Pneumonia is a common diagnosis in general practice and is associated with significant morbidity and mortality. Current estimates of pneumonia incidence in the UK are based on studies more than a decade ago and little is known about longer term outcomes in pneumonia patients. Though much is known about the aetiology of pneumonia and predictors of mortality, an emerging area for research is the relationship between commonly prescribed drugs in general practice and pneumonia. The aims of this thesis were first, to determine overall incidence and mortality for pneumonia and how these vary by socio-demographic characteristics like age, sex, deprivation; and second, to investigate whether statins, angiotensin converting enzyme inhibitors (ACEIs) and gastric acid suppressants like proton pump inhibitors (PPIs) and histamine 2 receptor antagonists (H2RAs) modify the risk of acquiring pneumonia and its prognosis. This study used data from The Health Improvement Network (THIN) database, a longitudinal database of anonymised computerised medical patient records from 330 United Kingdom (UK) general practices at the time of data extraction in 2006. A cohort design was used to determine pneumonia incidence and mortality in the UK. Case-control, case-series and cohort study designs were used to investigate associations between the various drug exposures and pneumonia. The overall incidence of pneumonia was 237 per 100,000 person-years (95 % confidence interval (CI): 235 to 239) and this rate was stable between 1991 and 2003. Pneumonia was more common in men and in children under the age of four years and adults over the age of 65 years. There was an increased incidence of pneumonia with higher levels of socioeconomic disadvantage. Pneumonia cases showed much higher all-cause mortality as compared to the general population, both in the short and long-term and this increase was independent of underlying comorbidity. After adjusting for potential confounders, current prescriptions for statins and ACE inhibitors were associated with a significant reduction in the risk of acquiring pneumonia. Current prescriptions for PPIs were associated with an increased risk of pneumonia. With regards the impact on mortality: the use of statins was associated with a lower risk of short and long-term mortality following pneumonia whereas the use of ACEIs was associated with a decreased mortality risk only in the short-term. No relationship was observed between prescriptions for PPIs, H2RAs and pneumonia mortality. This study shows that caution must be exercised while prescribing proton pump inhibitors especially in patients known to be at high risk of pneumonia. There is also a potential role for statins in preventing pneumonia in at-risk patients and improving pneumonia outcomes but this will necessitate clinical trials to determine adequate dose, duration and safety profiles before any prescribing policy recommendations are made.

There are many surgical implanted devices in current use and all are prone to biomaterial-related infections (BRI) associated with staphylococcal biofilm formation. BRI are usually associated with S. epidermidis or S. Aureus and are characterized by treatment failure and chronicity resulting in reoperation, removal of the implant, and loss of function or death. Staphylococcal small colony variants (SCVs) may be generated by exposure to sublethal concentrations of antibiotics or nutrient limitation which may occur in biofilms. Although the characteristics of S. aureus SCVs have been well studied, little information on SCVs of S. epidermidis and their potential role in BRI is currently available. This study was designed to investigate the biochemical and phenotypic characteristics of S. epidermidis SCVs to further identify characteristics which may contribute to their ability to cause these increasingly important infections. Exposure to two to four times the gentamicin MIC led to the emergence of stable S. epidermidis SCVs, and the ability to produce SCVs was strain dependent. These variants were isogenic by PFGE and less immunogenic by western blotting, and SDS-PAGE analysis of whole cell preparations and cell wall fractions showed altered protein profiles when compared to wild type strains. S epidermidis SCVs were resistant to aminoglycosides such as amikacin and/or netilmicin and they were thiamine and/or menadione auxotrophs. Chemiluminescence assays showed a decreased ATP content reflecting the deficiency in electron transport systems which results in a growth rate – all characteristics similar to those of S. aureus SCVs. Analysis of virulence factor production indicated that S. epidermidis SCVs showed increased lipolytic and proteolytic activity when compared to those of S. aureus. Some S. epidermidis SCVs showed phase variation in exopolysaccharide production which enabled them to be more adherent to uncoated plastic -a property that may also be important for the later stages of development of biofilms. Invasion assays demonstrated that some S. epidermidis and S. aureus SCVs were internalised by HUVECs by a receptor-mediated mechanism which differed from that of the wild type strains. Interaction of staphylococci with HUVECs induced cytokine production but SCVs stimulated production of IL1, IL-6 and IL-8 at lower concentrations than their related wild type parents in the first 6 hours of co-incubation. SCVs were also less damaging to the HUVEC cell line after 24 hours when compared to wild type strains. This study supports the suggestion that a switch to the S. epidermidis SCV phenotype could be a mechanism exploited by the wild type strains to facilitate their survival inside the host. The chronicity and increased antibiotic resistance associated with BRI could in part, be explained by the characteristics of SCVs identified in this study. In particular the ability to survive intracellularly combined with reduced immunogenicity and resulting decreased cytokine production, may contribute to persistence of infection. Although SCVs are resistant to some antibiotics, surviving intracellularly may further protect staphylococci from other drugs which are unable to enter mammalian cells. Resistance may be further enhanced for some strains in biofilms where enhanced polysaccharide production may also limit antibiotic access.

Since discovery H. pylori has been one of the most intensively researched bacteria. Although the majority of those infected remain asymptomatic it can lead to serious diseases which carry significant morbidity and mortality. The most serious complication of H. pylori infection is gastric cancer and one of the most effective ways to reduce the associated mortality is to detect pre-malignant disease, as this develops in a step wise manner. Using advanced endoscopy is one way to detect pre-malignant conditions but due to the variety in endoscopic techniques and mucosal classifications the diagnosis is often dependent on histology. This work aimed to develop simple, accurate classification systems to detect H. pylori associated disease. The sensitivity and specificity of magnification Narrow Band Imaging for detecting H. pylori gastritis was 69% and 67%, intestinal metaplasia 87% and 97% and dysplasia 92% and 98% respectively. H. pylori is also associated with iron deficiency anaemia but the mechanisms remain unclear. In children it has been proposed that H. pylori disrupts iron regulatory mechanisms via the peptide hepcidin but this has not been extensively researched in adults. Serum hepcidin was significantly lower in H. pylori infected anaemic individuals and anaemic individuals without evidence of infection when compared to controls (9-fold, p=0.009 and 5-fold, p < 0.0001 respectively). These results are opposite to data from children, possibly explained by the presence of gastric atrophy. The cellular localisation of ferroportin was different in the H. pylori infected group which could be due to local cytokine production. Gaining a better understanding of this mechanism could aid the development of more targeted investigation and treatment. However, with regards to allergic and autoimmune conditions, there is growing evidence to suggest H. pylori is inversely associated. It is believed that any benefit associated with H. pylori is confined to childhood when the immune system is developing. A significant reduction was seen in IL10+ Tregs (p=0.0029) after successful eradication suggesting the removal of H. pylori may have systemic consequences on the immune system that are still not fully understood. This work has highlighted the use of endoscopic techniques to identify individuals at risk of disease. It has also described the effects of eradication on the immune system which potentially could have implications for individuals with allergic conditions with regards to eradication therapy.

In the human gastric mucosa, an inflammatory response stimulated by H. pylori infection can lead to gastric cancer and peptic ulcer disease. Expression of the i1 active variant of Vacuolating Cytotoxin A (VacA) by the colonising bacterial strain has been identified as an independent risk factor for disease. VacA skews the adaptive immune response towards a regulatory phenotype to promote persistent H. pylori colonisation. In H. pylori-infected individuals, regulatory T cells (Tregs), which suppress inflammation through mechanisms including interleukin-10 (IL-10) production, are thought to play a role in protection against extra-gastric diseases such as multiple sclerosis and oesophageal cancer. IL-10 is an immunomodulatory cytokine which is expressed by several immune cell types including regulatory B cells (Bregs), whose role in H. pylori infection is unclear. Blood was donated by uninfected and infected patients, and those who underwent successful eradication of their H. pylori infection. A flow cytometry antibody panel was developed to quantify the relative frequencies of peripheral blood Bregs and Tregs, and investigate differences according to H. pylori status. Mice were also infected with H. pylori to determine VacA i1 versus i2 differences in the induced regulatory B and T cell frequencies. Stool samples were collected from patients to develop a VacA i-region PCR-based diagnostic test. Results showed that compared to during H. pylori infection, the proportion of IL-10-producing Tregs in the peripheral blood of patients declined after successful eradication therapy. A pilot study in mice revealed B lymphocytes to be another important source of IL-10, and the population expanded after H. pylori infection. In a study of H. pylori-positive, H. pylori-negative and H. pylori-eradicated patients, there were no significant differences in peripheral blood Breg or IL-10+ Breg frequencies. Data from an expanded mouse study using blood and spleen showed that VacA variants in a colonising H. pylori strain did not induce differences in Breg or Treg frequencies 9 weeks after wildtype or mutant H. pylori SS1 infection. The H. pylori 16S gene was successfully detected in stool DNA samples and could be used to determine infection status, but the development of a vacA i-region PCR-based typing stool test was unsuccessful. Previous work in the research group has identified how Treg frequencies are associated with H. pylori infection and disease. While Bregs are capable of producing IL-10 after stimulation, their role in H. pylori infection in mice and humans appears to be limited. The consistency of peripheral blood Treg frequencies in patients from their infected state until two years post-eradication is a start to understanding whether H. pylori-induced extra-gastric protection may also be maintained after eradication. While stool remains a promising resource for non-invasively diagnosing H. pylori infection worldwide, there are strong concerns about contamination and reproducibility which are unlikely to be overcome for use in a clinical setting.

Background: After three decades, Human Immunodeficiency Virus (HIV) continues to pose significant threats globally. The efforts to curb the HIV epidemic have required investment in research, with clinical trials being a major focus, to develop HIV prevention, treatment, and cure interventions. A large portion of such research has been undertaken within low income settings, due to the high burden of HIV and the availability of willing volunteers within this setting. HIV research calls for the implementation of ethical research practice which is informed by policy guidelines. However, current policies are largely informed by inputs from high income countries, and lack the voices of those closely involved in research implementation. In order to contribute to ethics policy development in HIV research, it is essential to involve different stakeholders by exploring their experiences/views on the issue. Existing research in this field has mainly explored experience of recruitment and trial conduct, while very little has been done on trial closure, indicating a significant evidence gap worth exploring. This research therefore sought to illuminate, explore and understand the significant issues regarding the care of HIV positive drug trial participants during closure of HIV clinical trials, within a low income setting, specifically, Uganda. Study aim: The study aimed to explore how care is perceived and enacted in HIV drug trial closure in Uganda, by addressing the following specific objectives: 1. From the perspective of research participants and research staff, to explore the views, opinions and understandings of the ethical/legal/moral post-trial obligations in HIV drug trials. 2. From the perspective of research staff, to explore the experiences, practices and processes related to care for HIV drug post-trial participants in a low income setting. 3. From the perspective of research participants, to explore the experiences of care at trial closure. 4. From the perspective of research participants, to explore the experiences of transitioning from HIV research to care/community. Methodology: The study adopted an interpretive-constructivist approach, and employed a social constructivist grounded theory methodology. The study included a total of 21 trial participants and 22 research staff from three different HIV drug trials, in two Ugandan research institutions. In addition, relevant ethical documents were reviewed from two of the included trials. Data collection and analysis followed the principles of grounded theory, with data collection and preliminary analysis being undertaken concurrently, and earlier data informing subsequent data collection. Data collection strategies included individual interviews, focus group discussions, and key informant interviews. Data was collected over a period of 10 months, from October 2014 to August, 2015. NVivo10 software was used to manage the data. Ethical approval was received from the University of Nottingham UK and The AIDS Support Organization (TASO) Uganda, Research Ethics Committees (RECs). The study was registered with the Uganda National Council for Science and Technology (UNCST), as SS 3608. Permission to conduct the research was granted by the respective research institutions, and written informed consent was received from all respondents. Findings: The findings showed that trial closure was often stressful for HIV positive participants in Uganda, and often resulted in negative psychological, socio-economic and health impacts. The negative effects mainly resulted from being stopped from accessing research related health care, which was of a significantly higher quality, and the inability to find alternative care to match the research standards. The main concerns which arose during the transition process of participants from HIV drug trials to usual care facilities include: the loss of the quality care and valued relationships in research, the need to find and link to alternative care facilities, the need to meet the increased financial needs, and worries about the effects/outcomes of research participation. These concerns demanded a range of additional care and supportive strategies from researchers (and other stakeholders). A conceptual model, the model of ‘Facilitated Transition’ was developed, which summarises the findings of this research and provides a diagrammatic representation of the research findings, showing the links and relationships between the different elements. The research established that the transition of HIV positive trial participants from research to usual care facilities is a process, which appears to consist of three overlapping phases. These phases include: The pre-closure phase which represents events occurring before the actual trial closure but that underpin post-trial care, the trial closure phase which is the active phase of the closure, in which trial participants are prepared and exited from the trials, and the post-trial phase which represents the events occurring after trial participants have been linked to post-trial care facilities until 12 months later. These phases are demarcated by specific time points, which reflect how the transition process evolves, proceeds and concludes. At the various phases of the process, specific concerns (care needs) arise, being influenced by the participants’ previous care experiences and perceptions, plus their health and socio-economic positions. Specific actions are required to proactively facilitate trial participants during these phases. These actions are underpinned by the perceived ethical and moral responsibilities of the researchers, and are principally aimed at establishing a continuum of HIV care and treatment after trial closure, promoting positive care experiences for trial participants during the transition, and enabling the settlement and adaptation of trial participants to care in the public healthcare system. Conclusions: This is the first known study to investigate perspectives on post-trial care among HIV positive trial participants in a low income setting, from those closely engaged in the research process. This study has provided novel contributions in the area of HIV research ethics and post-trial care in general. The study has established that trial closure involving HIV positive participants raises significant ethical, moral and practical concerns in the Ugandan context. The findings further demonstrated that current post-trial care practice does not meet all the care needs of the HIV positive trial participants. Existing ethical recommendations on post-trial care place an emphasis on the need to ensure access to trial drugs and provision of trial results, where as less attention is given to other important aspects, as revealed in this research. To meet the post-trial care needs of HIV positive participants in Uganda, a comprehensive trial closure strategy is required. In addition to the already existing aspects of post-trial care, the new strategy should aim to: (i) address the financial needs of trial participants through financial assessment, support and empowerment, (ii) provide practical support during linkage to post-trial care, and (iii) offer post-trial follow-up to monitor and support the participants. Implementing these recommendations may require involvement of various stakeholders, including researchers, ethics authorities, research funders and donors, public healthcare workers, families, trial participants, and the community. Recommendations for future research: Further research is required to ascertain the rates of linkage to care, and to assess the health outcomes of post-trial participants following trial exit. In addition, a study to target the views of other stakeholders, such as the public healthcare facility workers, the family, and ethics authorities on post-trial care may be essential to understand better the ways in which to support HIV positive trial participants in Uganda. Furthermore, a longitudinal prospective study on a larger sample is required to test the model proposed in this research. And finally, there is need to deliberate more on the ethical and moral implications of financial benefits in HIV research involving HIV positive participants in a low income setting.

Background: The immunological as well as the psycho-social impact, of living with HIV/AIDS transform HIV/AIDS into a multidimensional process. Stigma and discrimination against people living with HIV/AIDS (PLWHA) are proposed as hostile scenarios increasing hopelessness and reducing perceived and real social support affecting people’s health status. Peer support strategies are proposed as key factors for dealing with this scenario; additionally, socio-cultural variables may determine the provision and perception of social support. Objectives: To enhance the understanding of the process of living with HIV/AIDS and the role played by social support and to suggest cooperative strategies for dealing with stigma and discrimination against PLWHA to improve people’s health. Sample and method: Five studies were conducted studying 37 HIV positive members and non-members of peer support organisations (PSOs) in Chile and England; nine healthcare professionals working with PLWHA; and three spokes persons from PSOs of PLWHA from Romania, England and Chile. Results: PSOs of PLWHA, which reflect a cooperative strategy used by PLWHA to deal with stigma and self-provide social support, appear to play an important and underexplored role in PLWHAs’ health status; this relationship is also affected by socio-cultural characteristics. A measure of PSS was developed and theoretical analysis lead to a linkage with Maslow’s hierarchy of needs. Personality characteristics were found critical for the success of PNI based interventions. Conclusions: Living with HIV/AIDS involves psychological and social complications. PSOs are a powerful cooperative strategy improving quality of life and general health; however, further research is needed to establish the real impact of PSOs over HIV+ people. Implications: The peer-support strategy of PSOs is a powerful but underused clinical strategy. Healthcare teams and PLWHA may benefit from including this strategy if cooperative work is carried out with PSOs.

Background: Allergic disease is uncommon in developing countries, especially in rural areas. A protective effect of helminth infection has been implicated as a potential explanation. Objectives: To determine whether reduced exposure to helminth infection is associated with a higher risk of allergen skin sensitisation and allergic disease, and whether such an association could be explained by a helminth-induced up-regulation of certain cytokines, in particular anti-inflammatory IL-10. Methods: We invited 1,742 rural Vietnamese schoolchildren to take part in a cross-sectional baseline survey followed by a randomised, double blind, placebo-controlled trial of anti-helminthic therapy at 0, 3, 6, and 9 months to compare the change in exercise-induced bronchospasm (primary outcome), wheeze, rhinitis, eczema, and allergen skin sensitisation (secondary outcomes) at 12 months. 244 secondary schoolchildren also had venous blood taken to measure helminth induced IL-10, IFN-gamma, IL-5, and IL-13. Out of these 244 children, 144 were infected with hookworm and had bloods taken again at 12 months. Results: Baseline survey 1,601 schoolchildren (92% of those eligible) in grades 1-9 aged 6-18 participated in the baseline survey. 0.4% (6/1601) of children had a fall in peak flow after exercise of at least 15%. Doctor-diagnosed asthma was equally rare (0.4%, 6/1601), while 5.0% (80/1601) of children had experienced wheezing over the past 12 months. 6.9% (110/1601) of parents reported that their children had suffered of hay fever in the past 12 months, and in 2.6% (41/1601) of cases this diagnosis was confirmed by a doctor. 5.6% of children (89/1601) reported an itchy rash over the past 12 months. 0.9% (14/1601) had a history of flexural involvement and on examination 0.5% (8/1601) proved to have flexural eczema on the day of the survey. Skin prick test positivity was commoner than allergic disease. 33.5% (537/1601) of children had at least one positive skin prick test (dustmites 14.4%, cockroach 27.6%). The cross-sectional analysis yielded only significant results for allergen skin sensitisation. In univariate analysis, sensitisation was less frequent in children with hookworm or Ascaris infection, and increased in those with better santitation, including flush toilets and piped drinking water. In multivariate analysis, the risk of allergen skin sensitisation to house dust mite was reduced in those with Ascaris lumbricoides infection (adjusted OR=0.28, 95% CI 0.10-0.78) and in children with higher hookworm burden (adjusted OR for 350+ versus no eggs per gram faeces=0.61, 0.39-0.96), and increased in those using flush toilets (adjusted OR for flush toilet versus none/bush/pit=2.51, 1.00-6.28). In contrast, sensitisation to cockroach was not independently related to helminth infection but was increased in those regularly drinking piped or well water rather than from a stream (adjusted OR=1.33, 1.02-1.75). Intervention study 1,566 children in grades 1-8 completed the baseline survey and all consented to be randomised to either anti-helminthic treatment or placebo. 1487 children (95%) completed the intervention study. There was no effect of therapy on the primary outcome, exercise-induced bronchoconstriction (within-participant mean % fall in peak flow from baseline after anti-helminthic treatment 2.25 (SD 7.3) vs placebo 2.19 (SD 7.8, mean difference 0.06 (95% CI -0.71-0.83), p=0.9), or on the prevalence of the secondary clinical outcomes questionnaire-reported wheeze (adjusted OR=1.16, 0.35-3.82), rhinitis (adjusted OR= 1.39, 0.89-2.15), or flexural eczema (adjusted OR=1.17, 0.39-3.49). However, anti-helmithic therapy was associated with a significant allergen skin sensitisation risk increase in the treatment compared to the placebo group (adjusted OR=1.31, 1.02-1.67). In post-hoc analysis this effect was particularly strong for children infected with Ascaris lumbricoides at baseline (adjusted OR=4.90, 1.48-16.19), the majority of whom were co-infected with hookworm. Cytokine profiles Hookworm-induced IL-10 was inversely related to allergen skin sensitisation (any positive skin prick test) at baseline, but this result missed conventional statistical significance (univariate OR=0.70, 0.48-1.03; adjusted OR=0.72, 0.44-1.18). No other cytokine response was associated with skin prick test positivity at baseline (univariate OR IFN-gamma=1.15, 0.71-1.85; univariate OR IL-5=0.84, 0.53-1.33). Similary, no significant changes in any of the cytokine profiles were observed following anti-helminthic therapy in the treatment compared to the placebo group (p=0.3 for all three cytokines). Conclusion The baseline study suggested that hookworm and Ascaris infection, sanitation and water supply independently reduce the risk of allergic sensitisation. The intervention study confirmed that helminth infection and allergic sensitisation are inversely related and that the effect of Ascaris and hookworm infections on skin prick test responses is additive. However, we found little evidence to suggest that this effect was mediated by IL-10. There was also insufficient evidence to suggest that loss of exposure to gut worms for 12 months results in an increase in clinical allergic disease. The effect of more prolonged de-worming warrants further research.

Background: The global policy focus of today’s HIV efforts and strategies is to reverse the spread of HIV/AIDS and provide care, treatment and support. A key component of this strategy is to increase individual HIV status awareness through expansion of HIV testing and counselling (HTC). However, the numbers tested still remain low and evidence suggests that there are significant missed opportunities for HIV testing in clinical settings. One key strategy to expand HTC in clinical settings has been to implement a policy of ‘provider initiated counselling and testing’ (PITC) in which all patients accessing health facilities for treatment are routinely offered a HIV test. The introduction of PITC has brought with it a ‘dilution’ of the previously lengthy and stringent testing process by doing away with signed informed consent and extensive pre and post test counselling. The previous process was recognised as a barrier to public health gains of HIV testing expansion, particularly as it differentiated an HIV test from other routine medical tests resulting in a sense of HIV exceptionalism. In its place, the PITC policy recommends an opt-out approach and replaces the extensive pre test counselling with an information giving session placing more emphasis on post test counselling in cases where the result is positive. This change has given rise to debates about the potential for PITC to infringe patients’ rights to informed consent and counselling especially in developing countries. Emerging evidence from the exploration of the PITC process within antenatal settings in the Sub Saharan Africa has revealed some of the complexities of implementing PITC guidelines in different cultural and healthcare contexts. These studies suggest that information giving and consent are difficult to apply in contexts characterized by healthcare worker dominance, lack of sufficient resources and time constraints. This study aimed to specifically investigate how patients and counsellors co-construct informed consent and perform counselling during the PITC consultation. It examined ‘real time’ patient-counsellor interaction within hospital outpatient and inpatient settings in Kenya, explored the patient’s experience of a routine HIV test and evaluated how stigma and patient – provider interaction norms influence the PITC process in this context. Methods: In order to explore the context of the routine testing consultation and the way the interaction played out, a qualitative research approach was adopted, utilizing multiple data collection methods (interviews, observations and audio recording of consultations). The study was carried out in two government run health facilities in Kenya’s capital, Nairobi. The intention was to follow patients through the PITC process, i.e. before testing, during the HIV test and (whenever possible) after the HIV test. To get a broader picture of the events during the routine HIV testing consultation, additional interviews were conducted with five nurse-counsellors whose consultations had been observed. Ethical approval was obtained from the Kenya National Research Council, Kenya Medical Research Institute and the Aga Khan University Ethics Committee. The data were analysed using Charmaz’s constructivist grounded theory approach which allowed for a systematic yet flexible approach to analysis. This method facilitated immersion and engagement with the data, and provided a means of managing the different data sets in the study and undertaking a process of constant comparison within and between data sets. Findings: Results from the study suggest that HIV remains a highly stigmatised illness in Kenyan society and is associated with death and immorality. This is still the case in spite of years of health promotion and high profile media campaigns raising awareness about HIV and the availability and effectiveness of treatment. The context of stigma shaped the consultation so that both patients and counsellors worked together to help patients to maintain a ‘moral face’. Patients tended to withhold information on risky sexual behaviour whilst the counsellors avoided inquiring into this domain. The PITC consultation was characterised by a counsellor dominated approach to communication and health promotion. Counsellor inputs were generic, highly scripted and didactic rather than patient-centred. As a result, the counsellors’ style of communication allowed little space for personalised risk assessment or for patients to ask questions or to express concerns. The findings suggest that informed consent enabling explicit refusal of the test offer was difficult to achieve in an environment where the HIV test was not framed as a choice and patients came to the health facility expecting to be told what to do. Nevertheless, in spite of the obvious lack of explicit informed consent and the counsellor dominated interaction, post test interviews revealed that patients were satisfied with the nature of the interaction. The study concludes that there is a considerable distance between the policy recommendations and their implementation on the ground due to the complexity of real world practice. Lay constructions about HIV (HIV stigma) and the existing norms of patient-provider interaction that are characterised by a passive patient and a dominant health care provider shape the way the consultation unfolds. PITC training programs and manuals need to include skills and strategies that can support counsellors manage an uncomfortable interaction and emphasis the need to ensure an individualized post test counselling is carried out. The thesis makes several contributions to knowledge. The study pays attention to the operationalization of PITC recommendations thus illuminating how the PITC policy is translated into practice within a developing country like Kenya. It informs the existing debates on how informed consent and counselling should be implemented. The study findings suggest that in spite of the global debates on what constitutes ideal informed consent and counselling, in practice, sociocultural norms shape how these issues are translated and implemented. However, the study indicates that diversion from the PITC policy recommendations does not necessarily constitute a disregard for the recommendations but, rather, is an attempt to adapt to the prevailing environment. The study methodology enabled unique insights to be gained on how counselling and consent are constructed and managed in the PITC setting through the use of observations / audio recording to examine ‘real time’ interactions. The research study has been able to illuminate barriers that are posed by sociocultural and organisational structures in the real world implementation of the PITC policy. Therefore, my study suggests that the national PITC policy needs to consider the practical problems faced on the ground in developing contextually appropriate recommendations for the conduct of PITC and implementation of key guidelines.

Background: The 2009-10 influenza A(H1N1) pandemic was the first pandemic influenza of the twenty-first century and presented the first major opportunity for the use of influenza vaccines en-masse during a pandemic scenario. National anticipatory policies of pandemic influenza vaccine preparedness were implemented, and vaccine guarantee agreements were activated. Large quantities of vaccines were purchased and made available to identified citizens over the course of the pandemic. The use of pandemic influenza vaccines has been examined in this research. Methods: A comparative health policy approach in five study countries (Sweden, New Zealand, Japan, Singapore, and Canada) was conducted. Qualitative interviews (n= 36) were undertaken in each country with key pandemic influenza response personnel (n = 39). Participants included public health officials, policy makers and clinicians engaged at national country response level. Interviews facilitated discussions surrounding the 2009-10 influenza A(H1N1) pandemic response and use of vaccines. Documentary examination of available records supplemented the analysis of the interview data. Results: Several interview themes were identified following data analysis of the use of pandemic vaccines in the study countries. Themes of the vaccine use included: single or multiple vaccine supplier routes; hemisphere variation; historical pandemic legacy; targeted populations; setting vaccination priorities; side effect concerns; perceived effectiveness of vaccines during the pandemic influenza response. The themes which were most prominent comprised the sourcing and distribution of the vaccines during the response and the associated communication challenges. The necessary prioritisation of vaccines caused extensive discussions and uneasiness by the pandemic influenza response personnel as the initial vaccines arrived in small quantities and required allocation, especially in circumstances where country’s intended for all/most citizens to eventually have access to the vaccine. The variation in timing of the vaccination campaigns and disease activity would suggest that subsequent influenza wave morbidities and mortalities could have been reduced if vaccines had been available more promptly. The southern hemisphere country, New Zealand, exemplified the circumvention of vaccine safety concerns through the use of a trivalent vaccine inclusive of H1N1. Conclusions: Pandemic vaccines were the cornerstone of two countries responses and were associated with high uptake rates. Vaccine discussions, such as prioritisation and essential workers estimates, can be established during interpandemic phases by pandemic influenza response personnel. The use of annual seasonal influenza vaccines that are inclusive of the novel pandemic influenza strain should play a greater role in future pandemic influenzas, should the vaccination campaign timing be appropriate, as this may reduce public anxiety concerning the perceived safety of novel vaccines. The use of the 2009-10 influenza A(H1N1) pandemic vaccines had varied in success and the lessons learnt from this event have important implications for future policy. Pandemic influenza response personnel are recommended to prepare as fully as possible during this interpandemic period.

Epstein Barr Virus (EBV) is a major risk factor in Multiple Sclerosis (MS), via as yet unclear mechanisms. Several hypotheses have been proposed to explain how EBV infection could cause MS and the aim of this thesis was to better understand the mechanisms of action of EBV in the context of MS studying a) the role of EBV in myelin antigen presentation by B cells and b) the association of HERVs with MS. In a non-human primate experimental autoimmune encephalomyelitis (EAE) model, an EBV-related lymphocryptovirus enables B cells to protect a proteolysis-sensitive immunodominant myelin oligodendrocyte glycoprotein (MOG) peptide (residues 35- 55) against destructive processing. This facilitates its cross-presentation to autoaggressive cytotoxic MHC-E-restricted cytotoxic T cells. The present study extends these observations to human B cells and identifies a key role of autophagy. EBV infection upregulated antigen presentation-related markers on B cells and activated the cross-presentation machinery. Although human MOG protein was degraded less in EBV-immortalized B-lymphoblastoid cell lines (LCL) than in uninfected B cells, induction of cathepsin G activity by EBV led to total degradation of the immunodominant peptides. Inhibition of cathepsin G or citrullination of the arginine residue within a LC3-interacting regions (LIR) motif of immunodominant MOG peptides abrogated their degradation. Internalized MOG co-localized with autophagosomes, which may protect it from destructive processing. Thus, EBV infection switched MOG processing in B cells from destructive to productive possibly facilitating cross-presentation of disease-relevant epitopes to CD8+ T cells. This mechanism could facilitate presentation of myelin autoantigens that may be involved in MS induction and progression. The first part of this thesis shows a possible EBV-mediated mechanism involved in MS pathogenesis, but it is likely that different mechanisms act alternatively or cumulatively in different individuals based on environmental and genetic differences. A further mode of action of EBV is through the activation of Human Endogenous Retroviruses (HERVs). In normal conditions HERVs are silenced or expressed at low levels, but in some pathological cases, like MS, their expression is higher than in the healthy population. We performed a systematic review and meta-analysis of the literature on the association between HERVs and MS. The systematic review suggested a strong association between HERV expression and MS, in particular with the HERV-W family. The meta-analysis showed odds ratios of 22, 44, and 6 for the expression of MSRVpol in serum/plasma, MSRVenv in PBMC and MSRVpol in CSF respectively. Furthermore, we confirmed the association experimentally. An increased expression of MSRV/HERV-Wenv and TLR4 RNA was detected in blood of MS patients compared with control groups and the viral protein Env was expressed mainly by B cells and monocytes, but not by T cells. Our finding that EBV infection can induce the expression of MSRV/HERV-Wenv is consistent with previous reports in the literature. We also established that such increased expression was not due to a repression of retroviral restriction factors in LCL. A further connection between HERVs and MS is supported by the observation that people infected by HIV may have a lower risk of developing MS than the HIV non- infected, healthy population. We found that the expression of MSRV/HERV-Wenv RNA in HIV-infected people was lower than in MS patients and similar to healthy controls. Nevertheless, there was no difference in MSRV/HERV-Wenv expression between antiretroviral drug -treated and -untreated HIV patients. The expression of MSRV/HERV-Wenv was also detected in vitro in LCL treated with different classes of antiretroviral treatments (ART) and only Efavirenz (NNRI) reduced MSRV/HERV- Wenv expression. In conclusion, taking in consideration the multifactorial aetiology of MS, it is likely that EBV infection and increased expression of MSRV/HERV-W are significant contributing factors in genetically predisposed individuals. This thesis helps to better understand the mechanisms of action of EBV and HERVs in the context of MS.