Emerging infectious diseases (EIDs) constitute an important global health security problem. During EID outbreaks, patient centred research can play a significant role in informing evidence-based care for patients, in calibrating public health responses, and in directing effective policy and research. However, to date, this type of research has been limited in impact. This thesis sets out to improve the value of patient centred research in combating EID outbreaks. It provides a structured analysis of what has previously constrained efforts to rapidly accumulate high-quality evidence. It provides primary data from research conducted during an outbreak, and conducted in an outbreak vulnerable setting. And it provides recommendations that aim to facilitate high-quality data collection in future events. This thesis contains four results chapters. Chapter 2 systematically reviews elements of the research response to two EID outbreaks of public health importance. Chapter 3 provides findings of a phase II clinical trial of an investigational therapy for Ebola virus disease (EVD), contextualises the utility of this and comparable work in improving patient care, and discusses the operational feasibility of such work during an epidemic. Chapter 4 focuses specifically on improving one element - disease characterisation - during EID outbreaks. It achieves this through presenting a systematic analysis of bias in the characterisation of EVD and recommends how to prioritise data gathering for high-risk pathogens. Chapter 5 exemplifies how clinical data collection practices can progress between outbreaks. It is the first stage of work undertaken to improve the clinical characterisation of communicable diseases in the vulnerable environment of refugee camps. This thesis demonstrates progress towards having higher quality clinical research conducted during the time frame of an epidemic. Future work can focus on the most important barriers to accelerating research, now that these have been more clearly defined.

Seroepidemiology aims to understand population-level exposure and immunity to infectious disease. Serological results are normally presented as binary outcomes describing the presence or absence of antibody, despite the fact that many assays measure continuous quantities. A population's antibody titers may include information on multiple serological states - naiveté, recent infection, non-recent infection, childhood infection - not just seropositivity or seronegativity. In the first part of this thesis, I investigate 20,152 general-population serum samples from southern Vietnam collected between 2009 and 2013 from which I report antibody titers to the influenza virus HA1 protein using a continuous titer measurement from a protein microarray assay. I describe titer distributions to subtypes 2009 H1N1 and H3N2, and using a model selection approach for mixture distributions, I determine that 2009 H1N1 is best described by four titer subgroups while H3N2 is best described by three titer subgroups. For H1N1, my interpretation is that the two highest-titer subgroups correspond to recent and historical infection, which is consistent with pandemic attack rates. For H3N2 however, right-censoring of titers makes interpretations difficult to validate. To move beyond this stationary interpretation of titers, I developed two methods for analyzing this serum collection as a time series. First, I attempted to analyze mixture categories in individual time windows. This approach did not lead to a consistent temporal picture of titer change; results differed by site and were sensitive to assumptions in the mixture fitting. Second, I attempted to fit a hybrid-dynamical model with free incidence parameters. This inference was robust to parameter assumptions, consistent across sites, and in agreement with the incidence reported in Vietnam's influenza surveillance network. In addition, my new approach showed evidence that there was a second silent wave of the 2009 influenza pandemic that was not recorded in national surveillance, which is this thesis' main novel result.

Influenza A virus (IAV) replication and transcription occur in the host cell nucleus; a feature which means both the viral genome (vRNA) and mRNA must be exported from the nucleus to the cytoplasm. The mechanism by which vRNA nuclear export is achieved has been well characterised, but how viral mRNAs are exported is poorly understood. The cellular NXF1-dependent mRNA export pathway has been shown to be involved in the export of some viral mRNAs, but how they are recruited to this pathway is unknown. Prior work from our laboratory showed that segment 7 mRNA was inefficiently exported to the cytoplasm in a sub-viral ‘minireplicon’ system, providing the first indication that there were viral requirements for IAV mRNA nuclear export. Further addition of individual viral polypeptides was tested and the effect on segment 7 mRNA export was analysed by fluorescent in situ hybridization (FISH) and confocal microscopy. This identified the NS1 protein as the viral factor required for efficient segment 7 nuclear export. Mutational studies on NS1 were carried out to unveil the mechanistic role of this protein in viral mRNA nuclear export, by plasmid transfection as well as in the context of recombinant viruses. These approaches indicated that both functional domains of NS1 were necessary to preserve the mRNA export function. Furthermore, these mutant proteins were used to examine the association between NS1 and the NXF1-dependent pathway in the context of mRNA nuclear export. Protein-protein and protein-RNA binding assays indicated that interactions between NXF1 and NS1, and NXF1 and segment 7 mRNA were necessary, but not sufficient to promote segment 7 viral mRNA export. Lastly, the role of NS1 protein in the nuclear export of viral mRNAs from other genome segments was studied. The intracellular localisation of most viral mRNAs was not affected by the absence of NS1 or the presence of an export-incompetent NS1 mutant protein. However, segment 4 mRNA exhibited a similar phenotype to segment 7 mRNA in showing a dependence on NS1 for efficient nuclear export. Overall, the results presented in this dissertation suggest that NS1 acts as an adaptor protein between the viral RNA synthesis machinery and cellular export pathway. This provides deeper insights for the characterization of a recently identified function of the IAV NS1 protein, of being required for the efficient nuclear export of mRNA from “late” kinetic class viral genes.

Innate immune cells, such as macrophages, are trained by the unique microenvironment of the tissue they occupy. This tissue influence can include the extracellular matrix, the presence of inflammatory stimuli or signals and, in some tissues, the microbiota. Most studies, however, have examined such tissue specific training in health whereas little is known about the possibility of immune re-training in the lung following acute inflammation. The lung extracellular matrix is important for mechanical stability and structural support, as well as influencing inflammation via altering cell adhesion, migration, survival, proliferation and differentiation. Matrix alterations are a feature of a number of significant chronic respiratory diseases that carry high clinical unmet need. These include idiopathic pulmonary fibrosis, cystic fibrosis and chronic obstructive pulmonary disease (COPD). On the other hand, the impact on matrix after acute inflammation and whether it is returned to its pre-infection state is relatively unexplored. In murine models, macroscopic examination of the lung following acute inflammation implies a return to a reasonable homeostatic state. However, using more sensitive techniques, we now show that this is not the case. In this thesis we test the premise that a more thorough interrogation of lung extracellular matrix by mass spectrometry will reveal long term alterations that are not visible by histology. After influenza virus infection, we demonstrate that heightened extracellular matrix persists in the lung tissue, often forming structures that were not present in health. Furthermore, basement membrane components, for example collagen IV and laminin, are reduced. In vitro investigations show that individual extracellular matrix components affect lung macrophage activity. For example, hyaluronan and fibronectin alter macrophage expression of microRNA species known to influence toll-like receptor responsiveness and fibrosis. We also describe an alteration in microRNA species in response to influenza virus infection as well as a non-infectious model of pulmonary inflammation using carbon nanotubes. Collectively, this implies that altered matrix composition impacts on the inflammatory tone of the lung innate immune system. It is therefore feasible that such changes following severe lung inflammation could be overcome by targeting abnormal matrix production or degradation.

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Sócio-Econômico. Programa de Pós-Graduação em Economia. / Made available in DSpace on 2012-10-23T23:48:48Z (GMT). No. of bitstreams: 1 262524.pdf: 519374 bytes, checksum: d7241e195df4a2650217a26b013cdf5b (MD5) / O surto de gripe aviária ocorrido no final de 2005, tendo como focos principais a União Européia e a Ásia, causou grandes perdas econômicas ao setor. O Brasil, apesar de ser considerado país livre da doença, também sofreu impactos por conta do grande volume de exportações de carne frango realizado pelo país, e que foram prejudicadas pela grande contração na demanda externa. O presente trabalho busca identificar impactos deste evento na volatilidade dos preços e dos retornos dos preços internos e externos da carne de frango. Além disso, foi realizado um estudo a respeito da relação entre o preço externo e interno da carne de frango. Por meio dos métodos de cointegração confirmouse a hipótese de existência de uma relação de longo prazo entre os preços internos e externos da carne de frango. Com relação aos impactos do surto na volatilidade de preços e retorno dos preços, os modelos GARCH construídos indicam o aumento da volatilidade no caso do retorno dos preços internos e a redução no caso do retorno dos preços externos. The outbreak of avian influenza occurred in late 2005, with the major targets being the European Union and Asia, generated great economic losses to the sector. Brazil, despite being considered a country free of this disease, also felt impacts due to chicken meat exports made by the country, which has been hampered by the large contraction in external demand. This study seeks to identify impacts of this event in the volatility of prices and returns of internal and external prices of chicken meat. Moreover, a study was conducted on the relationship between the external and internal price of chicken meat. Through the methods of cointegrating confirmed the possibility of existence of a external and domestic prices of chicken meat. With relation of the impacts of the outbreak of volatility in prices and return prices, the models constructed GARCH indicate the increased volatility in the case of return on domestic prices and a reduction in case of return on external prices.

Submitted by Alessandra Portugal (alessandradf@ioc.fiocruz.br) on 2013-09-20T15:50:30Z No. of bitstreams: 1 Cristiane Maia Alves.pdf: 1063313 bytes, checksum: a48ab6ac753935673b07a64282e7821b (MD5) / Made available in DSpace on 2013-09-20T15:50:30Z (GMT). No. of bitstreams: 1 Cristiane Maia Alves.pdf: 1063313 bytes, checksum: a48ab6ac753935673b07a64282e7821b (MD5) Previous issue date: 2012 / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil / O vírus Influenza é o agente infeccioso que mais afeta o trato respiratório dos seres humanos, resultando em altos índices de morbidade e mortalidade. Este vírus pertence à família Orthomyxovirida, apresenta RNA fita simples, octa-segmentado, de polaridade negativa e possui um envelope lipoproteico no qual estão inseridas as glicoproteínas hemaglutinina e neuraminidase. Já foi demonstrado que a infecção por Influenza gera alterações no metabolismo celular, porém, não foi descrito, até o momento, qual seria o mecanismo de ação relacionado. Em nosso trabalho, decidimos analisar mais a fundo essas alterações metabólicas relacionadas à infecção por Influenza A. Para tal, resolvemos investigar os efeitos da inibição da via glicolítica e do silenciamento da enzima chave de regulação da via, a enzima PFK-1, sobre a replicação viral. Inicialmente, utilizamos células MDCK infectadas com MOI de 5,0 e verificamos o efeito da inibição de umas das etapas finais desta via metabólica sobre a replicação do vírus. Observamos que, em 24 horas pós-infecção, a inibição da glicólise provocou uma redução da replicação do vírus Influenza, porém, em 48 horas pós–infecção, a inibição desta via promoveu um aumento da replicação viral. Verificamos, também, que o silenciamento das isoformas L, M e P da enzima PFK-1, em 24 horas pós-infecção, promoveu uma significativa diminuição do título viral. Diante disto, decidimos investigar quais as etapas do ciclo replicativo estariam sendo afetadas pelo silenciamento desta enzima e observamos que, tanto a adsorção como a penetração de material genético no núcleo celular foram afetadas pelo silenciamento da PFK-1, principalmente pela inibição da isoforma P. Esses resultados sugerem que a enzima PFK-1 tem um importante papel na infecção pelo vírus Influenza podendo, inclusive, ser um possível alvo terapêutico. / The Influenza virus is the major infectious agent that affects the respiratory tract of humans, resulting in high morbidity and mortality. This virus belongs to Orthomyxovirida family and presents single-stranded, octa-segmented, negative polarity RNA and has a lipoprotein envelope in which are inserted the hemagglutinin and neuraminidase glycoproteins. It has been shown that Influenza infection causes changes in cellular metabolism, however, not been described up to now, which would be related mechanism of action. In our work, we decided to further analyze these metabolic changes related to infection with Influenza A. To this end, we decided to investigate the effects of inhibition of glycolytic pathway and the silencing of key regulatory enzyme of this pathway, the enzyme PFK-1, on viral replication. Initially, we used MDCK cells infected with m.o,.i.5.0 to check the effect of inhibition of some final stages of this pathway on virus replication. We observed that, in 24 hours postinfection, the inhibition of glycolysis resulted in a reduction of the replication of Influenza viruses, but at 48 hours post-infection, the inhibition of this pathway leads to an increase in viral replication. We also verified that silencing of L, M and P isoforms of PFK-1, at 24 hours post-infection, caused a significant decrease in viral titer. So, we decided to investigate which steps of the replicative cycle were being affected by the silencing of this enzyme and found that both the adsorption and penetration of genetic material in the cell nucleus were affected by the silencing of PFK-1, mainly by inhibiting P isoform. These results suggest that the enzyme PFK-1 plays an important role in the Influenza virus infection and may it also be a potential therapeutic target.

Submitted by Alessandra Portugal (alessandradf@ioc.fiocruz.br) on 2013-09-24T15:06:55Z No. of bitstreams: 1 Dissertação de Mestrado Paola Cristina Resende Silva.pdf: 1538372 bytes, checksum: 8c68a244d3e53f424ddb574f985bcad8 (MD5) / Made available in DSpace on 2013-09-24T15:06:55Z (GMT). No. of bitstreams: 1 Dissertação de Mestrado Paola Cristina Resende Silva.pdf: 1538372 bytes, checksum: 8c68a244d3e53f424ddb574f985bcad8 (MD5) Previous issue date: 2010 / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil / Globalmente, as infecções causadas pelos vírus Influenza constituem um importante desafio para a Saúde Pública. Os vírus Influenza B pertencem à família Orthomyxoviridae, seu genoma viral é constituído por um RNA de fita simples e polaridade negativa. O processo de drift antigênico favorece o contínuo aparecimento de novas variantes virais, o que demanda a reformulação anual da vacina. No início década de 80, foi observada a divergência do vírus Influenza B em duas linhagens antigênica e filogeneticamente distintas: B/Victoria/2/87-like (Vic87) e B/Yamagata/16/88-like (Yam88), que tem co-circulado em diferentes países na última década. O objetivo deste estudo consiste na identificação e caracterização molecular das linhagens de Influenza B circulantes em diferentes regiões brasileiras durante as epidemias de 2004 a 2008, com base no sequenciamento dos genes Hemaglutinina (HA) e Neuraminidase (NA). Ainda, padronizamos a metodologia de Eletroforese em Gel com Gradientes Desnaturantes (DGGE), visando à rápida tipagem dos vírus B. Diferentes substituições nos genes da HA e NA foram encontradas. Evidenciamos a co-circulação de ambas as linhagens no período estudado, contudo, não observamos a ocorrência de rearranjo gênico e nem a emergência de cepas resistentes aos inibidores de neuraminidase, com base nos genes investigados. No período 2006-2008, observamos a adequada concordância entre as cepas circulantes e as cepas vacinais preconizadas para uso no Hemisfério Sul. Entretanto, o mesmo não foi verdadeiro para o período 2004-2005. Finalmente, o protocolo de DGGE desenvolvido pode ser eficientemente utilizado para fins de rápida tipagem das linhagens de Influenza B. Os achados deste estudo contribuem para a melhor compreensão sobre a variabilidade dos vírus Influenza B e os mecanismos envolvidos na sua evolução molecular, bem como o padrão de circulação das linhagens virais no Brasil e sua correspondência com as vacinas para Influenza, anualmente administradas no Hemisfério Sul. Este conjunto de informações são de grande relevância para a contínua adequação e implementação das políticas e estratégias voltadas ao controle e prevenção de infecções por Influenza na nossa população. / Worldwide, Influenza infections are a major Public Health issue. Influenza B virus is classified into the Orthomyxoviridae family, the viral genome consists of a single strand RNA and negative polarity. Because of antigenic drift, novel viral variants are continuously rising, what demands the annual review of vaccine formulation. In the early 80´s, was observed the divergence of Influenza B into two distinct antigenic and phylogenetic lineages – B/Victoria/2/87-like (Vic87) and B/Yamagata/16/88-like (Yam88), was observed. In some countries, these strains have been co-circulating in the last 10 years. The aim of this study was to investigate the circulation patterns of Vic87 and Yam88 among different Brazilian regions during the 2004-2008 epidemics, based on haemagglutinin (HA) and neuraminidase (NA) sequencing. Moreover, a Denaturing Gradient Gel Electrophoresis (DGGE) protocol was standardized for rapid typing of Flu B typing into Yam88-like and Vic87-like strains. Different Aminoacid substitutions in the HA and NA were encountered. Along the studied period, our findings showed that both viral lineages have been co-circulating in Brazil. Moreover, no evidence of reassortant nor NA inhibitor-resistant viruses was found. From 2006 to 2008, an adequate match between vaccine and circulating strains was met. However, it was not true for 2004-2005 years. Finally, our DGGE protocol can be successfully used as a rapid Flu B strain typing test. Our findings contribute for a better figure of Flu B genetic variability and its molecular evolution mechanisms, in addition to the circulation patterns of Flu B lineages in Brazil, and their respective association with the vaccine strains used in the Southern Hemisphere. Altogether, these are pivotal information to continuously tailor and implement Public Health policies on behalf of the control and prevention of Influenza infections.

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências da Saúde. Programa de Pós-Graduação em Enfermagem. / Made available in DSpace on 2012-10-26T05:53:04Z (GMT). No. of bitstreams: 1 299963.pdf: 3817695 bytes, checksum: 61efb7853a18ffd59942f69c2d665bcb (MD5) / A doença Influenza é conhecida há centenas de anos, mas apesar disto, e de atualmente existir uma vacina comprovadamente eficaz para sua prevenção, continua sendo uma das principais causas de morbimortalidade e gastos financeiros com saúde no mundo. Nos hospitais, a vacinação contra Influenza dos profissionais de enfermagem, reveste-se em fator de biossegurança não só para os mesmos, mas também para os pacientes vulneráveis sob seus cuidados. Este estudo tem como objetivos: fazer o diagnóstico da situação vacinal em relação à Influenza dos profissionais de enfermagem do Hospital Universitário da Universidade Federal de Santa Catarina (HU/UFSC); identificar as crenças e conhecimentos que os profissionais da Diretoria de Enfermagem (DE/HU/UFSC) possuem a respeito deste assunto; estimular a prática da biossegurança através da vacinação dos servidores de enfermagem do HU/UFSC mediante a construção de uma cartilha educativa e, elaborar uma proposta de protocolo para obtenção de cobertura adequada permanente desta vacina. Métodos: O estudo inicialmente tomou como referência o perfil dos vacinados e não vacinados na Campanha Anual de Vacinação contra Influenza 2010. Em seguida calculou-se amostra (n = 265) representativa das categorias: enfermeiro, técnico e auxiliar de enfermagem da DE/HU/UFSC, suficiente para medir com 95% de confiança para as prevalências esperadas. Todos os 265 profissionais selecionados por sorteio responderam a um formulário baseado no Modelo de Crenças em Saúde. A partir das respostas obtidas, foi elaborado e analisado um Banco de Dados nos programas estatísticos Epidata 3.1 e EpiData Analysis, respectivamente. Os achados mais significativos foram tomados como referência para implementação de: (1) Ações educativas, que iniciaram com a elaboração de uma cartilha intitulada "Influenza/Gripe - O Profissional da Saúde precisa Saber" e, incluíram também, Oficinas de Sensibilização, cursos de capacitação e treinamento de vacinadores. (2) Ações administrativas institucionais que culminaram com o detalhamento organizacional da Campanha Anual de Vacinação contra Influenza no formato de um Protocolo e, (3) Ações políticas, através do envolvimento dos órgãos gestores da instituição a fim de sancionar e viabilizar e efetividade das ações propostas visando a Campanha de Vacinação contra Influenza 2011 e posteriores. Resultados: A cobertura vacinal encontrada na instituição foi de 49,8% em 2009, 92,4% em 2010 e 95,4% em 2011. A adesão encontrada foi ligeiramente maior no sexo feminino (92,8%), entre os separados/divorciados (95,0%), na faixa etária entre 41-50 anos (96,5%), nos formados há mais de 20 anos (94,9%), nos que trabalham há mais de 20 anos na instituição (94,0%), nos que atuam na emergência (94,9%), naqueles que possuem mais de um vínculo empregatício (92,6%), nos que não co-habitam com crianças (95,5%), não co-habitam com idosos (93,3%), naqueles que co-habitam com doentes crônicos (95%), possuem nível médio de instrução. Este profissional se vacinou em seu próprio setor de trabalho motivado por uma atitude de auto-proteção. Além disso, este profissional crê na severidade e transmissibilidade da doença para si e para os pacientes sob seus cuidados. Acredita ainda nos benefícios gerados pela vacinação contra Influenza. Este estudo resultou ainda na elaboração, impressão e distribuição para todo o corpo de enfermagem do HU/UFSC da Cartilha "Influenza/Gripe - O Profissional da Saúde Precisa Saber" e também na construção e impressão de um "Protocolo para Adesão dos Servidores de Enfermagem à Vacinação contra Influenza a ser usado na instituição". Considerações Finais: Os achados de cobertura de 92,5% em 2010 e de 95,4% em 2011, considerados excepcionais dentro da atual realidade mundial, refletem a existência de uma cultura de biossegurança relacionada a este tema, incorporada ao longo de uma década de ações educativas, de divulgação e acessibilidade. A construção da cartilha educativa e do protocolo, pretende, contribuir não só para a manutenção e sedimentação dessa cultura dentro da instituição, mas, também, de outros hospitais que desejem organizar/estruturar seus serviços de vacinação. / Influenza is known to humanity for hundreds of years, but despite this and the existence of a provenly effective vaccine for its prevention, the disease continues to be one of the main sources of morbidity and mortality and financial expenses in the world of healthcare. In hospitals, the vaccination against influenza for nursing professionals is a factor of biosecurity not only for nurses, but also for the vulnerable patients under their care. This study has the following objectives: diagnose the situation of flu vaccination among nursing professionals at the university hospital at the federal University at Santa Catarina (HU/UFSC); identify the beliefs and knowledges that the professionals of the department of nursing at the (DE/HU/UFSC) have about this issue; stimulate the practice of biosecurity through vaccination of nursing employees at HU/UFSC through the development of an educational primer and, prepare a proposed protocol to obtain permanent suitable coverage of this vaccine. Methods: The study initially used as a reference the profile of those vaccinated and not vaccinated in the annual Vaccination Against Influenza Campaign 2010. It then calculated a representative sample (n=265) of the categories: nurses, nurse technicians and nursing assistants at the DE/HU/UFSC, sufficient for measuring with 95% reliability the expected prevalences. All of the 265 professionals selected randomly responded to a formula based on the Model of Healthcare Beliefs. From the responses obtained, a database was prepared and analyzed using the statistical programs Epidata 3.1 and EpiData Analysis respectively. The most significant findings were used to guide the implementation of: (1) Educational actions, which were initiated with the primer named "Influenza/Flu - The Healthcare Professional Must Know" and included, too, Sensibilization Workshops, capacitation courses and training for the vaccinators. (2) Institutional administrative actions that resulted in the organizational detailing of the Annual Vaccination Campaign against the Influenza in the format of a Protocol and, (3) Political actions, through the involvement of the institutional manager sectors to approve the proposed actions aiming the Influenza Vaccination Campaign 2011 and posterior campaigns. Results: The coverage of the vaccine found at the institution was 49.8% in 2009, 92.4% in 2010 and 95.4% in 2011. The profile of the professional most adherent to the campaign is slightly greater in females (92.8%), divorced (95.0%), from 41-50 years old (96.5%), graduated for more than 20 years (94.9%), has been working for more than 20 years in the institution (94.0%), work in the Emergency Sector (94.9%), has more than one job, (92.6%), does not live with children (95.5%), does not live with elderly (93.3%), lives with chronical sick people (95.0%), has average level of education. This professional was vaccinated within his work sector, motivated by an attitude of self-protection. He recognizes the severity and transmissibility of the disease to herself and to patients under her care. She also believes in the benefits generated by the flu vaccine. This study resulted in the development, printing and distribution to all nursing professionals from HU/UFSC of the Primer "Influenza/Flu - The Healthcare Professional Must Know" and also the construction and printing of a "Protocol to Adherence of the Nursing Professional to the Vaccination against Influenza to be used in the institution". Final considerations: The findings of coverage of 92.5% in 2010 and of 95.4% in 2011 were considered exceptional within the current global reality, and reflect the existence of a culture of biosecurity related to this issue, incorporated over a decade of activities aimed at education, promotion and accessibility. The construction of the educative primer and the protocol intends to contribute not only to maintain and sediment this culture in the institution, but also in other hospitals that wish to organize their vaccination services.

<b>Introduction:</b> Respiratory Syncytial Virus is the major viral cause of lower respiratory tract disease in young children worldwide, with the greatest burden of disease in infants aged 1-3 months. Consequently, vaccine development has centered on a vaccine to directly protect the infants in this age group. The fundamental problem is that these young infants are poor responders to candidate RSV vaccines. This thesis focuses on the use of mathematical models to explore the merits of vaccination. <b>Methods:</b> Following development and analysis of a simple non-age-structured ODE model, we elaborate this to a Realistic Age Structured model (RAS) capturing the key epidemiological characteristics of RSV and incorporating age-specific vaccination options. The compartmental ODE model was calibrated using agespecific and time series hospitalization data from a rural coastal Kenyan population. The determination of Who Acquires Infection From Whom (WAIFW) matrix was done using social contact data from 1) a synthetic mixing matrix generated from primarily household occupancy data and 2) a diary study that we conducted in the Kilifi Health and Demographic Surveillance System (KHDSS). The vaccine was assumed to elicit partial immunity equivalent to wild type infection and its impact was measured by the ratio of hospitalized RSV cases after to before introduction. of vaccination. Uncertainty and sensitivity analysis were undertaken using Latin Hypercube Sampling (LHS) and partial rank correlation respectively. Given the importance of households in the transmission of respiratory infections, an exploratory household model was developed to capture the transmission dynamics of RSV A and B in a population of households. <b>Results:</b> From the analytical work of the simple ODE model, we have demonstrated that the model has the potential to exhibit a backward bifurcation curve within realistic parameter ranges. Both the diary and the synthetic mixing matrices had similar characteristics i.e. strong assortative mixing in individuals less than 30 years old and strong mixing between children less than 5 years and adults between 20 and 50 years old. When the two matrices were jointly linearly regressed, their elements were well correlated with an R2 ~ 0.6. The RAS model was capable of capturing the age-specific disease and the temporal epidemic nature of RSV in the specified location. Introduction of routine universal vaccination at ages varying from the first month of life to the 10th year of life resulted in optimal long-term benefit at 7 months (for the diary contact model) and 5 months (for the synthetic contact model). The greatest benefit arose under the assumption of age-related mixing with the contact diary data with no great deal of effectiveness lost when the vaccine is delayed between 5 and 12 months of age from birth. Vaccination was also shown to change the temporal dynamics of RSV hospitalizations and also to increase the average age at primary infection. From the sensitivity analysis, we identified the duration of RSV specific maternal antibodies, duration of primary and tertiary infections as the most important parameters in explaining the imprecision observed in predicting both the age specific hospitalizations and the optimal month at vaccination. Results from the household model have demonstrated that the household epidemic profile may be different from the general population with strong interaction of the viruses in the household that do not necessarily reflect at the population level. <b>Conclusion:</b> The synthetic matrix method would be a preferable alternative route in estimating mixing patterns in populations with the required socio-demographic data. Retrospectively, the synthetic mixing data can be used to reconstruct contact patterns in the past and therefore beneficial in assessing the effect of demographic transition in disease transmission. Universal infant vaccination has the potential to significantly reduce the burden of RSV associated disease, even with delayed vaccination between 5 and 12 months. This age class represents the group that is being targeted by vaccines that are currently under development. More accurate data measuring the duration of RSV specific maternal antibodies and the duration of infections are required to reduce the uncertainty in the model predictions.

Made available in DSpace on 2015-07-22T20:50:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-03-31 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O Bocavírus Humano (HBoV) é um parvovírus recentemente descoberto em isolados de secreções respiratórias humanas. Pesquisado em todo o mundo, sua detecção é muito variável de 1,3% a 19%. Há poucos estudos no Hemisfério Sul, particularmente no Brasil, sendo que a maioria relata maior incidência em crianças. Assim, investigamos crianças e adultos com infecção respiratória aguda e diferentes grupos de risco para doenças respiratórias em amostras de swabs, lavados e aspirados nasofaríngeos coletados de pacientes com sintomas de infecção aguda do trato respiratório. Quinhentos e trinta e quatro amostras provenientes de sete diferentes grupos de risco, entre 2001 e 2008 foram investigadas para presença de DNA HBoV através da amostra de PCR de acordo com o protocolo de Allander, et al. 2005. Em geral, 3% das crianças (8/264) e 0,4% dos adultos (1/270) foram positivos: 2,4% (3/127) das crianças da creche 4,8% (5/103) das crianças com cardiopatia congênita, 0,9% adultos transplantados de medula óssea (1/112), mas nenhum dos profissionais de saúde (83), adultos transplantados renais (31) e pacientes do pronto atendimento (44 adultos e 34 crianças). Três crianças da cardiopatia congênita apresentaram infecção leve, e 4 dos 7 pacientes co-infectados com Rinovírus apresentaram dispnéia e chiado. Os sintomas mais comumente observados foram coriza, tosse, febre que foram observados geralmente em mais de 50% dos casos positivos para HBoV. Estes dados sugerem que a infecção por HBoV em adultos mesmo em imunodeprimidos não é relevante e a elevada taxa de co-infecção observada em crianças aponta a necessidade de melhor avaliação do papel do HBoV na patogênese entre pacientes co-infectados. / The Human Bocavirus (HBoV) is a recently discovered parvovirus isolate from human respiratory secretions. Published reports pointed to detection rates from 1.3% to 19%. Limited data is available from Southern hemisphere circulation and, particularly in Brazil, there are some reports with a high incidence in children. We investigated samples from children and adults and other risk groups for respiratory diseases with acute respiratory infection. Five hundred thirty four samples collected from seven different risk groups between 2001 and 2008 were investigated for DNA HBoV by in house PCR adapted from Allander (2005). In general, 3% of children (8/264) and 0.4% of adults (1/270) were HBOV positive: 2.4% (3/127) of children from day care, 4.8% (5/103) of children with congenital heart disease, 0.9% of adult bone marrow transplant (1/112), but none of the health care workers (83), adult renal transplantation patients (31) and community patients in the emergency department (44 adults and 34 children). Commonly observed symptoms were runny nose, cough and fever which were usually observed in more than 50% of cases positive for HBoV. The three children with heart disease had mild infection but four co-infected patients with Rhinovirus had dyspnea and wheezing. These data suggest that HBoV infection among adults, including immunocompromised patients is not relevant. Children co-infection is highly observed and this fact highlights the need for better assessment of the HBoV role in the pathogenesis of symptomatic patients. / FAPESP: 2008/50352-2 / TEDE / BV UNIFESP: Teses e dissertações