risk of transmission is described in HIV/HBV co-infected women. Chronic hepatitis is a well-recognized risk factor for hepatocellular carcinoma (HCC). The presence of specific HBV mutations has been reported in chronic and HCC patients and is used in algorithms for the prediction of HCC in CHB patients in Asia. While these mutations are extensively described in male patients, little is known regarding the antenatal and paediatric populations. This study aimed to determine the prevalence of HBV infection in HIV-exposed infants and to investigate the presence of HCC-related mutations in pregnant women and HIV-exposed children in SA. Residual samples of infants born to HIV-infected mothers were collected from the P1041 study previously conducted in SA. HBV markers (HBsAg, anti-HBs and anti-HBc) were tested on the Architect (Abbott). HBsAg positive samples were tested for HBV DNA to determine HBV viral loads. HBV strains were characterised by sequencing of the HBsAg gene and genotypes were determined by phylogenetic analysis using HepSEQ (www.hepseq.org.uk). For the HCC-related mutations investigation, samples and data were collected from three HBV-related studies: the NHLS Paediatric Study, an Antenatal Study and the current study. Pre-S, basal core promoter (BCP) and pre-core data was collected from all samples. Multiple alignments were formed and the nucleotide sequences of these extracts were translated into protein sequences. These protein sequences were compared manually to the HBV reference genes to identify HCC-related mutations. Of 850 HIV-exposed infants tested, three infants were positive for both HBsAg and HBV DNA. Two samples show evidence of past, but cleared HBV infection. Sequence analysis showed that the infants were infected with a subgenotype A1. At follow up, only one infant and mother were able to be traced and contacted. The infant was HIV-infected and had been on an ART regimen, including lamivudine for two years. HBV testing showed that the infant was HBsAg positive and had an undetectable viral load. Core sequence analysis showed clustering between mother and infant sequences. Transmission of mutant HBV previously associated with HCC prompted the question of what the prevalence of mutations in the antenatal and paediatric population is. In this investigation of HCC-related mutations study, a higher prevalence of combined pre-S, BCP and pre-core mutations was found in HIV-infected as compared to HIV-uninfected women. This study shows that vertical transmission is occurring in HIV-exposed infants in SA despite HB vaccination. Data described in this study suggests the importance of HB vaccination closer to the time of birth in SA. Moreover, data on the higher prevalence of HCC-related mutations in HIV-infected pregnant women provide a background for further longitudinal studies to confirm these findings and their implications in SA. / AFRIKAANSE OPSOMMING: As gevolg van die beskikbaarheid van die Hepatitis B virus (HBV) entstof , het horisontale transmissie van die virus drasties in Suid-Afrika (SA) verminder. Ten spyte hiervan, is daar steeds ‘n hoë risiko van perinatale transmissie van swanger vroue na hulle babas, dit word veral gesien met MIV/HBV positiewe vroue. Dit is wyd beskryf dat vroue wat mede-besmet is met MIV/HBV gewoonlik beheer verloor oor hulle immuunstelsel, wat lei tot ‘n hoër mate van HBV replikasie en dus ‘n hoër risiko van virus oordrag. Kroniese hepatitis is wel bekend as ‘n hoë risiko faktor vir HCC. Die teenwoordigheid van spesifieke HBV mutasies in kroniese en HCC pasiënte word alreeds in Asië gebruik in sekere algoritmes en formules om infeksie aan te dui en te voorspel. Hierdie mutasies is omvattend beskryf in manlike pasiënte, maar baie min is bekend in voorgeboorte en pediatriese gevalle. In hierdie studie het ons die teenwoordigheid van HCC-verwante mutasies in swanger vroue en MIV-blootgestelde kinders in Suid-Afrika ondersoek. Monsters is verkry van babas gebore van MIV-positiewe moeders van die P1041 studie wat voorheen in SA gedoen is. Die HBV merkers (HbsAg, teen-HBs en teen-HBc) was op die Architect (Abbott) getoets. HBsAg positiewe monsters was getoets vir HBV DNA om die virale lading te bepaal. Die verskeidenheid HBV stamme was gekarakteriseer deur die virus se nukleïensuur volgordes te bepaal. Die verskillende genotipes is bepaal deur filogenetiese analises te doen met behulp van die HepSEQ (www.hepseq.org.uk) program. Vir die HCC-verwante mutasie studie is monsters en data vergelyk met 3 HBV-verwante studies: die NHLS pediatriese studie, ‘n voorgeboorte studie en hierdie spesifieke studie. Voor-S, basale kern promoter en voor-kern data was van alle monsters bekom. ‘n Veelvoudige belyning was gedoen met die nukleïensuur volgordes van die verskeie DNA ekstrakte, wat daarna vertaal is in proteïen volgordes. Hierdie proteïenvolgordes translasie was by hand vergelyk met verwysings gene om die relatiewe HCC mutasies te probeer identifiseer. Van die 850 blootgestelde MIV babas wat getoets is, het 3 positief getoets vir beide HbsAg en HBV DNA. Twee monsters het bewys van verlede , maar vrygestelde HBV infeksie. Data analise bewys dat die babas met subtipe A1 besmet was. Ons kon slegs een moeder en baba paar opvolg en kontak vir verdere toetse. Die baba was MIV-positief en was op antiretrovirale behandeling , insluitend lamivudine, vir ten minste 2 jaar. HBV toetse het gewys dat die baba HbsAg positief is en ‘n onopspoorbare virale lading gehad het. Kern nukleïensuur volgorde analise het groepering getoon tussen die ma en baba se virus monsters . Die transmissie van die mutante HBV wat geassosieer is met HCC het gelei tot die vraag wat die voorkomssyfer is van hierdie spesifieke mutasies in die voorgeboorte en pediatriese populasies in SA. In hierdie studie het ons ‘n hoër gekombineerde voorkomssyfer gevind van die voor-S, basale kern promoter en voor-kern mutasies in MIV-positiewe vroue, in vergelyking met MIV-negatiewe vroue. Hierdie studie bewys dus dat vertikale transmissie van HBV in blootgestelde MIV babas steeds plaasvind, ten spyte van HBV inenting. Die data wat in hierdie studie beskryf was dui daarop dat die belangrikheid van HBV inenting nader aan die tyd van die geboorte in SA gegee moet word.As gevolg van die hoë voorkomssyfer van HCC-verwante mutasies in swanger vroue, is daar verdere longitudinale studies nodig om hierdie bevindinge en hul implikasies in SA te bevestig.

MSc (Microbiology) / Department of Microbiology / Background: Prostate cancer (PCA) is a major health concern in males, particularly those above 40 years old. It is the most common form of cancer in males worldwide, including South Africa. In South Africa, the rate of histologically diagnosed prostate cancer is 40 per 100 000 in whites and 14 per 100 000 in blacks, and 1 in 8 men will develop PCA in their lifetime. Several reports have suggested the association of viruses in the pathogenesis of prostate cancer. Objectives: This study was aimed at identifying Hepatitis B virus (HBV), human papilloma virus (HPV) and human herpes virus type 8 (HHV-8), implicated in other forms of cancer, in a cohort of South African patients with either PCA or benign prostatic hyperplasia (BPH); and to seek possible associations thereof. Methods: The study group comprised 187 male patients recruited from Polokwane Hospital presenting with either PCA (staged by Gleason scores) or BPH. Enzyme-linked immunosorbent assay was used to detect antibodies to HHV-8 and HPV; and to detect hepatitis B surface antigen (HBsAg) in the plasma of the study subjects. Total DNA was extracted from plasma and targeted for the identification of HBV and HHV-8 DNA by nested PCR protocols. The HBV nested PCR protocol amplifies a 336bp fragment of the overlapping surface polymerase gene of HBV. The HHV-8 nested protocol amplifies a 233bp fragment of the ORF 26 gene of HHV-8. Amplified DNA products were purified, sequenced by the Sanger protocol and phylogenetically analysed for viral genotypes. The Chi-square test was used to infer statistically significant differences in the level of detection of viruses and the stage of prostate cancer development. Results: Of the 187 participants, a seroprevalence of 4.8% (9/187, HBsAg), 5.3% (10/187, HPV IgG antibody) and 27% (33/124, HHV-8 IgG antibody) were observed. HBsAg was detected more in individuals with BPH than those without and this was statistically significant at ( 2=6.0, p< 0.05). HHV-8 DNA was detected more in individuals in the 60-79 years age range and this was statistically significant at ( 2=61.1, p< 0.05). Occult HBV infection (that is the presence of HBV DNA in the absence of HBsAg) was detected in 23/178 (12.9%) of patients. Taking into account occult HBV infection, the overall prevalence of HBV was 17.7%. HBV genotype E was more prevalent (86.7%) followed by genotype A (13.3%). HHV-8 genotypes K and R were inferred. Apparently, this is the first report on the identification of HHV-8 genotypes K and R from South Africa. Conclusion: The current study has demonstrated for the first time, the presence of genotypes K and R of HHV-8 in South Africa. This study also suggests that there is a high level of occult genotype E HBV infection. Future studies will explore the virome in prostate cancer biopsies.