abstract: In the field of infectious disease epidemiology, the assessment of model robustness outcomes plays a significant role in the identification, reformulation, and evaluation of preparedness strategies aimed at limiting the impact of catastrophic events (pandemics or the deliberate release of biological agents) or used in the management of disease prevention strategies, or employed in the identification and evaluation of control or mitigation measures. The research work in this dissertation focuses on: The comparison and assessment of the role of exponentially distributed waiting times versus the use of generalized non-exponential parametric distributed waiting times of infectious periods on the quantitative and qualitative outcomes generated by Susceptible-Infectious-Removed (SIR) models. Specifically, Gamma distributed infectious periods are considered in the three research projects developed following the applications found in (Bailey 1964, Anderson 1980, Wearing 2005, Feng 2007, Feng 2007, Yan 2008, lloyd 2009, Vergu 2010). i) The first project focuses on the influence of input model parameters, such as the transmission rate, mean and variance of Gamma distributed infectious periods, on disease prevalence, the peak epidemic size and its timing, final epidemic size, epidemic duration and basic reproduction number. Global uncertainty and sensitivity analyses are carried out using a deterministic Susceptible-Infectious-Recovered (SIR) model. The quantitative effect and qualitative relation between input model parameters and outcome variables are established using Latin Hypercube Sampling (LHS) and Partial rank correlation coefficient (PRCC) and Spearman rank correlation coefficient (RCC) sensitivity indices. We learnt that: For relatively low (R0 close to one) to high (mean of R0 equals 15) transmissibility, the variance of the Gamma distribution for the infectious period, input parameter of the deterministic age-of-infection SIR model, is key (statistically significant) on the predictability of the epidemiological variables such as the epidemic duration and the peak size and timing of the prevalence of infectious individuals and therefore, for the predictability these variables, it is preferable to utilize a nonlinear system of Volterra integral equations, rather than a nonlinear system of ordinary differential equations. The predictability of epidemiological variables such as the final epidemic size and the basic reproduction number are unaffected by (or independent of) the variance of the Gamma distribution for the infectious period and therefore for the choice on which type of nonlinear system for the description of the SIR model (VIE's or ODE's) is irrelevant. Although, for practical proposes, with the aim of lowering the complexity and number operations in the numerical methods, a nonlinear system of ordinary differential equations is preferred. The main contribution lies in the development of a model based decision-tool that helps determine when SIR models given in terms of Volterra integral equations are equivalent or better suited than SIR models that only consider exponentially distributed infectious periods. ii) The second project addresses the question of whether or not there is sufficient evidence to conclude that two empirical distributions for a single epidemiological outcome, one generated using a stochastic SIR model under exponentially distributed infectious periods and the other under the non-exponentially distributed infectious period, are statistically dissimilar. The stochastic formulations are modeled via a continuous time Markov chain model. The statistical hypothesis test is conducted using the non-parametric Kolmogorov-Smirnov test. We found evidence that shows that for low to moderate transmissibility, all empirical distribution pairs (generated from exponential and non-exponential distributions) for each of the epidemiological quantities considered are statistically dissimilar. The research in this project helps determine whether the weakening exponential distribution assumption must be considered in the estimation of probability of events defined from the empirical distribution of specific random variables. iii) The third project involves the assessment of the effect of exponentially distributed infectious periods on estimates of input parameter and the associated outcome variable predictions. Quantities unaffected by the use of exponentially distributed infectious period within low transmissibility scenarios include, the prevalence peak time, final epidemic size, epidemic duration and basic reproduction number and for high transmissibility scenarios only the prevalence peak time and final epidemic size. An application designed to determine from incidence data whether there is sufficient statistical evidence to conclude that the infectious period distribution should not be modeled by an exponential distribution is developed. A method for estimating explicitly specified non-exponential parametric probability density functions for the infectious period from epidemiological data is developed. The methodologies presented in this dissertation may be applicable to models where waiting times are used to model transitions between stages, a process that is common in the study of life-history dynamics of many ecological systems. / Dissertation/Thesis / Ph.D. Applied Mathematics for the Life and Social Sciences 2014

Submitted by Haroudo Xavier Filho (haroudo.xavierfo@ufpe.br) on 2016-03-29T19:03:03Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Doutorado_POSCA_VilmaMacedo_2015.pdf: 2539315 bytes, checksum: f902199f34f31cb9dbedb12dc56463ff (MD5) / Made available in DSpace on 2016-03-29T19:03:03Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Doutorado_POSCA_VilmaMacedo_2015.pdf: 2539315 bytes, checksum: f902199f34f31cb9dbedb12dc56463ff (MD5) Previous issue date: 2015-08-18 / CNPq / FACEPE / A sífilis gestacional é uma doença infecciosa, transmitida verticalmente, e está associada a diversos desfechos negativos na gravidez que são evitáveis quando detectada e tratada de forma precoce. As recomendações atuais para o controle da sífilis reforçam a necessidade de priorizar intervenções globais em prevenção, diagnóstico e tratamento oportuno com atenção a grupos populacionais mais expostos. O objetivo desta tese foi estudar os fatores que influenciam a ocorrência e o tratamento para sífilis em mulheres atendidas em sete maternidades públicas do Recife – PE. O documento foi estruturado nos seguintes capítulos: revisão da literatura, método, resultados apresentado sob a forma de dois artigos originais, considerações finais e recomendações. O estudo foi desenvolvido a partir de uma pesquisa mais abrangente, do tipo caso-controle, que recrutou 1.206 mulheres a partir da admissão nas maternidades, conforme local de residência e resultado do exame de VDRL (Venereal Disease Research Laboratory). Para cada resultado de VDRL reagente sob qualquer titulação, buscavam-se, na sequência posterior de ordem de admissão, duas com resultados de VDRL não reagentes, durante os anos de 2013/2014. O primeiro artigo analisou os fatores de risco sociodemográficos, comportamentais e de assistência à saúde relacionados à ocorrência de sífilis em mulheres residentes e atendidas em maternidades públicas da cidade do Recife – PE. Utilizou-se um delineamento do tipo caso-controle que considerou o resultado da sorologia ELISA (Enzyme-Linked Immunosorbent Assay). A amostra foi constituída de 561 mulheres, das quais 239 eram reagentes (casos) e 322 eram não reagentes (controles) ao ELISA. Os resultados mostraram que os fatores de risco à sífilis gestacional estavam relacionados a menor escolaridade, ausência de acesso ao telefone, religião católica, ocorrência de quatro ou mais gestações, maior número de parceiros sexuais nos últimos doze meses, início do uso de drogas antes dos dezoito anos, assim como à utilização de drogas ilícitas pelo companheiro. Além destes, ao número insuficiente de consultas ao pré-natal e ao relato de história anterior de infecção sexualmente transmissível. O segundo artigo teve como objetivo caracterizar o perfil sociodemográfico, reprodutivo e assistencial segundo a situação do pré-natal, o registro do VDRL e o tratamento para sífilis em mulheres admitidas em maternidades públicas de uma capital do Nordeste do Brasil, entre 2013 e 2014. Trata-se de um estudo transversal, com uma amostra de 1.206 mulheres residentes em Pernambuco nos anos de 2013/2014. Os resultados evidenciaram entraves para o controle da transmissão vertical da sífilis. Do total, 91,3% das mulheres realizaram o pré-natal. O registro do VDRL no cartão de pré-natal estava ausente em 23,9% e destas, a maior parte iniciou o acompanhamento no último trimestre da gestação. O pré-natal não se mostrou efetivo na prevenção e rastreio da sífilis, uma vez que 34,1% apresentaram-se reagentes ao VDRL na admissão à maternidade. Entre as mulheres não tratadas para sífilis no pré-natal, apenas 57,7% e 46,2% cumpriram as recomendações de iniciar o acompanhamento no primeiro trimestre gestacional e realizar seis ou mais consultas, em contraste com as que receberam tratamento com valores de 70% para as duas situações, respectivamente. A ocorrência da sífilis na gestação está associada ao baixo nível de escolaridade, a piores condições socioeconômicas, a comportamentos de maior vulnerabilidade e acompanhamento pré-natal insatisfatório. Notou-se, também, obstáculos no diagnóstico e tratamento da sífilis durante o pré-natal, tornando ainda mais complexo o controle nessa população. / Gestational syphilis is an infectious disease transmitted vertically. It is associated with many negative outcomes during pregnancy, which can be avoided when the disease is detected and treated early. The current recommendations for controlling syphilis reinforce the need of prioritizing global preventive interventions, diagnosis, and timely treatment, paying special attention to more exposed groups. The objective of this thesis was to study the factors that influence the occurrence of syphilis and its treatment in women attending seven public maternity hospitals in Recife – PE. The document was structured into the following chapters: literature review, method, results presented in the form of two original articles, final considerations, and recommendations. The study was developed from a more comprehensive case-control study, which recruited 1,206 women during hospital admission according to their address and Venereal Disease Research Laboratory (VDRL) test. For every woman recruited with a positive VDRL test result regardless of titer, two consecutive women with negative VDRL test results were recruited by order of admission during 2013 and 2014. The first article analyzed the sociodemographic, behavioral, and health care risk factors related to the presence of syphilis in women from Recife/PE attending the city’s maternity hospitals. A case-control design took into account the result of the Enzyme-Linked Immunosorbent Assay test. The sample consisted of 561 women, of which 239 were ELISA positive (cases) and 322 were ELISA negative (controls). The results showed that the risk factors for gestational syphilis were related to lower education level, no access to a telephone, being Catholic, occurrence of four or more pregnancies, higher number of sexual partners in the last twelve months, illicit drug use before age 18 years, illicit drug use by partner, inadequate number of prenatal care visits, and a reported history of sexually transmitted diseases. The second article aimed to characterize the sociodemographic, reproductive, and health care profile according to prenatal care adequacy, VDRL records, and treatment for syphilis of women attending public maternity hospitals in a state capital in the Brazilian Northeast between 2013 and 2014. The cross-sectional study included 1,206 women from Pernambuco recruited between 2013 and 2014. The results evidenced obstacles for controlling vertical syphilis transmission. In total, 91.3% of the women received prenatal care. The VDRL test result was not recorded in 23.9% of the prenatal care cards and most of these women began prenatal care during the last trimester of pregnancy. Prenatal care did not effectively prevent and screen syphilis since 34.1% of the women had positive VDRL test result on hospital admission. Among women who did not receive treatment for syphilis during prenatal care, only 57.7% and 46.2% followed the recommendations to begin follow-up during the first trimester of pregnancy and to attend six or more visits. On the other hand, 70% of the women who received treatment began follow-up during the first trimester of pregnancy and attended six or more prenatal care visits. The occurrence of gestational syphilis is associated with low education level, low socioeconomic level, more vulnerable behaviors, and unsatisfactory prenatal care. Obstacles for controlling syphilis in this population were also present.

Introduction: the mother-to-child transmission is the main route of acquisition of HIV in children and the progressive increase of the epidemic in women of reproductive age significantly influences the epidemic in childhood. With the results of prophylaxis with antiretroviral, the possibility of transmission decreased considerably, but is still an important public health problem. Objective: to describe the time series of the clinical, epidemiological and laboratory of children born from mothers HIV positive or with AIDS in Sergipe and followed at referral center for STD / AIDS from January 1990 to December 2011. Methods: this is a retrospective cohort study. We recorded clinic and registry data from all HIV-infected pregnant women and exposed children from: notification system disorders (SINAN), file reference center for HIV / AIDS (CEMAR), referral maternity, system laboratory (SISCEL) and mortality system (SIM). The analyses were differentiated according to five specific objectives. At first, it was analyzed using the protocol AIDS clinical trial group (ACTG 076) in reference maternity HIV / AIDS for the period 1994-2010. We included HIV positive mothers from July 1994 to April 2010. In the second objective we did a prevalence survey to estimate the number of HIV positive pregnant using the capture-recapture method in the state of Sergipe in the period 1990-2011. The third was a retrospective cohort study to evaluate the risk factors associated with vertical transmission and the rate of mother to child transmission in Sergipe in the period 1990-2010. The fourth objective trends observed mortality in a cohort of children infected with HIV in the period 1993-2011. The fifth and last observed prevalence and risk factors for late diagnosis of HIV in infants exposed vertical transmission. Results: we identified 561 HIV-exposed children in the study period. Of these, 467 (83.24%) performed diagnostic test for HIV and 101 (18%) were infected by the virus. Of these, 467 (83.24) performed diagnostic test for HIV, 101 (18%) were infected, and 61 (10.8%) were still under investigation. In multivariate analysis of maternal factors for HIV infection in children, antiretroviral prophylaxis in children was a protective factor (aOR 0:07, 95% CI 0:01 to 0:41, p=0.003). Breastfeeding was marginally associated with increased chance of transmission (adjusted Odds Ratio [aOR] 4.52, CI 95% 0.78-0.17, p=0.092). The risk for breastfeeding over the study period was 91.0%, and transmission decreased from 91 per 100 live births before 1997 to 2 per 100 in 2011 following adoption of the prevention protocol. Of the 101 infected, twentyone children died with a median age at 4.3 years (IQR, 1.5-5.6 ears). In multivariable analysis, after adjusting for current treatment, the risk of death was 57% lower for children born after 2001 compared to those born before (adjusted relative risk [ARR] 0.43,IC95% 0.20-0.96, p <0.005). Lack of prenatal care (p=0.09) and breastfeeding (p=0.07) were marginally associated with late diagnosis. Was observed using the ACTG 076 was fully (during pregnancy, during delivery and after childbirth) utilized in only 31.8% of the participants. We estimate the population of HIV-seropositive pregnant women in the State of Sergipe between 2000 and 2010, using the capture-recapture method (CRC), that there were in total 1110 HIV seropositive pregnant women; therefore, 381 (34.3%) women were not captured by any of the three official systems registrations. Conclusion: the vertical transmission declined over the study period. Nevertheless, capitation of pregnant women and early initiations of preventive measures need to improve as soon as early HIV diagnosis in children for these populations to enjoy the benefit of the prophylactic and therapeutic/prophylactics measures including no infection, longer survival and better quality of life. / Introdução: a transmissão materno infantil, principal via de aquisição do vírus HIV em crianças e o aumento progressivo da epidemia nas mulheres em idade reprodutiva influenciam decisivamente a epidemia na infância. Com os resultados de profilaxia com antirretrovirais, a possibilidade de transmissão diminuiu consideravelmente, mas ainda constitui um problema relevante de saúde pública. Objetivo: descrever a série histórica da situação clínica, epidemiológica e laboratorial de crianças, filhas de mães soropositivas ao HIV ou com aids nascidas em Sergipe e acompanhadas no centro de referência em DST/Aids no período de janeiro de 1990 a dezembro de 2011. Métodos: Trata-se de uma coorte retrospectiva. Para compor o banco de dados, levantaram-se informações sobre nascimento e acompanhamento clínico no Sistema de Notificação de Agravos (SINAN), em arquivos do centro de referência em HIV/aids (CEMAR), em maternidade de referência, em sistema de exames laboratoriais (SISCEL) e em sistema de mortalidade (SIM). Os métodos para análise foram diferenciados de acordo com cinco objetivos específicos propostos. No primeiro, analisou-se uso do protocolo Aids Clinical Trial Group (ACTG 076) em maternidade de referência para HIV/aids no período de 1994 a 2010. No segundo realizou-se uma estimativa de gestantes HIV reagentes pelo método de captura e recaptura no estado de Sergipe no período de 1990-2011. O terceiro objetivo foi identificar fatores de riscos maternos para infecção pelo HIV em crianças expostas e a taxa de transmissão materno-infantil em Sergipe no período de 1990-2010. O quarto objetivo observou tendências de mortalidade em coorte de crianças infectadas pelo vírus HIV no período de 1993 a 2011. O quinto e último verificou prevalência e fatores de risco para diagnóstico tardio do HIV em crianças expostas por transmissão vertical. Resultados: foram identificadas 561 crianças expostas. Dessas, 467 (83,24) realizaram teste diagnóstico para HIV, constatando-se 101 (18%) infectadas e 61 (10,8%) ainda em investigação. Na análise multivariada sobre fatores maternos para infecção pelo HIV na criança, a profilaxia antirretroviral na criança foi um fator protetor (aOR 0.07, 95% CI 0.01-0.41, p=0,003). Amamentação foi marginalmente associada ao aumento da chance de transmissão vertical (aOR 4,52, Intervalo de Confiança [IC] 95% 0,78-26,17). A transmissão materno-infantil decresceu de 91% antes de 1997 para 2% em 2011, acompanhando o mesmo crescimento na adoção dos protocolos de prevenção. Das 101 infectadas, 21 morreram com a média de idade de 4,3 anos (IQR, 1,5-5,6 anos). O risco de morte foi 57% menor para crianças nascidas após 2001 quando comparadas com as nascidas antes (Risco relativo ajustado [aRR] 0,43; IC95% 0.20-0.96, p<0.05). Na análise sobre fatores de risco para diagnóstico tardio na coorte de 55 crianças infectadas no período de 2002 a 2011, 42(76,5%) foram diagnosticadas tardiamente, acima de 12 meses de idade. Foi observado o uso do protocolo ACTG 076 nas três fases (antirretroviral na gestação, durante e após o parto), sendo utilizado de forma completa somente em 31,8% dos participantes. Pelo método de captura e recaptura, estimou-se, para o período de 2000 a 2010, 1.110 gestantes, tendo sido observada subnotificação de 381 casos (34,3%) que não constavam nos sistemas oficiais de cadastramento dos pacientes. Conclusão: a transmissão vertical decresceu durante o período estudado, mas, apesar disso, captação de gestantes e iniciação precoce de profilaxia com antirretroviral necessitam ser melhoradas, assim como o diagnóstico precoce pelo HIV em crianças, para haver o benefício de medidas profiláticas e/ou terapêuticas e, consequentemente, sobrevida mais longa e melhor qualidade de vida.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2015-03-24T17:25:34Z No. of bitstreams: 2 Tese - Joseneide Teixeira Câmara - 2014.pdf: 2654661 bytes, checksum: 45d6b37146cb1b9be595aa54c97b9a6a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2015-03-24T17:27:34Z (GMT) No. of bitstreams: 2 Tese - Joseneide Teixeira Câmara - 2014.pdf: 2654661 bytes, checksum: 45d6b37146cb1b9be595aa54c97b9a6a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-03-24T17:27:34Z (GMT). No. of bitstreams: 2 Tese - Joseneide Teixeira Câmara - 2014.pdf: 2654661 bytes, checksum: 45d6b37146cb1b9be595aa54c97b9a6a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-05-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The vertical transmission of infection from mother to child, and may increase morbidity and mortality of both mother and child, when not diagnosed and by suitably dealest, causing a serious public health problem. This study aimed to estimate the prevalence of antibodies to toxoplasmosis, rubella, cytomegalovirus, hepatitis B, syphilis and HIV among pregnant women in Caxias, Maranhão, Brazil and identify the main factors associated with seropositivity for Toxoplasma gondii infection in pregnant women attending two referral centers Caxias, MA. Descriptive, observational, cross-sectional study of 561 pregnant women who received prenatal care at two clinics reference to prenatal high risk in the period July 2011 to December 2012, the outpatient clinics of Maternity Carmosina Coutinho (MCC) and the Specialized Center for Maternal and Child Care (CEAMI). Serological tests for toxoplasmosis, rubella, cytomegalovirus, hepatitis B were performed by a laboratory conveniado to the municipality by the same trained technician, and for syphilis and HIV were performed in the Counseling and Testing Center (ATC) in the city laboratory. And a small sample of whole blood from five pregnant IGM reagent for Toxoplasma gondii and their respective newborns was processed at the Institute of Tropical Pathology and Public Health in the Department of Parasitology UFG for performing Polymerase Chain Reaction (PCR). Statistical analysis was performed using SPSS version 20.0 Windows, using the chi-square tests of association and Odds Ratio (95%CI), considering a significance level of 5%. It was found to be positive for HIV was 0.4%, 2.0% syphilis, rubella and cytomegalovirus IgG reactivity were 93.6% and 87.8% respectively without reactive IgM, HBsAg was negative for all pregnant women in the sample tested. Regarding toxoplasmosis in 437 (77%), 124 susceptibility (22.1%) and 5 (0.9%) women with active infection. Found no significant association between toxoplasmosis susceptibility and age, location, income, education, sewerage, number of pregnancies and gestational age. Variables with significant association (p≤0.05) were seropositive pregnant women who are multiparous (p=0.036), living with dogs stuck at home (p=0.001), and consumption of raw kibbeh (p=0.036). The frequency of seropositivity of these infectious diseases of vertical transmission in pregnant women seen at antenatal care in the city of Caxias-MA is considered high, but are similar to those described in other regions of Brazil. Pregnant women who are multiparous who perform consumption of raw kibbeh and live with dogs that do not wobble on the street, had more chance of becoming infected with Toxoplasma gondii, thus guidance on primary prevention measures and quarterly serological monitoring should be strengthened these infections of pregnant women, since it is important to identify and/or prevent congenital infection measured. / A transmissão vertical das infecções da mãe para o filho e pode aumentar a morbimortalidade do binômio mãe-filho. Quando não diagnosticadas e tratadas adequamente, e ocasionam um sério problema de saúde pública. Este estudo objetivou estimar a soroprevalência de anticorpos para toxoplasmose, rubéola, citomegalovírus, hepatite B, sífilis e HIV entre gestantes em Caxias, Maranhão, Brasil e identificar os principais fatores associados à soropositividade para o Toxoplasma gondii (T. gondii) em gestantes atendidas em dois centros de referência em Caxias–MA. Estudo descritivo, observacional, transversal, com 561 gestantes que realizaram a assistência pré-natal em dois ambulatórios de referência para pré-natal de alto risco, no período de julho de 2011 a dezembro de 2012, nos ambulatórios da Maternidade Carmosina Coutinho (MCC) e no Centro Especializado de Assistência Materno-Infantil (CEAMI). Os testes sorológicos de toxoplasmose, rubéola, citomegalovírus, hepatite B foram realizados por um laboratório conveniado ao município, e para sífilis e HIV foram realizadas no laboratório do Centro de Testagem e Aconselhamento (CTA) do município. Uma amostra de sangue total das cinco gestantes IGM reagente para o T. gondii e de seus respectivos recém-nascidos foi processada no Instituto de Patologia Tropical e Saúde Publica da UFG no Setor de Parasitologia para a realização de Reação em Cadeia da Polimerase (PCR). A análise estatística foi realizada com o programa SPSS versão 20.0 Windows, usando os testes de associação qui-quadrado e Odds Ratio (IC95%), considerando-se o nível de significância de 5%. Constatou-se que a soropositividade para HIV foi de 0,4%, sífilis 2,0%, rubéola e citomegalovírus a reatividade de IgG foram de 93,6% e 87,8% respectivamente sem IgM reativa, HBsAg foi não reagente para todas as gestantes da amostra. Em relação ao T. gondii 437 (77,9%) foram soropositivas, a susceptibilidade em 124 (22,1%) e 5 (0,9%) gestantes com infecção ativa. Não foi observada associação significativa entre soropositividade para toxoplasmose e idade, procedência, renda, escolaridade, rede de esgotos, número de gestações e idade gestacional. As variáveis com associação significativa (p≤0,05) para soropositividade foram gestantes que são multigestas (p=0,036), convívio com cães presos em casa (p=0,001), e consumo de quibe cru (p=0,036). A frequência de soropositividade dessas doenças infecciosas de transmissão vertical em gestantes atendidas no pré-natal, no município de Caxias-MA é considerada alta, mas encontram-se semelhantes aos descritos em outras regiões do Brasil. As gestantes que são multigestas que realizam consumo de quibe cru e convivem com cães presos em casa, apresentaram mais chance de se infectar com o Toxoplasma gondii, assim, deve ser reforçada orientações sobre medidas de prevenção primária e o monitoramento sorológico trimestral dessas infecções às gestantes, uma vez que são medidas importantes para identificar e/ou prevenir as infecções congênitas.

Made available in DSpace on 2014-08-20T14:37:53Z (GMT). No. of bitstreams: 1 dissertacao_debora_scopel.pdf: 765310 bytes, checksum: dc0bea20bd4a62c37e4145ef858b7894 (MD5) Previous issue date: 2013-02-27 / The development and use of drugs with the ability to prevent or strike an infection are indispensable for human and animal health. However, the antiviral drug arsenal is still small and has serious use restrictions, like small activity range, limited therapeutic usage and several degrees of cytotoxicity. The objective of this work was to evaluate the antiviral activity of an antibacterial peptide isolated from the intestinal contents of the fish Piau-com-pinta (Leporinus sp.), named P34. Its cytotoxicity was analyzed in different cell lineages, in order to evaluate its antiviral activity. This study was performed against viruses with different phenotypical and genotypical features like: canine adenovirus type 2 (CAV-2), canine coronavirus (CCoV), canine distemper virus (CDV), canine parvovirus type 2 (CPV-2), equine arteritis virus (EAV), equine influenza virus (EIV), feline calicivirus (FCV) and feline herpesvirus type 1 (FHV-1). It was observed antiviral activity, in vitro, against EAV and FHV-1, both enveloped viruses, with RNA e DNA genomes, respectively. A virucidal effect was observed when P34 was incubated for different periods of time with EAV at 37 °C. Transmission electronic microscopy analysis suggests that the peptide P34 binds and promotes lesions to the viral envelope. The peptide P34 does not have virucidal activity against FHV-1 and although its mechanism of action is not completely elucidated, it is possible to suppose that P34 interferes in the adsorption process of FHV-1. Thus, the peptide P34 may represent an antimicrobial substance with potential application in the prevention and treatment of viral infections caused by FHV-1 and EAV. / O desenvolvimento e o uso de fármacos antivirais capazes de prevenir ou combater uma infecção são imprescindíveis para a saúde do homem e dos animais. Entretanto, o arsenal de fármacos antivirais permanece pequeno e apresenta graves restrições de uso, tais como reduzido espectro de atividade, utilidade terapêutica limitada e vários graus de toxicidade. O objetivo desse trabalho foi avaliar atividade antiviral de um peptídeo antibacteriano isolado do conteúdo intestinal do peixe Piau-com-pinta (Leporinus sp.), denominado P34. Sua citotoxicidade foi determinada em diferentes linhagens celulares, visando posterior avaliação da atividade antiviral. Foram realizados ensaios antivirais frente a vírus com diferentes características genotípicas e fenotípicas: adenovírus canino tipo 2 (CAV-2), coronavírus canino (CCoV), vírus da cinomose canina (CDV), parvovírus canino tipo 2 (CPV-2), vírus da arterite equina (EAV), vírus da influenza equina (EIV), calicivírus felino (FCV) e herpesvírus felino tipo 1 (FHV-1). Foi observada ação antiviral, in vitro, contra EAV e FHV-1, ambos vírus envelopados, com genomas RNA e DNA, respectivamente. Foi observado efeito virucida, contra o EAV, quando o P34 foi incubado por diferentes períodos a 37 °C. A análise por microscopia eletrônica de transmissão sugere que o peptídeo P34 faz ligação e promove lesão do envelope viral. O P34 não possui atividade virucida contra o FHV-1 e embora o mecanismo de ação não tenha sido completamente elucidado, é possível supor que o P34 interfira no processo de adsorção do FHV-1. Dessa maneira, o peptídeo P34 pode representar uma substância com potencial aplicação na prevenção e tratamento das infecções pelo FHV-1 e pelo EAV.

L'évaluation médico-économique (EME) joue un rôle de plus en plus important dans le développement des recommandations cliniques et les décisions de prix et remboursement des produits de santé, notamment des vaccins. L'EME des vaccins fait l'objet de procédures et de recommandations méthodologiques spécifiques, distinctes des médicaments, dans de nombreux pays. Cette thèse illustre et répertorie les différentes questions méthodologiques concernant l'EME des programmes de vaccination sur la base de six études : estimation de la morbidité, mortalité et coûts liés aux infections à cytomégalovirus chez les receveurs de greffe d'organe solide ; description de l'état de santé subjectif et qualité de vie liée à la santé chez les femmes atteintes de candidose vulvovaginale récurrente (CVVR) ; revue critique des EME de la vaccination de rappel contre la coqueluche ; revue critique des EME de la vaccination contre le rotavirus ; analyse coût-efficacité de la vaccination antigrippale chez les personnes de 50 à 64 ans ; analyse coût-efficacité d'un vaccin antigrippal quadrivalent en Ontario. L'EME des programmes de vaccination nécessite de prédire l'effet d'un vaccin dans la vie réelle à partir d'essais cliniques, ce qui est particulièrement difficile pour plusieurs raisons : l'épidémiologie d'une infection peut varier dans le temps et l'espace, la réduction du risque d'infection après vaccination est différente de celle du risque de maladie, et la vaccination peut conduire à une augmentation ou diminution du risque chez les personnes non-vaccinées. De plus, la mesure et la valorisation des effets sur la qualité de vie soulèvent des questions méthodologiques et requièrent des choix normatifs liés aux faits que de nombreux vaccins ciblent les enfants, et que la réduction du risque peut améliorer la qualité de vie en dehors des périodes de maladie. Nous établissons finalement des recommandations pour les futures EME de programmes de vaccination, concernant la définition des stratégies à comparer, le choix de structure de modèle, l'estimation des paramètres cliniques et épidémiologiques, et la mesure et la valorisation de la qualité de vie et des coûts / Economic evaluation plays an increasingly important role in the development of clinical recommendations and pricing and reimbursement decisions for healthcare interventions, and particularly for vaccination. Specific processes and methodological recommendations have been developed for the economic evaluation of vaccines in many countries. This thesis identifies and illustrates different methodological questions about the economic evaluation of vaccination programs based on six studies: estimation of morbidity, mortality and costs associated with cytomegalovirus infections among receivers of solid organ transplant; description of subjective health state and quality of life among women with recurrent vulvovaginal candidosis; critical review of economic evaluations of pertussis booster vaccination; critical review of economic evaluations of rotavirus vaccination; cost-effectiveness analysis of influenza vaccination for people aged 50 to 64 years; cost-effectiveness analysis of a quadrivalent influenza vaccine in Ontario. The economic evaluation of vaccines requires predicting the effectiveness of vaccination based on clinical trial data, which is particularly difficult for several reasons: the epidemiology of an infection may vary over time and space, the effectiveness against infection may differ from effectiveness against disease, and vaccination may lead to an increase or decrease in the burden of disease among non-vaccinated persons. In addition, the measurement and valuation of effects of vaccination on quality of life raises methodological questions and requires normative choices related to the facts that many vaccines target children and that the reduction in risk may improve quality of life outside illness periods. We finally establish recommendations for future economic evaluations of vaccination programs, related to the definition of vaccination strategies to compare, the choice of model structure, the estimation of clinical and epidemiological parameters, and the measure and valuation of quality of life and costs

Assessing the genetics of wild animal populations aims to understand selective pressures, and factors whether it be inbreeding or adaptation, that affect the genome. Although numerous techniques are available for assessing population structure, a major obstacle in studying wild populations is obtaining samples from the animals without having to capture them, which can lead to undue distress and injury. Therefore, biologists often use non-invasive sampling methods (i.e., collection of feces, hair) to extract host DNA. In this study, new DNA extraction protocols were developed that improved the quality and quantity of DNA obtained from fecal matter. Fecal samples aged up to Day 6 as well as field samples with unknown days since defecation were successful in individualization of the contributors using microsatellites and were further used to demonstrate kinship. Neutral markers such as short tandem repeat, and mitochondrial D-loop sequences are used for assessing relatedness and evolutionary relationships and can mutate without detrimental effects on the organism. Loci, such as the major histocompatibility complex (MHC), adapt more rapidly under selective pressure such as parasite load, or resistance to diseases and support natural selection processes. Analysis of the neutral microsatellites in Big Summit feral horse population demonstrated a population lacking diversity and trending towards being an inbred population. However, examination of the MHC genes showed maintenance of greater variation that may be the result of selection pressures. The MHC similarity and lower genetic demarcation between geographically separated horse populations further indicated effect of selection pressures in preserving diversity at the MHC genes. Although such molecular markers are used in profiling populations, the current study was also successful in demonstrating the use of individual odor profiles as an additional profiling tool. Volatile organic compounds (VOC) obtained from hair of domestic horses were able to individualize horses as well as differentiate between horse breeds and display kinship. The relation of genetics to odor phenotype is of interest as the inherent polymorphic nature of MHC genes has the potential to generate unique combinations of genotypes that presumably produce distinct odor phenotypes. Subsequently, this study was able to show a significant correlation between MHC genotypes and VOC odor profiles in horses. Understanding the relationship between MHC and odor using domestic horses with known relatedness provides evidence that these same correlations may be applicable to wild equids and dictates their harem hierarchal social structure.

The purpose of this study was to determine the prevalence of Lyme Disease (LD) bacteria in adult Ixodes pacificus ticks collected from the mountains of San Bernardino County in Southern California. Seven hundred fifty four I. pacificus adults were collected from the Pacific Crest Trail and adjacent areas. The Polymerase Chain Reaction (PCR) was used to screen ticks for Borrelia burgdorferi infection by targeting two different DNA loci. Oligonucleotide primers targeting both the ospA and fla genes were used in the assay. Ticks were processed in pools of three, and genomic DNA from the ticks was extracted with a commercial mini-kit utilizing silica matrix spin-columns. All ticks tested negative for B. burgdorferi infection regardless of primer pair used. In addition, ticks were negative following examination by dark-field microscopy. This study confirms previous reports that the prevalence of LD in Southern California is quite low.

La modélisation des maladies infectieuses représente un outil important pour évaluer la vulnérabilité d'une population à l'introduction d'un nouveau agent pathogène. La possibilité d’enregistrer les contacts responsables de la propagation des maladies représente à la fois une ressource et un défi pour les modèles épidémiques. En particulier, l'interaction entre la dynamique des maladies et l'évolution dans le temps des structures de contact influence la façon dont les agents pathogènes se propagent, en changeant les conditions qui mènent à une flambée épidémique (seuil épidémique). Jusqu'à maintenant, les chercheurs n'ont caractérisé le seuil épidémique sur des structures de contact qui évoluent dans le temps que dans des contextes spécifiques. En utilisant un formalisme multi-couches, nous calculons analytiquement le seuil épidémique sur un réseau temporel générique. Nous utilisons cette méthode pour évaluer l'impact de la résolution temporelle et la durée du réseau sur l'estimation du seuil. De plus, grâce à cette méthode, nous évaluons la vulnérabilité globale de différents systèmes à l'introduction d'agents pathogènes, et en particulier nous analysons les réseaux de mouvements des bovins. Les données de contact souvent ne sont pas disponible en temps réel, et cela limite notre capacité de prévision. Pour répondre à ça, nous développons une méthodologie numérique pour prédire le risque épidémique ciblé, qui repose uniquement sur les données de contact passées. Notre travail fournit de nouvelles méthodologies pour évaluer et prédire le risque associé à un agent pathogène émergent, à la fois à l'échelle de la population et en ciblant des hôtes spécifiques. / Infectious disease modeling represents a powerful tool for assessing the vulnerability of a population to the introduction of a new infectious pathogen. The increased availability of highly resolved data tracking host interactions is making epidemic models potentially increasingly accurate. Integrating into them all the features emerging from these data, however, still represents a challenge. In particular, the interaction between disease dynamics and the time evolution of contact structures has been shown to impact the way pathogens spread, changing the conditions that lead to the wide-spreading regime, as encoded in epidemic threshold. Up to now researchers have characterized the epidemic threshold on time evolving contact structures only in specific settings. Using a multilayer formalism, we analytically compute the epidemic threshold on a generic temporal network, accounting for several different disease features. We use this methodology to assess the impact of time resolution and network duration on the estimation of the threshold. Then, thanks to it, we assess the global vulnerability of different systems to pathogen introduction, and in particular we analyze the networks of cattle trade movements Data collection strategies often inform us only about past network configurations, and that limits our prediction capabilities. We face this by developing a data-driven methodology for predicting targeted epidemic that relies only past contact data. Our work provides new methodologies for assessing and predicting the risk associated to an emerging pathogen, both at the population scale and targeting specific hosts.

Previously, our lab demonstrated that heterologous immunity could result in either gain or loss of protective immunity and alteration in immune pathology following infection by a second un-related pathogen. One of the prototypical models to study T cell-mediated heterologous immunity involves two distantly related arenaviruses, namely lymphocytic choriomeningitis virus (LCMV) and Pichinde virus (PV). Each virus encodes a cross-reactive CD8 epitope that has six out of eight in amino acid (aa) similarity with respect to its counterpart at the position 205-212 of the nucleoprotein (NP205). Heterologous challenge between LCMV and PV results in 1) expansion of the cross-reactive NP205-specific CD8 T cell responses and alteration of the immunodominance hierarchy and 2) partial protective immunity (heterologous immunity). Our lab showed that cross-reactive NP205-specific CD8 T cell receptor (TCR) repertoires become extremely narrowed following a heterologous challenge between LCMV and PV. Therefore, I questioned if LCMV NP205 epitope escape variants could be isolated during a dominant but narrowed crossVI reactive NP205-specific CTL response. In the first part of my thesis, I describe the isolation of a LCMV NP-V207A CTL escape variant in vivo using PV-immune animals challenged with LCMV clone 13. The LCMV NP-V207A variant contains a point mutation, which results in the switching of valine to alanine at the third non-anchoring residue of the LCMV NP205 CD8 epitope. Immunization of mice with the LCMV NP-V207A variant results in a significantly diminished cross-reactive NP205-specific CD8 T cell response. This suggests that the point mutation is responsible for the loss in the immunogenicity of the LCMV NP205 CD8 epitope. In addition, an in vitrorescued(r) recombinant LCMV variant (r/V207A) that encodes the original mutation also induces a highly diminished cross-reactive NP205-specific CD8 T cell response in mice. In agreement with the result obtained from the intracellular cytokine assays (ICS), MHC-Ig dimers loaded with the LCMV NP205 (V-A) peptide could only detect a minute population of cross-reactive NP205-specific CD8 T cells in mice infected with r/V207A variant virus. All the data indicate that the point mutation results in a significant loss in immunogenicity of the LCMV NP205 CD8 epitope. So far, no direct link between the cross-reactive NP205-specific CD8 T cells and heterologous immunity had been established in this system. Therefore, we immunized mice with either LCMV WT or the LCMV NP-V207A variant virus and showed that a significant loss of heterologous immunity is associated with the group immunized with LCMV NP-V207A variant virus. Again, r/V207Aimmune animals also displayed a significant loss in heterologous immunity following PV challenge. This suggests that the cross-reactive NP205-specific CD8 T cells mediate the majority of heterologous immunity between LCMV and PV in vivo. In comparison to the PV-immune control group, PV clearance kinetics mediated by the cross-reactive NP205-specific CD8 T cells were significantly delayed. Finally, these data also suggest that bystander activation plays very little role in heterologous immunity between LCMV and PV. Many studies in murine systems and humans suggest that cross-reactive T cells are often associated with immune pathology. We showed that in mice that were sequentially immunized with PV and LCMV (PV+LCMV WT double immune mice), there was a development of a high incidence and high level of immune pathology known as acute fatty necrosis (AFN) following a final PV challenge. The data suggest that these cross-reactive NP205-specific CD8 T cells might play an important role in immune pathogenesis. Therefore, we asked if the cross-reactive NP205-specific CD8 T cells play a role in immune pathogenesis by comparing the incidence of AFN between the (PV+LCMV WT) and the (PV+LCMV NP-V207A) double immune mice following a final PV challenge. In agreement with our hypothesis, the result showed the (PV+LCMV NP-V207A) double immune mice developed a significantly lower incidence of AFN compared to the (PV+LCMV WT) double immune mice. However, linear correlation studies comparing the frequency of different antigen-specific CD8 T cell populations within the (PV+LCMV WT) double immune mice before challenge and the severity of AFN following the PV challenge suggest that two opposing antigen-specific CD8 T cell populations are involved in determining the final outcome of the immune pathology. The PV NP38-45-specific CD8 T cell response (PV NP38) appears to be more protective than the cross-reactive NP205-specific CD8 T cell response. In addition, a positive linear correlation between the ratio of cross-reactive NP205 to PV NP38 and the severity of AFN seem to suggest that these cross-reactive populations are important contributors to immune pathogenesis. Peptide titration studies examining the functional avidities to different antigenic specificities suggest that both populations consist of high avidity TCR and peptide MHC (TCR:pMHC) interactions. However, skewing within the cross-reactive NP205 specific CD8 T cell response towards the LCMV NP205 epitope response in one of the (PV+LCMV WT) double immune mice suggests that cross-reactive NP205 specific CD8 T cells could constitute a sub-optimal response to a PV challenge. In summary, I questioned what might be some of the immunological consequences of heterologous immunity in this model. First of all, we have established a direct link between the cross-reactive NP205-specific CD8 T cell response and heterologous immunity in LCMV and PV. Second of all, I demonstrated that a LCMV NP205 epitope escape variant could be selected in vivo under the conditions of heterologous immunity. In addition, I showed that PV clearance kinetic was significantly delayed in cross-reactive NP205-mediated heterologous immunity as compared to homologous challenge. Finally, we demonstrated that cross-reactive NP205-specific CD8 T cells could play an important role in immune pathogenesis in this model. However, correlation data indicate that two opposing antigen-specific CD8 T cell populations could ultimately decide the outcome and magnitude of immune pathology in each individual mouse. All the data presented above strongly suggest that the cross-reactive NP205 CD8 T cells play a crucial role in immune pathology in this model system by 1) interfering with the regular establishment of immunodominance hierarchy orders, or 2) exhibiting a sub-optimal protective immunity due to the nature of the cross-reactive epitope.