Understanding of the viral and host factors that determine time for progression to acquired immunodeficiency syndrome (AIDS) in individuals infected with human immunodeficiency virus type 1 (HIV-1) could aid in the design of an effective HIV-1 vaccine. Human leukocyte antigen (HLA) class I profile is strongly and consistently associated with differential rates of HIV-1 disease progression, however the mechanisms explaining this are not well understood. It has been hypothesised that “protective” HLA alleles select escape mutations in functionally important epitopes in the conserved group specific antigen (Gag) protein resulting in HIV-1 attenuation, which may result in slower disease progression. Many of the studies investigating the fitness cost of Gag escape mutations have concentrated on a few pre-selected mutations and have not assessed fitness consequences in the natural sequence background. Furthermore, the majority of studies have focussed on HIV-1 subtype B, while HIV-1 subtype C is the most prevalent subtype worldwide. Therefore, in the present study, a large population-based approach and clinically-derived Gag-protease sequences were used to comprehensively investigate the relationship between immunedriven sequence variation in Gag, viral replication capacity and markers of disease progression in HIV-1 subtype C chronic infection. The influence of Gag function on HIV-1 disease progression was further investigated in early HIV-1 subtype C infection. It was also hypothesised that Gag may contribute significantly to overall HIV-1 fitness and towards fitness differences between HIV-1 subtypes. Materials and Methods Recombinant viruses encoding Gag-protease, derived from antiretroviral naïve HIV-1 subtype C chronically (n=406) and recently (n=60) infected patients as well as a small subset of HIV-1 subtype B chronically infected patients (n=25), were generated by electroporation of an HIV-inducible green fluorescent protein (GFP)-reporter T cell line with plasmaderived gag-protease PCR products and linearised gag-protease-deleted NL4-3 plasmid. The replication capacities of recombinant viruses, as well as intact HIV-1 isolates from peripheral blood mononuclear cells of patients chronically infected with HIV-1 subtype C (n=16), were assayed in the GFP-reporter T cell line by flow cytometry. Replication capacity was defined as the slope of increase in percentage infected cells from days 3-6 following infection, normalised to the growth of a wild-type NL4-3 control. Replication capacities were related to patient HLA alleles and markers of disease progression (viral load, CD4+ T cell count, and rate of CD4+ T cell decline in chronically infected patients, and viral set point and rate of CD4+ T cell decline in recently infected patients). Replication capacities were compared between isolates and recombinant viruses encoding Gag-protease from the same isolates, as well as between HIV-1 subtype B and C recombinant viruses matched for viral load and CD4+ T cell count. Bulk sequencing of patient -derived gagprotease amplicons was performed and mutations were identified that were significantly associated with altered viral replication capacity. The fitness effect of some of these mutations was directly tested by site-directed mutagenesis followed by assay of the mutant viruses. Results In HIV-1 subtype C chronic infection, protective HLA-B alleles, most notably HLA-B*81 (p<0.0001), were associated with lower replication capacities. HLA-associated mutations at low entropy sites (i.e. conserved sites) in or adjacent to Gag epitopes were associated with lower replication capacities (p=0.02), especially the HLA-B*81-associated 186S mutation in the TL9 epitope (p=0.0001). The fitness cost of this mutation was confirmed in site-directed mutagenesis experiments (p<0.001), and the co-varying mutations tested did not significantly compensate for this fitness cost. Replication capacity also correlated positively of an HIV-inducible green fluorescent protein (GFP)-reporter T cell line with plasmaderived gag-protease PCR products and linearised gag-protease-deleted NL4-3 plasmid. The replication capacities of recombinant viruses, as well as intact HIV-1 isolates from peripheral blood mononuclear cells of patients chronically infected with HIV-1 subtype C (n=16), were assayed in the GFP-reporter T cell line by flow cytometry. Replication capacity was defined as the slope of increase in percentage infected cells from days 3-6 following infection, normalised to the growth of a wild-type NL4-3 control. Replication capacities were related to patient HLA alleles and markers of disease progression (viral load, CD4+ T cell count, and rate of CD4+ T cell decline in chronically infected patients, and viral set point and rate of CD4+ T cell decline in recently infected patients). Replication capacities were compared between isolates and recombinant viruses encoding Gag-protease from the same isolates, as well as between HIV-1 subtype B and C recombinant viruses matched for viral load and CD4+ T cell count. Bulk sequencing of patient -derived gagprotease amplicons was performed and mutations were identified that were significantly associated with altered viral replication capacity. The fitness effect of some of these mutations was directly tested by site-directed mutagenesis followed by assay of the mutant viruses. Results In HIV-1 subtype C chronic infection, protective HLA-B alleles, most notably HLA-B*81 (p<0.0001), were associated with lower replication capacities. HLA-associated mutations at low entropy sites (i.e. conserved sites) in or adjacent to Gag epitopes were associated with lower replication capacities (p=0.02), especially the HLA-B*81-associated 186S mutation in the TL9 epitope (p=0.0001). The fitness cost of this mutation was confirmed in site-directed mutagenesis experiments (p<0.001), and the co-varying mutations tested did not significantly compensate for this fitness cost. Replication capacity also correlated positivelyof an HIV-inducible green fluorescent protein (GFP)-reporter T cell line with plasmaderived gag-protease PCR products and linearised gag-protease-deleted NL4-3 plasmid. The replication capacities of recombinant viruses, as well as intact HIV-1 isolates from peripheral blood mononuclear cells of patients chronically infected with HIV-1 subtype C (n=16), were assayed in the GFP-reporter T cell line by flow cytometry. Replication capacity was defined as the slope of increase in percentage infected cells from days 3-6 following infection, normalised to the growth of a wild-type NL4-3 control. Replication capacities were related to patient HLA alleles and markers of disease progression (viral load, CD4+ T cell count, and rate of CD4+ T cell decline in chronically infected patients, and viral set point and rate of CD4+ T cell decline in recently infected patients). Replication capacities were compared between isolates and recombinant viruses encoding Gag-protease from the same isolates, as well as between HIV-1 subtype B and C recombinant viruses matched for viral load and CD4+ T cell count. Bulk sequencing of patient -derived gagprotease amplicons was performed and mutations were identified that were significantly associated with altered viral replication capacity. The fitness effect of some of these mutations was directly tested by site-directed mutagenesis followed by assay of the mutant viruses. Results In HIV-1 subtype C chronic infection, protective HLA-B alleles, most notably HLA-B*81 (p<0.0001), were associated with lower replication capacities. HLA-associated mutations at low entropy sites (i.e. conserved sites) in or adjacent to Gag epitopes were associated with lower replication capacities (p=0.02), especially the HLA-B*81-associated 186S mutation in the TL9 epitope (p=0.0001). The fitness cost of this mutation was confirmed in site-directed mutagenesis experiments (p<0.001), and the co-varying mutations tested did not significantly compensate for this fitness cost. Replication capacity also correlated positively with baseline viral load (p<0.0001) and negatively with baseline CD4+ T cell count (p=0.0004), but not with subsequent rate of CD4+ T cell decline (p=0.73). In HIV-1 subtype C recent infection, replication capacities of the early viruses did not correlate with subsequent viral set points (p=0.37) but were significantly lower in individuals with below median viral set points (p=0.03), and there was a trend of correlation between lower replication capacities and slower rates of CD4+ T cell decline (p=0.09). Overall, the proportion of host HLA-specific Gag polymorphisms in or adjacent to epitopes was negatively associated with replication capacities (p=0.04) but host HLA-B-specific polymorphisms were associated with higher viral set points (p=0.01), suggesting a balance between effective Gag CD8+ T cell responses and viral replication capacity in influencing viral set point. A moderate statistically significant correlation was found between the replication capacities of whole isolates and their corresponding Gag-protease recombinant viruses (p=0.04) and the replication capacities of the subtype C recombinant viruses were significantly lower than that of the subtype B recombinant viruses (p<0.0001). The subtype-specific difference in the consensus amino acids at Gag codons 483 and 484 was found in site-directed mutagenesis experiments to largely contribute to the fitness difference between subtypes, possibly by influencing budding efficiency. Discussion The data support that protective HLA alleles, in particular HLA-B*81, attenuate HIV-1 through HLA-restricted CD8+ T cell-mediated selection pressure on Gag. Results suggest that viral replication capacity determined by sequence variability in Gag-protease has an impact on HIV-1 disease progression, but also indicate that a balance between HLA-driven fitness costs and maintenance of effective CD8+ T cell responses is important in determining clinical outcome. Gag-protease was observed to significantly contribute to overall HIV-1 replication capacity and variability in this region between HIV-1 subtypes B and C is suggested to partly explain the difference in viral fitness between these subtypes. Specific mutations in Gag-protease associated with viral attenuation were identified and it was also observed that mutations in conserved Gag regions carried the greatest cost to HIV-1 replication capacity. Overall, the data support the concept of, and may assist in the rational design of, an HIV-1 vaccine in which immune responses are directed towards several conserved epitopes, particularly in Gag, with the aim to constrain immune escape (thereby maintaining effective CD8+ T cell responses) and attenuate HIV-1 (in the event of partial escape), resulting in slower disease course and reduced HIV-1 transmission at the population level. / Thesis (Ph.D.)-University of KwaZulu-Natal, 2011.

Subtype C accounts for the majority of HIV infections and in South Africa, is the dominant subtype. The Gag cleavage sites of subtype C viruses show a high degree of natural variation compared to subtype B and group M sequences, with the p2/NC site having the highest degree of variation among all cleavage sites and between all subtypes. This study therefore aimed to determine the functional effect of this variation on viral fitness. A library of drug naïve subtype C sequences were screened using computational analysis to predict binding affinity between HIV protease and the Gag substrate at the p2/NC site. Ligands with high predicted affinity had hydrophobic cleavage sites with substantial diversity at positions P5-P3. Lower ranking ligands were mostly similar to the consensus subtype C. Three ligands were selected for fitness assays from each the high ranking and low ranking groups. Chimeric viruses expressing selected cleavage sites were generated by site directed mutagenesis. Replication capacity assays of these viruses showed moderate differences in fitness but failed to demonstrate a correlation with computational estimates of binding affinity. Enzymes assays were performed to further investigate substrate preferences and the binding mechanism of protease. To this end, recombinantly expressed HIV-1 protease was tested against a range of substrates the matching the p2/NC cleavage sites used in the replication capacity assay. Results of the enzyme assay did not correlate with either the computation studies or the replication capacity assay results, suggesting a sequence independent binding and recognition mechanism of HIV-1 protease. Taken together the results suggest that processing of Gag is determined by tertiary folding of the polyprotein and not amino acid sequence at the cleavage site. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2012.

In sub-Saharan Africa, women carry a disproportionate burden of the Human Immunodeficiency Virus Type 1 (HIV-1) pandemic. The high risk of HIV acquisition in these women and the variability in their disease progression is not fully understood. Natural Killer (NK) cells, which are innate immune antiviral lymphocytes, present systemically and at mucosal surfaces, may play a role in preventing HIV acquisition and/or altering disease progression, as they are key early mediators of the response to viral infections and are equipped to kill infected cells. The purpose of this study was to evaluate the role of NK cells in HIV-1 acquisition and following acquisition, in disease progression. The study participants were selected women who were participating in a randomized controlled trial assessing the effectiveness of 1% Tenofovir gel in preventing HIV-1 (CAPRISA 004 trial). The study design was a case-control study nested within the cohorts followed up in the CAPRISA 004 trial. In this trial, 889 sexually-active women aged 18-40 years were randomized to receive Tenofovir or placebo gel and prospectively followed. Assessment of HIV infection was performed monthly by rapid HIV-1 antibody tests, supplemented by HIV-1 RNA polymerase chain reaction (PCR), p24 Western blotting and/or ELISA. Samples obtained prior to the first positive rapid antibody test were retrospectively tested by HIV specific PCR to identify window period infections. The date of infection in this study was estimated as the midpoint between the last negative and first positive antibody test, or 14 days prior to the first HIV-1 RNA-PCR positive result. Multi-parametric flow cytometry techniques developed and validated in healthy blood donors were used to asses the bidirectional relationship between NK cells and HIV-1. To simulate in vivo interaction between NK cells and autologous HIV infected cells, an in vitro infection and coculture assay was used in addition to conventional assays of NK cell recognition of HLA-deficient cell lines. These were supplemented with measurement of plasma cytokines by Luminex and microbial products by ELISA. In this study, 44 cases who acquired HIV-1 were sampled prior to infection and 39 controls who remained HIV-1 negative despite high behavioural exposure at the timepoint when their preceding sexual activity was highest. To understand how HIV infection affected NK cells during early HIV-1 infection, the first sample obtained after acquisition was studied and compared to preinfection samples from the same participant. The case and control groups were broadly similar in the proportions using tenofovir gel, proportions infected with HSV-2 and number of sexual partners but tended to be marginally older than cases (27.6 vs 23.3 years). By design control women had higher sexual activity than cases (mean 11 vs. 5.7 sex acts per month). The frequency of IFN-γ secreting NK cells from women who acquired HIV infection were significantly lower than from women who remained uninfected in response to 721 cells-an EBV transformed B cell line (background-adjusted median 13.7% vs. 21.6%; p=0.03) and to autologous HIV infected T-cells (background-adjusted median 0.53% vs. 2.09%; p=0.007). NK cells from HIV acquirers displayed impaired proliferation but enhanced spontaneous degranulation compared with non-acquirers after co-culture with HIV uninfected or infected autologous T-cell blasts. Adjusting for age, gel arm, HSV-2 infection status and levels of NK cell activation, IFN-γ+ NK cell responses to autologous HIV infected cells were associated with reduced odds of HIV acquisition (OR 0.582; 95% CI 0.35-0.98; p=0.04). In addition, even in the absence of ex vivo stimulation, HIV acquirers had higher levels of generalised innate immune activation measured by systemic cytokine concentrations (TNF-α, IL2, IL-7 and IL12p40), peripheral blood platelet concentrations (p=0.038), and non-specific ex vivo NK cell activation (p<0.001). Generalised NK cell activation measured directly ex vivo without stimulation was associated with acquisition. Further, if innate immune activation was assembled as a principal component in an unsupervised fashion but taking into account all the measures made, it was significantly associated with HIV acquisition (OR adjusted for age, tenofovir gel use, and HSV-2 status for PC with innate immune factor loadings 11.27; 95% CI 1.84- 69.09; p=0.009). The causes of preinfection innate immune activation could not be established in this study but the degree of activation could not be explained by microbial translocation as both HIV acquirers and non-acquirers had similar levels of plasma lipopolysaccharide (LPS), soluble CD14 (sCD14) and intestinal fatty-acid binding protein (I-FABP). Similarly, both HIV acquirers and non-acquirers had similar NK cell and cytokine responses to Toll-like Receptor (TLR)-2, 3 or 7/8 agonists 11. During early HIV-infection, NK cells demonstrated significantly higher activation (p=0.03), expression of Killer-cell immunoglobulin-like Receptors (KIR) (p=0.006) and expression of chemokine receptor 7 (CCR7, p<0.0001) compared with prior to acquisition. Although NK cells had reduced cytolytic potential following HIV acquisition, antiviral IFN-γ secretion appeared to be preserved. NK cell responses were not different between tenofovir and placebo gel recipients, but women who acquired HIV whilst using tenofovir gel had higher gag-specific IFN-γ CD4+ T-cell responses during early infection. Overall, the findings suggest that the frequency of NK cells producing IFN-γ specifically after co-culture with HIV-1 infected target cells was associated with protection from HIV-1 acquisition but, generalised, non-specific activation of NK cells and other innate immune components enhanced HIV acquisition. Since neither microbial translocation nor TLR responsiveness were associated with pre-existing immune activation further studies will be required to identify the drivers of generalised innate immune activation. Methods to dampen generalised innate immune activation and/or augment specific NK cell antiviral responses in women at risk for HIV-1 may reduce HIV-1 acquisition. During primary HIV-1 infection, NK cells underwent impairment of cytolytic function but not IFN-γ secretory function; this may affect their ability to affect disease progression. Although Tenofovir gel did not alter innate immune responses in women with breakthrough infection, it preserved HIV-specific Tcell immune responses, the consequences of which need further exploration. Understanding how Tenofovir gel mediated preservation of adaptive immune responses may lead to interventions that will reinforce protective host responses. In conclusion, innate immune responses by NK cells have been shown to impact HIV acquisition; HIV-specific IFN-γ responses by NK cells were protective while generalised NK activation was detrimental. The causes of innate immune activation are not known but these effects were independent of the impact of Tenofovir gel. Future prevention strategies targeting mucosal transmission of HIV should assess their impact on NK cell responses, to avoid general innate immune activation and enhance their ability to protect against HIV acquisition. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2013.

Infection with HIV-2 has important implications for the diagnosis, treatment and management of the infection. The objective of this study was to describe the seroprevalence and molecular epidemiology of HIV-2 in KwaZulu-Natal – the province with the highest HIV prevalence in South Africa, which in turn is the country with the highest HIV prevalence in the world. HIV-1 positive samples were screened using a rapid test for HIV-2. Samples showing antibody positivity were subject to molecular confirmation by PCR and / or serological confirmation by Western blot. There was a large difference in results (10.6% by Western blotting versus 0% by PCR). This discrepancy between molecular and serological confirmation by Western blot. There was a large difference in results (10.6% by Western blotting versus 0% by PCR). This discrepancy between molecular and serological confirmation was attributed to cross-reacting antibodies. The use of rapid tests and Western blots for HIV-2 diagnosis in South Africa, should, therefore, be interpreted with caution. Based on the results of this study, HIV-2 is most probably not present in KwaZulu-Natal. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, Durban, 2013.

KwaZulu-Natal has the highest prevalence of HIV in South Africa. The prevalence of dual infection in a normal-risk population in this region is unknown. Dual HIV infection has important implications for diagnosis, treatment response and vaccine development. This cross-sectional study aimed to establish and optimize methods for subtyping and detection of dual infection in KZN. Samples were from chronically-infected patients on ARV treatment within the ARV Rollout Programme, from sites throughout KZN. Subtyping of the samples was performed using HMA. Four samples had indeterminate results by HMA and were then cloned and sequenced. Phylogenetic analysis showed that one of the four samples was a dual infection. This study showed 1/46(2%) samples to be dually infected which suggests that the prevalence of dual infection is low in the sample population. The low prevalence of dual infection reported could be due to the low-risk profile of the sample population. It was concluded that the low prevalence of dual infection is unlikely to have a considerable impact on HIV management. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, 2007.

Autopsy liver material from patients having died of chronic liver disease, cirrhosis, hepatocellular carcinoma (HCC) and causes unrelated to liver diseases was examined by dot blot hybridisation for the presence of HBV DNA. The results indicate that of the patients with chronic liver disease 6/9 were positive for HBV DNA in the liver tissue; of the patients with HCC 3/4 were positive for HBV DNA; of the patients with cirrhosis 4/4 showed the presence of HBV DNA in the liver. Thus by this technique 13/17 (76%) of these patients, all of whom were HBsAg positive, were shown to have HBV DNA present in liver tissue. However, autopsy liver samples were found to be unsuitable for Southern blot hybridisation. Biopsy liver/tumour tissue was examined for the presence of integrated or non-integrated HBV DNA by Southern blot analysis using the enzymes Eco R1 and Hind 111. 5/5 patients who were both HBsAg and HBeAg positive had extrachromosomal HBV DNA and 2/5 also showed the presence of integrated HBV DNA. 3/4 patients who were HBsAg positive and HBeAg negative had extrachromosomal HBV DNA and all three also had integrated HBV DNA. One control patient was negative for both markers and also for Southern blot hybridisation with the HBV DNA probe. These results support the hypothesis that HBV is a factor in the development of HCC, and indicate that the dot blot hybridisation method would be suitable for routine evaluation of patients with chronic liver disease or cirrhosis. / Thesis (M. Med.)-University of Natal, Durban, 1987.

As South Africa begins its National HIV-1 treatment program, it is urgent that we collect data that will help define the phylogenetic relationships, transmissibility and drug responsiveness of C viruses. In this thesis, data is presented on the genetic diversity of locally circulating drug naive subtype C strains, as an indication of their natural susceptibility to antiretroviral drugs, prior to the national roll-out of antiretroviral therapy. At the time this thesis was initiated, antiretroviral therapy was only available in South Africa in a few clinical trials and in the private sector, and it was therefore difficult to obtain large numbers of samples from treatment-experienced patients. Nevertheless, valuable information on the prevalence and patterns of resistance mutations in subtype C infected patients was obtained from small studies on patients receiving HAART, concomitant HAART and TB treatment, HAART and treatment for Kaposi Sarcoma, and single dose nevirapine for the prevention of mother-to-child transmission of HIV-1 infection. The results show that the general antiretroviral drug naive population do not harbour any major resistance-associated mutations to the currently available protease and reverse transcriptase inhibitors, with no differences in genetic variation between the different ethnic groups infected with subtype C. Phenotyping of some of these isolates showed that they were susceptible to the available protease and reverse transcriptase inhibitors, and hyper-susceptible to the protease inhibitor, Lopinavir. Phylogenetic analysis of recent and retrospective subtype C isolates showed that there are multiple lineages of subtype C viruses circulating in South Africa, indicative of multiple introductions of subtype C across its many borders. Polymorphisms in the protease, reverse transcriptase and C2-V5 region of envelope in these drug naive samples lead to significant variation in the number, type and location of potential phosphorylation sites. There was also variation in the cleavage sites controlling the initiation and rate of Gag and Gag-Pol processing (p2/NC) and the activation of protease (TFP/p6gag) suggesting that there may be important differences in the way that B and C viruses regulate polyprocessing and virion assembly. Similar to studies on subtype B, 10 to 18% of the patients on HAART developed drug resistance. However, those on concomitant HAART and TB treatment developed resistance as early as one month after starting treatment. Generally, the resistance mutations that were seen were consistent with those seen in treatment experienced subtype B isolates. Of note was the high level of resistance to the entire class of NNRTIs. This could be reflective of the predominant use of NNRTI-based regimens, as well as the low genetic barrier in this class of drugs. The NNRTI mutations included the V106M mutation that is considered a signature mutation of EFV experienced subtype C isolates. Resistance was high (40%) in mothers and infants 6 weeks after each received a single dose of NVP. K103N was most common mutation in the mothers, while Y181C was most common in the infants. Of note were the changes in functional properties caused by these mutations, by the introduction or alteration of putative myristoylation and phosphorylation sites in the RT. Taken together, these data suggests that the pattern of resistance in African patients will be similar to that observed for the treatment of subtype B infection. However, patients should be closely monitored for viral rebound very early on in treatment. Also, given the high rate of resistance in mothers and infants after single dose NVP, the search for safer regimens to prevent MTCT should be intensified. Although the mechanisms are unknown, our results indicate that several of the phosphorylation-related substitutions in the pol and env genes of KZN and other C viruses are highly conserved and positively selected. It will be important to determine whether these sites play an important role in the replicative capacity and proteolytic processing of C viruses, and in viral entry. These data provide important benefits for public health policy and planning and for future patient treatment management. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2004.

The study of retroviruses has been of pivotal significance to the field of biomedical science, where it has provided fundamental insights into the processes underlying both viral and non-viral carcinogenesis. Ovine pulmonary adenocarcinoma (OP A), a contagious lung cancer of sheep and goats, has emerged over the past three decades as an invaluable model of human epithelial cancers. It is one of the very few animal models of retrovirus induced neoplasia of epithelial tissues, whereas most other such animal models of human cancers pertain to the haematopoietic system. OP A represents a unique, naturally occurring, inducible, outbred animal model of peripheral lung carcinomas, and is caused by a betaretrovirus - jaagsiekte sheep retrovirus (JSRV) - that is receiving increasing attention in the fields of retrovirology and lung cancer research. JSRV exists in two highly homologous, yet molecularly distinct forms. The first is an exogenous form of the virus that is transmitted horizontally from one animal to another. This form is infectious and the direct cause of OP A. The other is an endogenous form, 15 to 20 proviral copies of which reside benignly in the genome of sheep and are transmitted vertically from one generation to the next. At the time this study commenced, no knowledge existed regarding the underlying pathogenic mechanism by which JSRV causes OPA. Even though the nucleotide sequence of exogenous JSRV had been elucidated seven years earlier, only limited sequence information was available on endogenous JSRVs. With a view towards identifying genetic regions or elements within exogenous JSRV that could potentially be implicated in its pathogenic function, this study began with the cloning of the first three full-length endogenous JSRV loci ever isolated from sheep. The DNA sequences of these full-length endogenous JSRV loci were determined and comprehensively analysed. Comparison with exogenous JSRV isolates revealed that the two forms of the virus are highly homologous, yet can be consistently distinguished in three short regions within the coding genes. Two of these reside in the gag gene, and one at the end of the env gene. These regions were named the variable regions (VRs) of sheep betaretroviruses. The JSRV VR3 in env was linked by our collaborators to the virus's ability to transform cells in tissue culture. The effects and biological significance of VRI and VR2 in gag are subtler and more difficult to determine. After identifying these regions, it became the objective of this study to develop relevant molecular tools that could be used to discern the significance of these variable regions in vivo, and to characterise these tools in vitro to assess their suitability for in vivo studies. The development of these tools entailed the design of a novel strategy that was implemented to precisely substitute the endogenous VRI and VR2 (individually and in combination) into an infectious molecular clone of exogenous JSRV. These chimeric constructs were shown to support retroviral particle release into the supernatant of transiently transfected cells in tissue culture. These particles were confirmed by independent experiments to have arisen specifically from transfection with the chimeric clones. Finally, the particles were shown to be capable of infecting cultured cells and of productively integrating their genomes into those of their host cells, rendering these particles fully competent retroviruses that can be used in the context of in vivo studies to determine the biological significance of VRI and VR2. This study has made a significant contribution to the further development of the OP A / JSRV model system of human epithelial lung cancers. It has also led to the design of a molecular substitution strategy that can be adapted to introduce any genetic region into a cloned DNA construct, regardless of the degree - or lack of interrelation - of the two DNA sequences, thereby creating a highly versatile molecular biological tool. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2007.

No abstract available. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2011.

HIV is known to affect the epidemiology, transmission, pathogenesis and natural history of HCV infection whilst studies on the effects of HCV on HIV have shown conflicting results and are confounded by the influence of intravenous drug use and anti-retroviral therapy. This study was conducted in KwaZulu-Natal Province in South Africa where HIV is predominantly a sexually transmitted infection. Intravenous drug use is rare in this region and the study population was naive to anti-retroviral therapy. For this study, specimens from selected sentinel sites submitted to a central laboratory for routine HIV testing were screened for anti-HCV IgG antibodies. HIV positive HCV-positive patients were compared to HIV-positive HCV-negative patients in a subgroup of patients within this cohort in order to determine if HCV sero-prevalence was associated with clinical outcomes in a linked anonymous retrospective chart survey. The prevalence of HCV was 6.4% and that of HIV, 40.2%. There was a significantly higher prevalence of HCV among HIV infected patients as compared to HIV negative patients (13.4% vs. 1.73% respectively). HCV-HIV co-infected patients had significantly increased mortality (8.3 vs. 21%). A significant association was found between HCV serostatus and abnormal urea and creatinine levels. Hepatitis B surface antigen seropo-sitivity was not found to be a confounding factor. This study has found that hepatitis C co-infection is more common in HIV positive individuals and is associated with an increased mortality and renal morbidity. / Thesis (M.Med.)-University of KwaZulu-Natal, Durban, 2008.