Abstract We investigated the relationship between prevalence and severity of clinical signs of Demodex cafferi infection in freeranging African buffalo (Syncerus caffer) and other factors such as age, sex, pregnancy status, and concomitant infections with bovine tuberculosis (BTB), Rift Valley fever (RVF), and brucellosis (BA). Approximately half of 203 buffalo examined in this study had clinical signs of demodicosis (cutaneous nodules); younger age classes had the highest prevalence and severity of lesions (x2521.4, df56, P50.0015). Nodules were generally limited to the head and neck region, but in severe cases were present over the entire animal. We found no significant association between clinical severity of the Demodex infection and gender, pregnancy status, or infection with BTB, RVF, or BA.

Objective: The objective of this thesis was to compare demographic and clinical characteristics and factors associated with advanced hepatic fibrosis between HIV and HIV-hepatitis B (HBV) co-infected patients. Methods: Proportional odds models were developed to investigate socio-demographic and clinical variables’ association on liver fibrosis determined by AST-to-Platelet-Ratio-Index (APRI). Results: HBV status and APRI values were available for 2,419 of 9,289 (26%) participants. 199 (9%) were HBV co-infected. Compared to HIV infected, HIV-HBV co-infected individuals were 2.19 (95% CI: 1.63, 2.90) and 1.68 (95% CI: 1.10, 2.53) times more likely to belong in a higher level of APRI category. Compared to HIV mono-infection, HIV-HBV co-infected participants on ARV therapy were less likely to have clinically significant or advanced fibrosis compared to mild or moderate fibrosis. Conclusion: We provide evidence in favour of an association between ARV therapy and reduced fibrosis in HIV-HBV co-infected population.

Magister Artium (Development Studies) - MA(DVS) / Tuberculosis (TB) infection is present in many people but it is sometimes latent until one’s immune system is compromised. As such, it increasingly manifests in people, especially those whose immune system has been compromised by e.g. HIV, as an opportunistic disease. TB is thus closely interlinked with HIV and efforts to eradicate TB have been integrated with the fight against HIV in South Africa. The study revealed that factors such as poverty and stigma - be it enacted or perceived - has an impact on how people with TB deal with the burden of having the disease. Using qualitative research as the choice of methodology and collecting data using observations, in-depth interviews and structured interviews among 18 participants the study focused on the ways in which people understand TB in an area that is known to have high HIV prevalence. The researcher explored people’s experiences with TB and investigated their understanding of the disease as well as explored how people on Directly Observed Treatment Strategy (DOTS) make sense of and interact with this programme in Gugulethu Township. During the study it emerged that people have significant understanding of TB and its symptoms but their initial reaction to those symptoms is selfmedication and this results in delayed treatment seeking. TB is stigmatised in Gugulethu despite some people acknowledging that the environment itself is partly to blame for the rapid spread of the disease. The study revealed that there is good healthcare provision in Gugulethu and it is accessible but the burden of suffering from TB is a difficult one that requires family support, financial support and good relations with clinic and hospital staff in order for one to adhere to treatment and recover from TB.

Humans are subject to infection with a wide range of commensal and pathogenic organisms. Each pathogen requires an appropriate immune response to eliminate or control the invading organism and minimise pathology. Many pathogens have evolved strategies to subvert or manipulate the immune response and establish on-going infections. Similarly acute respiratory infection with virulent strains of influenza A virus are often poorly controlled by the immune system and can cause severe immunopathology and even fatality as a result of an inappropriate and excessive inflammatory response called a ‘cytokine storm’. Morbidity due to influenza infection and exacerbation by the immune response can vary greatly between individuals. The effect of underlying infection on the immune system could contribute to the variation in response. The aim of this project was therefore to determine if co-infection with two pathogens that establish on-going infections could alter the immune response to influenza A and impact the outcome of infection. Persistent infections with filarial helminths can cause debilitating disease and significantly impact the immune response toward a skewed TH2 or regulatory phenotype in order to control pathology. In contrast, infection with gammaherpesviruses in an immunocompetent host causes an initial inflammatory ‘anti-viral’ response before becoming an asymptomatic, latent infection. In an immunocompromised host, gammaherpesviruses can reactivate and lead to clinical presentation of disease. This suggests that these viruses require an on-going immune response to control all stages of infection. Both filarial helminths and gammaherpesviruses are common infections in human populations and therefore mouse models of these infections provide relevant systems to study their potential role in influenza virus infections. In a BALB/c murine co-infection model, latent infection with the rodent gammaherpesvirus MHV-68 led to significantly decreased weight loss and clinical signs following high dose infection with A/WSN/33, (a H1N1 influenza A virus). This was coupled with decreased immunopathology in the lung and fewer infiltrating lymphocytes in the alveolar spaces and around larger airways, although infectious virus titres were not significantly reduced. This response was coupled with a decreased production of inflammatory cytokines and chemokines in co-infected mice 6 days post infection which correlated with the amelioration of pathogenesis in these animals. A repeat of the study in 129Sv/Ev IFNγR knock out mice showed the same protective effect in the co-infected mice, suggesting IFNγ is not critical for the protective phenotype. Mice infected with latent MHV-68 alone showed a significant increase in expression of T cell chemokines in the lung and alveolar macrophages had a significantly increased production of suppressor of cytokine signalling (SOCS-1) suggesting latent MHV-68 infection may impact the phenotype of macrophages in the lung, modulating the response to influenza co-infection. A co-infection model with a persistent rodent filarial helminth, Litomosoides sigmodontis and A/WSN/33 was also established in BALB/c mice. The L4 developmental stage of L. sigmodontis infection had no impact on co-infection with A/WSN/33. Adult stage worms, however, appeared to have a protective effect against A/WSN/33 pathogenesis. Co-infected mice had significantly delayed weight loss and clinical signs 3-5 days post infection. CD4+ and CD8+ T cells in the lung draining lymph nodes had significantly reduced TH1 and TH2 phenotypes (measured by cytokine production) compared with singly infected controls. IFNγ secreting CD4+ T cells in the lungs of co-infected mice also secreted increased levels of IL-10, suggesting an increase in regulation of the inflammatory response to A/WSN/33. At the full patent stage of L. sigmodontis infection, co-infection with A/WSN/33 led to increased clinical signs and significantly exacerbated weight loss. CD4+ and CD8+ T cells in the lung draining lymph nodes were inflammatory in L. sigmodontis infected mice alone as well as co-infected mice and there were no differences in the percentage of CD4+ T cells in the lung secreting IL-10 and IFNγ between co-infected and influenza infected mice. A loss in regulatory responses during the patent stage of L. sigmodontis infection may therefore contribute to the loss of protection against A/WSN/33 at this time point within the co-infection model. Understanding the impact of an underlying infection on the immune system could provide immune mechanisms that could be exploited to increase vaccine efficacy against influenza and similarly help to provide better treatment for individuals infected with influenza A. These results may also help predict the outcome of influenza A infection in individuals already infected with highly immunogenic, on-going infections.

Hepatitis is an infectious disease that affects millions of people worldwide. The current project seeks to achieve two objectives: 1) To understand how hepatitis policies affect hepatitis prevalence in prison, and 2) To understand how hepatitis prevalence in prison affects the general population. Using a content analysis of correctional policies available through each state Department of Corrections (DOC) and secondary data from the 2010 Census, Centers for Disease Control and Prevention, and Corrections Compendium; hepatitis prevalence and policies are analyzed. The content analysis employed for this study revealed that some states have more comprehensive policies than others. However, all states may benefit from modifying their policies to meet recommendations constructed by the Federal Bureau of Prisons. Findings from descriptive statistics also suggest changes in HIV prevalence and policies positively affect hepatitis C prevalence. Future research should be dedicated to examining how personal interactions in prison also affect prevalence rates.

Infection & Immunity / Currently, there are 38 million people living with human immunodeficiency virus (HIV-1) worldwide and there were 680,000 HIV-related deaths in 2020 alone. The greatest cause of mortality in people living with HIV (PLHIV) is infection with opportunistic pathogens such as tuberculosis (TB), which accounts for one third of HIV-related deaths. PLHIV are 20 times more susceptible to TB and co-infection leads to significantly worsened outcomes in terms of both diseases. Humanized mouse (hu-mouse) models, which possess human immune cells for HIV to infect, have been useful for HIV research. Our aim is to create hu- mouse models of HIV, TB and co-infection to investigate disease progression, immune responses, therapeutics, prevention and vaccination. NOD-Rag1null-IL2rgnull (NRG) mice are highly immunocompromised mice that are traditionally used to generate hu-mouse models. We are also developing NRG mice that are transgenic for human HLA-DR4 and HLA-A2 (DRAG-A2) and similar mice have been reported to have improved immune responses. NRG and DRAG-A2 mice were humanized with hematopoietic stem cells obtained from human umbilical cord blood. DRAG-A2 mice had significantly higher engraftment success rates (defined as the percentage of mice with >10% hCD45+) as well as higher overall CD45+ leukocyte, CD4+ T cell, CD19+ B cell and CD14+ monocyte reconstitution in the blood compared to huNRGs. huNRG mice were permissive to infection with JR-CSF or NL4.3-Bal-Env HIV-1 intravaginally or systemically. huDRAG-A2 mice were also infected intravaginally with NL4.3-Bal-Env HIV-1. huDRAG-A2 mice, but not huNRGs, produced HIV-specific IgG, indicating improved immune responses. huNRG mice were infected intranasally with mCherry-Erdman, YFP-H37Rv or H37Rv Mtb. huDRAG-A2 mice were also infected with H37Rv. Human immune cell involvement and human-like granuloma formation was observed using flow cytometry and immunohistopathology. These findings show that the DRAG-A2 model may be optimal for investigating HIV, TB and co-infection, which continue to be serious global health concerns. / Thesis / Master of Science (MSc) / Human immunodeficiency virus (HIV) and tuberculosis (TB) are infectious diseases that affect millions of people worldwide every year. The greatest cause of death in people living with HIV is co-infection with TB and HIV-positive individuals are much more likely to get TB. Humanized mouse (hu-mouse) models possess human immune cells for HIV to infect and are useful for studying HIV. Our goal is to create hu-mouse models of HIV, TB and HIV/TB co-infection that will allow us to study how these diseases interact. We are currently developing a traditional hu-mouse model (known as NRG), as well as an improved next-generation model (known as DRAG-A2) with a more functional immune system. Both models have been successfully infected with HIV or TB. Only DRAG-A2 mice were able to make antibodies against HIV. The improved DRAG-A2 model will enable future studies on HIV, TB and co-infection, which continue to be understudied global problems.

Le virus influenza peut être responsable d’infections respiratoires sévères. Les pneumonies bactériennes post-influenza font partie des complications les plus graves et S. aureus est l’une des bactéries les plus fréquemment retrouvée dans ce contexte. L’efficacité des traitements dans ces infections graves est modérée ce qui souligne l’importance de progresser dans la compréhension de la physiopathologie de ces infections graves. Une réponse immunitaire inadéquate (soit excessive, soit trop faible) à l’infection pulmonaire joue un rôle considérable dans la gravité du tableau clinique et le pronostic du patient. Nous avons montré que le virus influenza potentialise l’inflammation et la cytotoxicité engendrée par des facteurs de virulence de S. aureus dans des monocytes isolés de témoins sains. Cependant l’étude du système immunitaire de patients hospitalisés pour grippe grave, a montré qu’au lieu d’être dans un état d’activation massive, il était en phase d’anergie et possédait une altération de la réponse immunitaire fonctionnelle en cas d’exposition à des facteurs de virulence de S. aureus. L’immunomonitoring de ces patients au pronostic sévère, qui permet la détermination de l’état pro- ou anti-inflammatoire dans lequel se trouve le patient pourrait participer à l’amélioration de la prise en charge de ces patients en permettant l’utilisation de traitements immunomodulateurs adaptés à la situation clinique de chaque patient. Cette problématique peut être étendue à d’autres co-infections virus bactérie et notamment au VRS. Nous avons étudié l’épidémiologie des co-infections VRS/bactérie chez l’adulte dans le contexte d’une pneumonie et nous avons observé qu’elle était similaire à celle des co-infections influenza bactérie. Cette connaissance de l’épidémiologie est importante afin d’adapter la prise en charge des patients / Post-influenza bacterial pneumonia is a leading cause of morbidity and mortality with severe influenza virus illness. Staphylococcus aureus is one of the most common pathogen found in this context. The severity of post-influenza Staphylococcus aureus pneumonia is due both to an inadequate responsiveness of the immune system (either too important or too weak) and to the weak efficacy of treatments used during these severe infections. A better knowledge of the pathophysiology of influenza/S. aureus co-infection is needed in order to improve patients care. In this study, we showed using in vitro experiments that influenza virus increased the inflammation and cytotoxicity induced by S. aureus virulence factors in human monocytes. However ex vivo experiments performed on leucocytes isolated from hospitalized patients with severe influenza showed an anergy of the immune system after exposition to S. aureus virulence factors. Immunomonitoring of patients with severe post-influenza Staphylococcus aureus pneumonia may allow to optimize the therapeutic regimen towards a more individualized immunomodulatory therapy. This can be extended to other viral bacterial co-infections including RSV. We studied the epidemiology of bacterial superinfections associated with RSV pneumonia in adults. Our results suggested that there was no main differences between the microbiological epidemiology of RSV/bacterial co-infections and influenza/bacterial co-infections. Knowledge of this epidemiology is important to assess to improve patients care

Les hépatites virales constituent un enjeu majeur de santé public dans le domaine des maladies infectieuses. L’enjeu pour les prochaines années sera de mettre en œuvre des stratégies de dépistage et de de prise en charge des hépatites virales et du VIH, en particulier chez les usagers de drogue par voie intraveineuse et dans les pays à ressources limitées. Dans ce travail de thèse nous avons évalué des outils et des stratégies nouvelles pour améliorer le diagnostic et la prise en charge des infections par le VIH et le VHC dans les pays du Sud. Notre première étude porte sur l’évaluation de la performance diagnostique de la primo-infection du VIH sur Dried serum spot (DSS) par rapport aux tests rapides. Cette étude a été rétrospectivement réalisée chez 39 cas diagnostiqué Primo-infection du VIH entre 2000 et 2012 au CHU de Montpellier. En comparant avec le résultat sur le DSS, nous avons réussi à avoir une sensibilité de 87.2% (34/39) avec PCR Ag/Ac combiné 4eGeneration (ElecsysCombi PT test reactive et Liaison XL test reactive) témoignant de la bonne performance de ce test. Nous avons réalisé par la suite une étude clinico-virologique chez 104 patients co-infectés par le VIH et le VHC à Haiphong, Vietnam (ANRS 12262). C’est pour la première fois qu’une telle étude descriptive (évaluation clinico-virologique, évaluation de la fibrose hépatique avec les marqueurs biologiques recommandés par l’OMS et également par le Fibroscan®) est réalisée dans cette population au Vietnam. L’évaluation clinique, l’analyse des tests biochimiques et virologique et celle de la fibrose par l’élastographie hépatique (Fibroscan®, Echosens) ont été réalisées Parmi 104 patients, 93 (89,4%) avaient des ARN du VHC détectable (médiane 6,19 (4,95 à 6,83 log10 UI / mL). La plupart des patients ont été infectés par les génotypes 1a/1b (69%) et les génotypes 6a/6e (26%). 43 patients (41,3%) présentaient une fibrose significative (≥ F2), dont 24 patients (23,1%) avec une fibrose extensive (F3) et/ou une cirrhose hépatique (F4). L’évaluation de la fibrose hépatique par l’élastométrie (Fibroscan®) est utilisée comme l’examen de référence à comparer avec le test APRI (AST-to-platelet ratio index) recommandé par l’OMS dans la prise en charge des patients infectés par le VHC dans les pays à ressource limitée, en prenant le cut-off élevé supérieur ou égale à 2, nous avons réussi à classifier les fibroses sévères/cirrhose hépatique avec une sensibilité à 90% et une spécificité à 84% (Se: 90%, Sp: 84%, AUROC = 0,93, IC 95%: 0,86 à 0,99).Notre dernière étude a évalué la réponse des marqueurs immunologiques à l’association de Peginterféronα (PegIFNα) et ribavirine. Nous avons étudié la concentration des 25 cytokines chez 30 patients co-infectés par le VIH et le VHC. Les résultats ont été comparés entre les patients classés « RVS » (réponse virologique soutenue) (RVS, n = 19) et les non-répondeurs (NR, n = 11). Le changement en concentration des cytokines lié à la thérapie PegIFNα-ribavirine a été observé chez les patients RVS et NR. Le changement en concentration sérique de l'IL-8, MIP-1β; et MCP-1 pourrait être associé à l'efficacité de la bithérapie PegIFNα-ribavirine chez les patients co-infectés par le VIH et le VHC.L’amélioration du dépistage et du diagnostic est un élément primordial faisant partie du contrôle de ces infections virales. Notre étude a renforcé l’hypothèse de l’utilité de DBS. Le Fibroscan® et les marqueurs biologiques (APRI Test) sont des outils intéressants pour l’évaluation de la fibrose hépatique dans les pays à ressources limitées. Mot clés : Co-infection HIV-VHC, usagers de drogues par voie intraveineuse, dried blood Ssot, fibrose hépatique, fibroscan, APRI, interféron pégylé, Vietnam. / Chronic viral hepatitis is a major public health issue worldwide in the field of infectious dis and mostly affects resource-constrained countries. The challenge for the resource-limited countries is to implement the strategies for screening and management of viral hepatitis, particularly for hepatitis C among people who inject drugs.In this thesis we have evaluated new tests and strategies to improved diagnosis and therapeutic monitoring of HCV and HIV infection in low resource setting. The first study evaluated the performances of HIV testing using filter paper (DSS – Dried serum spot) compared with rapid tests during the early phase of HIV infections. A total of 39 serum samples form newly diagnosed HIV infected persons was included. Fourth generation immunoassays (ElecsysCombi PT test reactive and Liaison XL test reactive) identified 34 out of 39 HIV early infections using dried serum spot, whereas the Determine TM HIV-1/2 rapid test detected 24 out of 39 HIV positive serum (87.2% vs 61.5% respectively, p = 0.009). Fourth generation Ag/Ab immunoassays performed on DSS had good performance for HIV testing during the early phases of HIV infection. In the second study, we conducted a cross-sectional study aimed to assess the proportion of clinically significant fibrosis in HIV/HCV-co-infected patients followed in Viet Tiep Hospital in Haiphong, Northern Vietnam. From February to March 2014, 104 HIV-HCV coinfected patients receiving antiretroviral therapy (ART) were prospectively enrolled. 93 (89.4%) had detectable HCV RNA, median 6.19 (4.95-6.83 Log10 IU/mL). Patients were mainly infected with genotypes 1a/1b (69%) and genotypes 6a/6e (26%). 43 patients (41.3%) had fibrosis ≥ F2 including 24 patients (23.1%) with extensive fibrosis (F3) and/or cirrhosis (F4). Using Fibroscan® as a gold standard, the high threshold (2) of AST-to-platelet ratio index (APRI) had very good performances for the diagnosis of extensive fibrosis/cirrhosis (Se: 90%, Sp: 84%, AUROC=0.93, 95%CI: 0.86-0.99).In the last study, the impact of pegylated interferonα (PegINFα) and ribavirin therapy on T cell immune response was explored in HIV/HCV coinfected patients. Concentrations of 25 cytokines and CD8+ T cell activation were monitored in HCV/HIV co-infected patients. Results were compared between patients retrospectively classified as sustained virological responders (SVR, n=19) and non-responders (NR, n = 11). High pretreatment concentrations of IP-10 (CXCL-10) and MCP-1 (CCL-2) were associated with poor anti-HCV response. Highest rise in MIP-1β; and MCP-1 levels was observed four weeks after anti-HCV treatment initiation in SVR compared to NR, whereas a decrease of IL-8 concentration was associated with treatment failure (p= 0.052). Treatment based on drugs having immunomodulating activities may benefits from immunomonitoring using multiplex techniques. In conclusion, improving access to HIV and HCV diagnosis and monitoring are critical toward the control of these infections. Our work performed illustrate how dried blood spot, point of care testing, Fibroscan and simplified assays may contribute to HIV and HCV care in low resource setting. Key word : Co-infection HIV-HCV, IV drug user, dried blood Spot, liver fibrosis, fibroscan, APRI, Pegylated interferon, Vietnam.

There are an estimated 2 billion individuals infected with Mtb, and 37.7 million people living with HIV (PLWH) worldwide. HIV/Mtb co-infection increases the risk of developing active tuberculosis by over 20-fold, and 210,000 of 1.5 million deaths from TB were among co-infected PLWH in 2020. Therefore, development of effective TB vaccination, particularly within the vulnerable PLWH population, is an urgent global issue. With limited in vivo models to study co-infection, humanized NRG (huNRG) mice and humanized DRAG-A2 mice (a next-generation of huNRG mice expressing HLA class I and II transgenes with improved human immune reconstitution, huDRAG-A2) are promising tools for HIV and TB reserach as they develop robust human immune cell populations and recapitulate many aspects of HIV or TB clinical disease. HIV/Mtb co-infection was investigated using huNRG and hu-DRAG-A2 mice in separate experiments where intravaginal (with DMPA pre-treatment) or intraperitoneal HIV-1 infection was administered, respectively, and intranasal infection of Mtb was administered 3.5 weeks later. Both huNRG and huDRAG-A2 mice recapitulated hallmark features of HIV/Mtb co-infection such as severe granuloma pathology, hCD4+ T cell depletion in lung and spleen tissue, and human like lung pathology such as Mtb-infected foamy macrophages in the granuloma. Co-infected huDRAG-A2 mice also displayed significantly higher bacterial burden in the lungs, increased extrapulmonary dissemination into spleen and liver, and significantly lower hCD4+ T cells in the peripheral blood post-Mtb infection when compared to the Mtb-only infected group. To investigate TB vaccine immunogenicity, huNRG and huDRAG-A2 mice were immunized with a novel trivalent vaccine, AdCh68MV. Upon intranasal immunization, both models showed trends of developing higher Mtb antigen-specific hCD4+ T cell responses in the lung and spleen. Overall, this project sets the initial stages of a pre-clinical HIV/Mtb co-infection model in huNRG and huDRAG-A2 mice appropriate for immune investigations, therapeutic and vaccination development. / Thesis / Master of Science in Medical Sciences (MSMS) / There are over 2 billion individuals infected with TB and 37.7 million people living with HIV (PLWH) worldwide. When someone is co-infected with both diseases, the risk of death is greatly increased. Research in co-infection and developing effective TB vaccination for PLWH are urgent global issues. Animal studies are currently limited because studying HIV requires human immune cells. Our lab has established humanized mice (hu-mice) that develop many different human immune cells and are useful for HIV/Mtb co-infection research. When hu-mice were co-infected, they showed more dying lung tissue, immune cell loss, and bacteria in the lungs. Hu-mice were also used to study human immune responses to a novel TB vaccine delivered to the lungs. Trends of higher immune responses towards TB were observed in the lung and spleen of immunized hu-mice. Overall, this project shows the utility of hu-mice as pre-clinical models of HIV/Mtb co-infection and Mtb vaccine studies.

The cause of the high HIV prevalence in sub-Saharan Africa is incompletely understood, with heterosexual penile-vaginal transmission proposed as the main mechanism. Heterosexual HIV transmission has a very low probability; further, a single estimation of heterosexual probability of HIV transmission fails to reproduce the variation associated with important biological cofactors. In particular, studies of HIV incidence suggest that co-infection with other infectious diseases influence the HIV transmission, and therefore might substantially vary the pattern of the spread of the infection. To assess the effect of co-infection on the spread of HIV, I developed and analyzed several mathematical and statistical models based on published data. The results show that despite the low probability of heterosexual transmission per sexual contact, the inclusion of individual variation generated by transient but repeated increases in HIV viral load associated with co-infections may provide a biological basis for the accelerated spread of HIV in sub-Saharan Africa, and raises the possibility that that the natural history of HIV in sub-Saharan Africa cannot be fully understood if individual variation in infectiousness is neglected. Co-infection might be a key explanatory variable for the rapid spread of HIV infection in sub-Saharan Africa; in fact, co-infection may be a necessary factor, rather than merely being a contributing factor, in the successful spread and survival of HIV in populations where heterosexual vaginal-penile contact is the main mechanism of transmission. Consequently, broad population based control strategies to decrease infectivity and reduce the incidence of other sexual and parasitic infectious diseases might be effective strategies in diminishing the spread of HIV in sub-Saharan Africa.