Avian influenza H5N1 is one kind of important bird flu. Unfortunately, this virus has swiftly evolved and become highly pathogenic to humans and poultry, resulting in 100% of death in infected poultry and over 60% of mortality among infected human population. Moreover, the virus tends to reassort with other influenza viruses, such as the current swine flu H1N1, to establish themselves in environments and further this epidemic all over the world. The World Health Organization (WHO) has in fact warned that highly pathogenic avian influenza H5N1 poses a graver risk of a global human pandemic than at any time since the Hong Kong outbreak (H3N2) in the 1960s. / Finally, avian influenza is an inter-disciplinary issue across virology, medical geography, and spatial epidemiology. How to quantify and integrate knowledge from different disciplines remains a challenge in fully understanding the disease. We propose a method to formally integrate genetic analysis that identifies the evolution of the H5N1 virus in space and time, epidemiological analysis that determines socio-environmental factors associated with H5N1 occurrence and statistical analysis that identifies outbreak dusters. Our integrated results show a significant advance in findings over reports in, for instance, Gilbert et al. (2008) and we believe our findings are more precise and informative in representing the occurrence and the space-time dynamics of H5N1 spread. Overall, unlike traditional influenza studies, our work sets up a solid foundation for the inter-disciplinary study of this and other spatial infectious diseases. / First, we apply multifractal detrended fluctuation analysis to determine the temporal scaling behavior of outbreaks in Asia, Europe, Africa, and the whole of the world between December 2003 to March 2009. Long-range correlation and multifractality, two important properties characterizing the scaling behavior of complex dynamics, are first detected in the outbreak time series. In addition, this study identifies different temporal scaling behaviors of outbreaks of these continents 8,nd specific seasonal patterns in Asia. These findings confirm our perspective that avian-influenza outbreak behaviors are self-similar over time and are spatially heterogeneous. / One key to preventing such a calamity is to obtain a thorough understanding of the mechanisms of avian influenza transmission and its spatio-temporal patterns of dispersal. The issues at stake are outbreaks' spatial and temporal patterns, the interrelationship of these with the evolution of influenza viruses in such a way that geography is understood as a dimension of the disease's virology, and the human and avian behaviors and socio-ecological environments associated with H5Nl spread. This thesis sets out to study these problems in detail and propose solutions. / Second, we conduct a spatial analysis for global trends and local clusters of H5N1 outbreaks at multiple geographical scales. Currently, the local K function used in a point pattern analysis searches outbreak clusters, assuming the disease is spatially homogeneous. The thesis proposes a much more efficient method to measure the degree of clusters accurately. The modified function works by weighting outbreaks through distances, counting the number of the weighted outbreaks for each lattice point no matter whether the disease emerges in a grid. This weighted local K function extends cluster analysis from a point pattern to lattice data. Spatial representation in these terms then seeks to explore local patterns of H5N1 over a continuous space. / Third, we study a set of socio-environmental factors, which are plausibly associated with the occurrence of H5N1. Spatial epidemiological models are built for predicting the disease at both continental and national levels, covering Indonesia, China, and the whole of East-Southeast Asia. We evaluate the statistical models using 1,000 bootstrap replicates, showing a consistently high rate of prediction, assessed by statistics: AUC, Kappa Index, and pseudo R square. / Ge, Erjia. / Advisers: Yee Leung; Tung Fung. / Source: Dissertation Abstracts International, Volume: 73-06, Section: A, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 169-197). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

The oxysterol, 25-hydroxycholesterol (25-HC), is important for sterol metabolism and emerging evidence suggests that 25-HC plays a more critical role in immunity and infection. However, the precise antiviral mechanism and the target of 25- HC remains unclear. Here efforts were made to investigate the link between viral infection and the triggering of the 25-HC associated interferon (IFN) response, and how this dynamically alters the endogenous level of 3-hydroxy- 3-methylglutaryl-CoA reductase (HMGCR), a key enzyme that catalyses the production of the precursor of cholesterol and oxysterols. In this thesis I have sought to specifically explore the temporal changes and role of HMGCR in DNA virus (cytomegalovirus) and RNA (Influenza) virus infections. I hypothesise that HMGCR is a target for 25-HC associated IFN-mediated host defence against viral infection. To characterise HMGCR and test this hypothesis, the following objectives were defined: (1). To establish an experimental system to quantitatively study the endogenous HMGCR protein level; (2). To investigate the mechanism of the down-regulation of HMGCR involved in the IFN-mediated innate immune response; (3). To study the behaviour of HMGCR in the influenza virus induced 25-HC associated IFN-mediated innate immune response; (4). To study the behaviour of HMGCR in the cytomegalovirus induced 25-HC associated IFN-mediated innate immune response. Chapter 3, describes establishing an experimental system for the quantification of endogenous HMGCR levels. Different protein detection methods, including a modified western blot protocol and immunostaining, were tested. The results of RNA interference of HMGCR demonstrate that under lipid-deficient condition with the supplementation of mevastatin (an HMGCR inhibitor) the modified western blot protocol specifically detects endogenous HMGCR. This chapter lays the foundational work for the temporal analysis and testing the role of HMGCR in infection. In Chapter 4, the mechanism of the degradation of HMGCR following 25-HC and IFN treatments, in wild-type and Ch25h−/− mouse bone marrow derived macrophages (BMDMs), was investigated. Similar to 25-HC, IFN-γ treatment results in the drop of both the transcript and protein abundance of HMGCR in wild-type BMDMs. Differential temporal analysis of RNA and protein alterations and the use of proteasome inhibitors reveals that both 25-HC and IFN-γ lead to a marked reduction of HMGCR protein via a proteasomal degradation mechanism within early times of treatments. Further, the immediate reduction of HMGCR levels induced by IFN-γ was completely abrogated in Ch25h−/− BMDMs. Hence, the reduction of HMGCR following IFN-γ treatment is due to the de novo synthesis in macrophages of 25-HC. However, the decrease of Hmgcr gene expression was observed in not only wild-type but also Ch25h−/− BMDMs, suggesting additional mechanisms for regulating Hmgcr RNA levels. These results demonstrate the mechanism of the down-regulation of HMGCR resulted from the induction of IFN response during viral infection, is only partially due the de novo synthesis of 25-HC. In chapter 5, influenza A virus was used to investigate the role of HMGCR in the IFN-mediated innate immune response. The inhibition of HMGCR by RNA interference inhibited viral growth, suggesting the requirement of HMGCR for optimal intracellular viral growth. Viral infection in wild-type murine BMDMs reduced the endogenous HMGCR levels. However, the reduction of HMGCR at early times was prevented in Ch25h−/− BMDMs. Intriguingly, the decrease of HMGCR at late time points was still observed in Ch25h−/− BMDMs. These results indicate that the down-regulation of HMGCR with influenza virus infection in BMDMs at early times is completely due to the de novo synthesis of 25-HC; whereas at late times alternative pathways or mechanisms exist. Additionally, human epithelial A549 cells and A549/PIV5-V cells that are deficient in STAT1 were used to study the role of IFN pathway in the down-regulation of HMGCR at late times during viral infection. Results from these studies show that at late times the reduction of HMGCR is due to IFN-independent mechanisms. Chapter 6, extends these investigations to the herpes virus murine cytomegalovirus and infection of BMDMs. HMGCR is known to be essential for cytomegaloviral infections and 25-HC, statin and RNAi inhibition of HMGCR restrict viral growth. 25-HC is shown to reduce HMGCR at immediate early times of infection. However, most notably, the down-regulation of HMGCR was also observed in Ch25h−/− BMDMs at late times with murine cytomegalovirus infected BMDMs. These results confirm that alternative pathways or mechanisms exist, playing roles in the crosstalk between cholesterol metabolism and innate immune response. Collectively, this study characterises the role of HMGCR in the 25-HC associated IFN-mediated host defence against viral infection. Results indicate that, in addition to the IFN-mediated host response, alternative pathways or other mechanisms also result in the down-regulation of HMGCR during viral infection. HMGCR is at the crossroad of different pathways or mechanisms, and is therefore not only targeted by 25-HC. Hence, further questions can be addressed from these results: (1). What are the alternative pathways or mechanisms for the down-regulation of HMGCR? (2). How do these pathways or mechanisms work in hosts’ immune system? Answering these questions can contribute to refining the pathway map of innate immunity and understanding the precise role of HMGCR, or even the sterol biosynthesis pathway, in hosts’ immune response against pathogens.

Objetivos: Avaliar a imunogenicidade e segurança da vacina anti-influenza A/H1N1 2009 em pacientes com dermatomiosite juvenil (DMJ) comparados com controles saudáveis e a possível associação entre taxas de soroconversão com dados demográficos, enzimas musculares, escores da DMJ, linfopenia e tratamento nos pacientes com DMJ atendidos em dois serviços de Reumatologia Pediátrica. Métodos: Trinta pacientes com DMJ entre 9 e 21 anos e 81 controles saudáveis foram imunizados com a vacina anti-influenza A H1N1/2009 sem adjuvante. Todos foram avaliados pré e 21 dias após a vacinação. As taxas de soroproteção e soroconversão, a média geométrica dos títulos de anticorpos (MGT) e o fator de aumento (FA) na MGT foram calculados. Foram analisados os eventos adversos (EAs), assim como: enzimas musculares, instrumentos de força muscular, presença de linfopenia e tratamento atual da DMJ. Resultados: Pacientes com DMJ e controles foram comparáveis em relação à mediana de idade atual [15,5 (9- 21) vs. 15 (9-21) anos, p=0,511] e frequência do sexo feminino (63% vs. 51%, p=0,286). A mediana do tempo de duração da DMJ foi de 5,5 (2-17) anos. Após a imunização, as taxas de soroconversão foram significantemente menores em pacientes com DMJ comparados com controles saudáveis (86,7% vs. 97,5%, p=0,044), enquanto soroproteção (p=0,121), MGT (p=0,992) e FA na MGT (p=0,827) foram semelhantes entre os grupos. As avaliações clínicas e laboratoriais na DMJ mostraram que as medianas dos escores de avaliação da atividade doença e enzimas musculares permaneceram estáveis no período do estudo (p > 0,05). Uma alta frequência de curso clínico crônico da doença foi observada em pacientes que não apresentaram soroconversão em comparação aos pacientes soroconvertidos (100% vs. 27%, p=0,012). Em relação à influência do tratamento, baixas taxas de soroconversão foram observadas em pacientes em uso de metotrexate (100% vs. 38%, p=0,036) e associação de prednisona, metotrexate e ciclosporina (50% vs. 4%, p=0,039). EAs locais e/ou sistêmicos foram leves e similares entre pacientes e controles (p > 0,05). Conclusão: Este foi o primeiro estudo que avaliou a vacina anti-influenza A H1N1/2009 na DMJ, identificando que o curso crônico da doença e a terapia imunossupressora são fatores que podem prejudicar a resposta humoral nos pacientes. Uma única dose da vacina foi soroprotetora nos pacientes avaliados, sem evidências de efeitos deletérios na atividade da doença / Objectives: To assess the immunogenicity and safety of influenza A H1N1/2009 vaccine in juvenile dermatomyositis (JDM) patients compared to age-matched controls and the possible association of seroconversion rates whith demographic, muscle enzymes, JDM scores, lymphopenia and treatment in JDM patients routinely followed at two Pediatric Rheumatology Units. Methods: Thirty JDM patients between 9 and 21 years old and 81 healthy age-matched controls were vaccinated with non-adjuvanted influenza A H1N1/2009 vaccine. All participants were evaluated pre- and 21 days postvaccination. Seroconversion and seroprotection rates, geometric mean titres (GMT) and factor increase (FI) in GMT were assessed. Adverse events, as well as muscle enzymes, JDM scores, lymphopenia and current treatment in JDM were also evaluated. Results: JDM patients and healthy controls had similar median of current age [15.5 (9-21) vs. 15 (9-21) years, p=0.511] and frequencies of female gender (63% vs. 51%, p=0.286). The median disease duration of JDM was 5.5 (2-17) years. After immunization, seroconversion rate was significantly lower in JDM patients compared to age-matched controls (86.7 vs. 97.5%, p=0.044), whereas seroprotection (p=0.121), GMT (p=0.992) and FI in GMT (p=0.827) were similar in both groups. Clinical and laboratorial evaluations revealed that JDM scores and muscle enzymes remained stable throughout the study (p > 0.05). A higher frequency of chronic course was observed in non-seroconvert compared to seroconverted (100% vs. 27%, p=0.012). Regarding treatment, a lower rate of seroconversion was observed in patients treated with methotrexate (100% vs. 38%, p=0.036) and in those with a combination of prednisone, methotrexate and cyclosporine (50% vs. 4%, p=0.039). Local and systemic adverse events were mild and similar in JDM patients and controls (p > 0.05). Conclusions: This was the first study that evaluated the influenza A H1N1/2009 vaccine in JDM, identified that chronic course and immunosuppressive therapy were factors hampering immune response in patients. A single dose of non-adjuvanted influenza A/H1N1 2009 vaccine was seroprotective in assessed patients with no evident deleterious effect in disease itself

Regulatory processes and history dependent behavior appear in many dynamical systems in nature and technology. For modeling regulatory processes, hybrid systems offer several advances. From this point of view, to observe the capability of hybrid systems in a history dependent system is a strong motivation. In this thesis, we developed functional hybrid systems which exhibit memory dependent behavior such that the dynamics of the system is determined by both the location of the state vector and the memory. This property was explained by various examples. We used the hybrid system with memory in modeling the gene regulatory network of human immune response to Influenza A virus infection. We investigated the sensitivity of the piecewise linear model with memory. We introduced how the model can be developed in future.

Submitted by admin tede (tede@pucgoias.edu.br) on 2018-11-19T16:59:56Z No. of bitstreams: 1 GISELLE ANGÉLICA MOREIRA DE SIQUEIRA.pdf: 1650143 bytes, checksum: 0a85747b640c1ee6d3c2dc446dececf7 (MD5) / Made available in DSpace on 2018-11-19T16:59:56Z (GMT). No. of bitstreams: 1 GISELLE ANGÉLICA MOREIRA DE SIQUEIRA.pdf: 1650143 bytes, checksum: 0a85747b640c1ee6d3c2dc446dececf7 (MD5) Previous issue date: 2013-12-19 / SIQUEIRA, Giselle Angelica Moreira de. Epidemic Influenza A (H1N1) 2009 in the state of Goiás/Brazil: cases and deaths. Dissertation (MSc in Environmental Sciences) – Catholic University of Goiás, Goiânia, 2013. Between late March and early April 2009, were the first reported cases of human infection caused by a new viral subtype Influenza A (H1N1) in Southern California and near San Antonio, Texas, USA, and then in Mexico and Canada. Until July 6, 2009, 905 cases were confirmed by the Ministry of Health, with reports of 23 states and the Federal District. This study described the profile of confirmed cases and deaths affected by Influenza A ( H1N1 ) in 2009 in the state of Goias and Brazil through a descriptive ecological study of confirmed cases and deaths affected by Influenza A virus (H1N1) 2009 in the State of Goias and Brazil between epidemiological weeks 16 th to 52 th, variables of research Influenza record, feeding SINAN Influenza Web were selected such as epidemiological week, age, gender, education, signs and symptoms, comorbidities, vaccination status, hospitalizations and evolution. Among the total number of cases reported during the epidemic , more than 45% were confirmed Influenza A (H1N1) in Goiás and in Brazil , with 14.9% and 3.9% subsequently died respectively. Females were predominant, those over 6 % were pregnant. The age range was found between 15 and 45 years, with the primary and secondary school levels observed schooling. Among the signs and symptoms , more than 95% of cases and deaths had fever, cough and dyspnoea, less than 30% had comorbid conditions, the occurrence of hospitalizations of cases was 96% and 45% in Goiás in Brazil, while hospitalization those who subsequently died was above 96%, less than 14% of cases and deaths have taken the vaccine against influenza (H1N1). It was concluded that it was possible to know the profile of cases and deaths from socio demographic and clinical characteristics during the epidemic period Influenza (H1N1) 2009 in Goias and Brazil, many lessons were learned that will assist in the consolidation of plans to tackle the unusual situations of epidemic and pandemic character and guide the development of public policies that will strengthen the surveillance system of disease, health care, implementation of laboratory diagnosis, mass vaccination and personal protection and respiratory hygiene network. / SIQUEIRA, Giselle Angélica Moreira de. Epidemia da Influenza A (H1N1) 2009 no estado de Goiás/Brasil: casos e óbitos. Dissertação (Mestrado em Ciências Ambientais) – Pontifícia Universidade Católica de Goiás, Goiânia, 2013. Entre o final de março e começo de abril de 2009, foram notificados os primeiros casos de infecção humana causada por um novo subtipo viral Influenza A (H1N1), no sul da Califórnia e próximo de San Antonio, no Texas, Estados Unidos, e, em seguida, no México e Canadá. Até o dia 06 de julho de 2009, 905 casos foram confirmados pelo Ministério da Saúde, com notificações de 23 estados e do Distrito Federal. Neste estudo foi descrito o perfil dos casos confirmados e óbitos acometidos por Influenza A (H1N1) em 2009 no Estado de Goiás e Brasil por meio de um estudo ecológico descritivo dos casos confirmados e óbitos acometidos pelo vírus Influenza A (H1N1) 2009 no Estado de Goiás e Brasil entre as semanas epidemiológicas 16ª a 52ª, foram selecionadas variáveis da ficha de investigação de Influenza, que alimenta o SINAN Influenza Web tais como semana epidemiológica, faixa etária, gênero, escolaridade, sinais e sintomas, comorbidades, situação vacinal, hospitalizações e evolução. Dentre o total de casos notificados durante a epidemia, mais de 45% foram confirmados por Influenza A (H1N1) em Goiás e no Brasil, sendo que 14,9% e 3,9% evoluíram para o óbito respectivamente. O gênero feminino foi predominante, destas mais de 6% eram gestantes. A faixa etária encontrada foi entre 15 a 45 anos, sendo o ensino médio e fundamental os níveis de escolaridade constatados. Dentre os sinais e sintomas, mais de 95% dos casos e óbitos apresentaram febre, tosse e dispneia, menos de 30% apresentaram comorbidades, a ocorrência de hospitalizações dos casos foi de 96 % em Goiás e 45% no Brasil, enquanto que a hospitalização dos que evoluíram para o óbito foi acima de 96%, menos de 14% dos casos e óbitos tomaram a vacina contra a Influenza (H1N1). Concluiu-se que foi possível conhecer o perfil de casos e óbitos a partir das características sócio demográficas e clínicas durante o período epidêmico da Influenza (H1N1) 2009 em Goiás e no Brasil, foram aprendidas muitas lições que auxiliarão na consolidação de planos de enfrentamento a situações inusitadas de caráter epidêmico e pandêmico e norteará a construção de políticas públicas que fortalecerá o sistema de vigilância da doença, da rede de atenção à saúde, implementação de diagnóstico laboratorial, vacinação massiva e medidas de proteção individual e higiene respiratória.

Surfactant proteins, SP-A and SP-D, are collagen-containing calcium-dependent (C-type) lectins, called, collectins. Their primary structure has four regions: a cysteine-linked N- terminal region involved in multimerization, a collagen region composed of Gly-X-Y repeats, coiled-coil neck region, and the C-terminal carbohydrate recognition domains (CRD) or C-type lectin domain. SP-A looks like a bouquet, while SP-D is a cruciform- like structure, with four arms of equal length. SP-A and SP-D have been shown to act as innate immune molecules at pulmonary as well as extra-pulmonary sites by binding to pathogens, allergens and apoptotic/necrotic cells via their CRD region. SP-A and SP-D can induce pathogen neutralization and enhanced phagocytosis. In addition, SP-A and SP-D can interact via CRDs with allergens and dampen allergic reaction in vitro and in vivo. This thesis examines in vitro interaction of a recombinant fragment of human SP-D containing neck and CRD regions (rhSP-D) with IAV and Aspergillus fumigatus, in addition to characterizing a dichotomy of the effects of SP-A and SP-D on dendritic cells in an attempt to explain how SP-A and SP-D modulate DC functions differentially. Experiments involving interaction of rhSP-D with IAV pandemic strain show that it can be a restrictive factor against the virus, in addition to modulating immune response by a macrophage cell line. The rhSP-D can have anti-A. fumigatus effect directly and indirectly in the context of pathogen as well as allergen. A comparison has been made between two recombinant fragments of SP-D that have been expressed with and without 8 Gly-X-Y repeats for their fungistatic properties. The effects of SP-A and SP-D on cultured DC maturation, and effector cytokine and proliferative response of co-cultured cells have also been examined in vitro.

Introdução: Em 13 de Setembro de 2009, a OMS reportou que existiam mais de 296.471 casos confirmados laboratorialmente de infecção pelo p-H1N1 2009. Ainda assim muitas questões permanecem, incluindo o papel de regras de probabilidade clínica e escores de gravidade de pneumonia adquirida na comunidade nestes pacientes. Nós descrevemos as características clínicas e epidemiológicas de pacientes internados por pneumonia adquirida na comunidade com ou sem infecção pelo p-H1N1. Objetivos: Verificar a incidência e características clínicas da pneumonia adquirida na comunidade associada com infecção pelo p-H1N1 2009, comparado as pneumonias adquiridas na comunidade sem infecção pelo p-H1N1 2009 e a aplicação de regras de probabilidade clínica e escores de gravidade de pneumonia. Métodos: Estudo observacional prospectivo avaliando pacientes consecutivos hospitalizados por pneumonia adquirida na comunidade por mais de 24 horas no HC-FMUSP. A infecção pelo p-H1N1 foi confirmada utilizando ensaios realtime PCR (RT-PCR). Os dados coletados incluíam variáveis clínicas e laboratoriais e 3 escores de gravidade de pneumonia: PSI (Pneumonia Severity Index), CURB-65 e o SMART-COP. Resultados: De 12 de julho a 17 de agosto de 2009, um total de 118 pacientes com pneumonia foram hospitalizados e RT-PCR realizado em 105 pacientes, infecção pelo p-H1N1 foi identificada em 53 pacientes. Comparado com os 52 pacientes sem infecção pelo p-H1N1, o grupo p-H1N1 apresentou significativamente mais coriza [razão de chances (RC): 6,09;intervalo de confiança 95% (IC95%): 1,72-21,52) e infiltrado bilateral (RC: 11,08; IC95%: 3,48-35,2).Um modelo clínico baseado em nossos resultados, incluindo infiltrado bilateral, febre, coriza e idade menor que 65 anos, foi capaz de predizer infecção pelo p-H1N1 2009 com sensibilidade de 90,6% e acurácia de 82% e com uma área sobre a curva (AUC) de 0,82. Nós também verificamos que, em pacientes com infecção pelo p-H1N1 2009, apenas 9,52% com escore SMART-COP entre 0-2 foram admitidos em UTI ou evoluíram para óbito intra-hospitalar comparado a 36,84% dos pacientes com escore PSI 1-2 e 51% dos pacientes com escore CURB-65 de 0-1. O prognóstico da pneumonia foi similar nos grupos com ou sem infecção pelo p-H1N1 2009. Conclusões: A pneumonia associada com infecção pelo p-H1N1 2009 possui apresentação clínica diferente de pacientes sem infecção pelo p-H1N1, entretanto, possuem prognóstico similar. Escores tradicionais de gravidade de pneumonia como PSI e CURB-65 tiveram desempenho ruim em pacientes com infecção pelo p-H1N1 e o escore SMART-COP foi o melhor preditor de internação em UTI em pacientes com pneumonia e infecção pelo p-H1N1. / Introduction: As of September 13, 2009, the WHO had reported over 296.471 laboratory-confirmed cases of p-H1N1 2009. However many questions remain unanswered, including the role of clinical prediction rules and community-acquired pneumonia severity scores. We describe clinical and epidemiologic characteristics of patients hospitalized for pneumonia at our tertiary hospital with laboratory-confirmed and laboratory-excluded H1N1 infection. Objectives: Verify the incidence and clinical characteristics of community-acquired-pneumonia associated with p-H1N1 2009 infection compared with community-acquired pneumonia without p-H1N1 infection and the applicability of clinical prediction rules and pneumonia severity scores. Methods: We prospectively reviewed medical chart in daily basis to collect data on that patients. H1N1 infection was confirmed in specimens using a real-time reverse transcriptase-polymerase-chain-reaction (RT-PCR) assay. The data collected included clinical and laboratorial variables and three pneumonia severity scores: Pneumonia Severity Index, CURB-65 and the SMART-COP rule. Results: From 12 of July through August 17, 2009, a total of 118 cases of pneumonia were hospitalized, and RT-PCR was performed in 105, indentifying p-H1N1 infection in 53 patients. Compared with the 52 patients without p-H1N1 infection , the p-H1N1 group presented significantly more often with rhinorrhoea (OR 6,09 IC 95 1,72-21,52) and bilateral infiltrates ( OR 11,08 IC 95 3,48-35,2), a clinical model based on our results and using bilateral infiltrates, fever, rhinorrhoea and age less than 65 years was capable of predict p-H1N1 infection with 90,6% sensitivity, 82% accuracy and area under the ROC curve (AUC) being 0.82. We also find that in the patients with pneumonia and p-H1N1 infection, only 9.52% of those with SMART-COP score of 0-2 presented ICU admission/in-hospital mortality, compared with 36.84% of those with PSI score of 1-2 and 51% of those with CURB-65 score of 0-1. The prognosis of pneumonia was similar in the patients with and without p-H1N1 2009 infection. Conclusions: Pneumonia associated with p-H1N1 2009 has different clinical presentation than in pneumonia patients without p-H1N1 infection, but the prognosis is similar. Traditional pneumonia severity scores like PSI and CURB-65 performed poorly in patients with p-H1N1 infection and the SMART-COP rule was the best predictor of ICU admission in pneumonia patients with p-H1N1 infection.

M. Tech. (Department of Biotechnology, Faculty of Applied and Computer Science), Vaal University of Technology. / Influenza-A virus is a single stranded negative sense RNA virus that is a member of a Orthomyxoviridae group. The virus is diverse and consists of 16 haemagglutinin (H) and 9 neuraminidase (N) glycoproteins subtypes that form a serotype. Avian influenza virus (AIV) has been detected in more than 100 bird species from 26 different families, although Anseriformes and Charadriiformes are considered the natural hosts of the virus. A 12-month study was conducted at the African Pride Irene Country Club lodge in Pretoria where the prevalence of AIV was monitored in a community of wild birds. The African Pride Irene Country Club lodge houses a population of wild bird species such as Egyptian geese (Alopochen aegytptiaca), Yellow-billed duck (Anas undulata), Red knobbed coot (Fulica cristata), African sacred ibis (Threskiornis aethiopicus) and Hadeda ibis (Bostrycha hagedash). A total of 3674 faecal samples were collected over a period of 12 months and screened for AIV group using the Matrix gene (M-gene) real time reverse-transcriptase PCR (rRT-PCR). Positive samples were submitted for virus isolation in embryonated chicken eggs. In addition, the RNAs were screened using H5 and H7 subtype specific rRT-PCR and a conventional universal RCR assay that targets the HA gene was also used. Polymerase Chain Reaction (PCR) products were requenced using Sanger sequencing and the viral isolates were subjected to Next Generation sequencing (NGS). Twenty percent of the samples tested positive for the AIV group and four virus subtypes were identified. One virus isolate was identified through NGS as H3N6; two through conventional PCR and Sanger sequencing as H9Nx and H6Nx. Of the twenty percent samples that tested positive for AIV 98% were identified as H7Nx by subtype specific through rRT-PCR. The highest frequency of AIV positive samples was detected between the months of January and February 2017 (20%), with smaller peaks detected in february and March 2016 (0.3%). Lower peaks were also detected between the months July and November 2016 (0.1%), respectively. A high prevalence of AIV was detected in the late summer months with a frequency of 65% positive, although a low prevalence was also detected in the autumn (0.6%) winter (0.6%) and spring 0.08%). Thus, the study provides a valuable insight into the seasonal prevalence of AIV in a heterogeneous wild duck population in Gauteng Province.

Heterologous immunity is a mechanism by which immunological memory within an individual, developed in response to a previous infection, plays a role in the immune response to a subsequent unrelated infection. In murine studies, heterologous immunity facilitated by cross-reactive CD8 T-cell responses can mediate either beneficial (protective immunity) or detrimental effects (e.g. enhanced lung and adipose immunopathology and enhanced viral titers) (Selin et al., 1998; Chen et al., 2001; Welsh and Selin, 2002; Nie et al., 2010; Welsh et al., 2010). Protective heterologous immunity results in enhanced clearance of virus during a subsequent infection with an unrelated pathogen. Such is the case when mice are immunized with lymphocytic choriomeningitis virus (LCMV) and subsequently challenged with Pichinde virus (PV) or vaccinia virus (VACV) (Selin et al., 1998). However, heterologous immunity may also mediate enhanced immunopathology as mice immunized with influenza A virus (IAV) and challenged with LCMV show increased viral titers and enhanced lung immunopathology (Chen et al., 2003). The role heterologous immunity plays during infection is not limited to the murine system. In fact, there have now been several reports of enhanced immunopathology due to heterologous immunity during human infections, involving viruses such as IAV, Epstein-Barr Virus (EBV), hepatitis C virus (HCV), and dengue virus (DENV) (Mathew et al., 1998; Wedemeyer et al., 2001; Acierno et al., 2003; Nilges et al., 2003; Clute et al., 2005; Urbani et al., 2005). Interestingly, in all reported cases in humans, heterologous immunity mediated enhanced immunopathology. Upon infection with EBV the clinical presentation can range from asymptomatic to severe, occasionally fatal, acute infectious mononucleosis (AIM) (Crawford et al., 2006b; Luzuriaga and Sullivan, 2010) which is marked by a massive CD8 lymphocytosis. This lympho-proliferative effect in AIM was shown to be partially mediated by reactivation of cross-reactive IAV-M1 58-66 (IAV-GIL) specific CD8 memory T-cells in HLA-A2 patients reacting to the EBV-BMLF1 280 (EBV-GLC) epitope (Clute et al., 2005). Interestingly, EBV infects ~90% of individuals globally by the third decade of life, establishing a life-long infection (Henle et al., 1969). However, it is unknown why 5-10% of adults remain EBV-sero-negative (EBV-SN), despite the fact that the virus infects the vast majority of the population and is actively shed at high titers even during chronic infection (Hadinoto et al., 2009). Here, we show that EBV-SN HLA-A2+ adults possess cross-reactive IAV-GIL/EBV-GLC memory CD8 T-cells that show highly unique properties. These IAV-GIL cross-reactive memory CD8 T-cells preferentially expand and produce cytokines to EBV antigens at high functional avidity. Additionally, they are capable of lysing EBV-infected targets and show the potential to enter the mucosal epithelial tissue, where infection is thought to initiate, by CD103 expression. This protective capacity of these cross-reactive memory CD8 T-cells may be explained by a unique T-cell receptor (TCR) repertoire that differs by both organization and CDR3 usage from that in EBV-seropositive (EBV-SP) donors. The composition of the CD8 T-cell repertoire is a dynamic process that begins during the stochastic positive selection of the T-cell pool during development in the thymus. Thus, upon egress to the periphery a naïve T-cell pool, or repertoire, is formed that is variable even between genetically identical individuals. This T-cell repertoire is not static, as each new infection leaves its mark on the repertoire once again by stochastically selecting and expanding best-fit effectors and memory populations to battle each new infection while at the same time deleting older memory CD8 T-cells to make room for the new memory cells (Selin et al., 1999). These events induce an altered repertoire that is unique to each individual at each infection. It is this dynamic and variable organization of the T-cell repertoire that leads to private specificity even between genetically identical individuals upon infection with the same pathogens and thus a different fate (Kim et al., 2005; Cornberg et al., 2006a; Nie et al., 2010). It is this private specificity of the TCR repertoire that helps explain why individuals with the same epitope specific cross-reactive response, but composed of different cross-reactive T-cell clones, can either develop AIM or never become infected with EBV. Our results suggest that heterologous immunity may protect EBV-SN adults against the establishment of productive EBV infection, and potentially be the first demonstration of protective T-cell heterologous immunity between unrelated pathogens in humans. Our results also suggest that CD8 T-cell immunity can be sterilizing and that an individual’s TCR repertoire ultimately determines their fate during infection. To conclusively show that heterologous immunity is actively protecting EBV-SN adults from the establishment of a productive EBV infection, one would have to deliberately expose an individual to the virus. Clearly, this is not an acceptable risk, and it could endanger the health of an individual. A humanized mouse model could allow one to address this question. However, before we can even attempt to address the question of heterologous immunity mediating protection from EBV infection in humanized mice, we must first determine whether these mice can be infected with, and build an immune response to the two viruses we are studying, EBV and IAV. We show here that these mice can indeed be infected with and also mount an immune response to EBV. Additionally, these mice can also be infected with IAV. However, at this time the immune responses that are made to these viruses in our established humanized mouse model are not substantial enough to fully mimic a human immune response capable of testing our hypothesis of heterologous immunity mediating protection from EBV infection. Although the immune response in these mice to EBV and IAV infection is not suitable for the testing of our model the data are promising, as the humanized mouse model is constantly improving. Hopefully, with constant improvements being made there will be a model that will duplicate a human immune system in its entirety. This thesis will be divided into 5 major chapters. The first chapter will provide an introduction to both general T-cell biology and also to the role of heterologous immunity in viral infection. The second chapter will provide the details of the experimental procedures that were performed to test our hypothesis. The third chapter will describe the main scientific investigation of the role of heterologous immunity in providing natural resistance to infection in human subjects. This chapter will also consist of the data that will be compiled into a manuscript for publication in a peer-reviewed journal. The fourth chapter will consist of work performed pertaining to the establishment of a humanized mouse model of EBV and IAV infection. The establishment of this model is important for us to be able to show causation for protection from EBV infection mediated by heterologous immunity.

Innate sensing of nucleic acids lies at the heart of antiviral host defense. However, aberrant activation of innate sensors by host nucleic acids can also lead to the development of autoimmune diseases. Such host nucleic acids can also be released from stressed, damaged or dying cells into the tissue microenvironment. It however remains unclear how the extracellular nucleic acids impacts the quality of the host immune responses against viral infections. Using a mouse model of influenza A virus (IAV) infection, we uncovered an important immune-regulatory pathway that tempers the intensity of the host-response to infection. We found that host-derived DNA from necrotic cells accumulates in the lung microenvironment during IAV infection, and is sensed by the DNA receptor Absent in Melanoma 2 (AIM2). AIM2-deficiency resulted in severe immune pathology highlighted by enhanced recruitments of immune cells, and excessive systemic inflammation after IAV challenge, which led to increased morbidity and lethality in IAV-infected mice. Interestingly, these effects of AIM2 were largely independent of its ability to mediate IL-1β maturation through inflammasome complexes. Finally, ablation of accumulated DNA in the lung by transgenic expression of DNaseI in vivo had similar effects. Collectively, our results identify a novel mechanism of cross talk between PRR pathways, where sensing of hostderived nucleic acids limits immune mediated damage to virus infected tissues.