Técnicas de genotipificação do Mycobacterium bovis baseadas na amplificação do DNA via PCR como MIRU-VNTR constituem importantes ferramentas na investigação epidemiológica da tuberculose bovina (TB) em áreas de baixa prevalência, como no Estado de Mato Grosso. Isto posto e diante de limitadas informações a respeito dos genótipos grassantes no Estado, foi realizado monitoramento nas linhas de inspeção sanitária pós-abate em 35 matadouros-frigoríficos sob inspeção oficial para detectar lesões granulomatosas sugestivas de TB e proceder a coleta e análise de amostras. Foram processadas e analisadas 167 amostras mediante isolamento bacteriano e técnicas moleculares. Através do método de genotipagem MIRU-VNTR, 49 isolados de M. bovis foram analisados aplicando-se 24 pares de primers diferentes. Desses, 20 marcadores de VNTR mostraram polimorfismo genético. O locus QUB26 apresentou alto poder discriminatório (h=0,66) enquanto ETRC (0,54), Mtub21 (0,5), QUB11b (0,33) e Mtub34 (0,31) mostraram moderada diversidade alélica. Os outros 15 loci (Mtub 04, 29 e 39; MIRU 04, 16, 23, 24, 26, 27, 31, 39 e 40; ETR A; ETR B; QUB 4156) revelaram baixo poder discriminatório (h=0,02 - 0,27). Quatro loci (MIRU 2, 10 e 20; Mtub30) não apresentaram diversidade alélica. Foram observados 28 perfis genéticos (V1-V28) nos isolados de M. bovis obtidos em 35 propriedades rurais. Dentre essas, 30 (85,71%) apresentaram somente 1 tipo de perfil genético. Apenas 19 amostras (38,77%) apresentaram perfil MIRU-VNTR único revelando a existência de isolados com o mesmo perfil MIRU-VNTR entre diferentes regiões geográficas no Estado. O isolamento, seguido da identificação molecular e discriminação genotípica por MIRU-VNTR em isolados de M. bovis constituíram fontes de relevantes informações auxiliares no desenvolvimento de estratégias de erradicação da TB na região de estudo. / Mycobacterium bovis genotyping techniques based on PCR amplification as MIRU-VNTR are important tools in the epidemiological investigation of bovine tuberculosis in areas of low prevalence, such as in the state of Mato Grosso. Based on limited information about the genotypes in state, post-slaughter sanitary inspection lines were monitored in 35 slaughterhouses under official inspection to detect granulomatous lesions suggestive of TB and to collect and analyze samples. 167 Samples were processed and analyzed by bacterial isolation and molecular techniques. Through the MIRU-VNTR genotyping method, 49 M. bovis isolates were analyzed by applying 24 different primer pairs. Of these, 20 VNTR markers showed genetic polymorphism. The QUB26 locus presented high discriminatory power (h = 0.66) while ETRC (0.54), Mtub21 (0.5), QUB11b (0.33) and Mtub34 (0.31) showed moderate allelic diversity. The other 15 loci (Mtub 04, 29 e 39; MIRU 04, 16, 23, 24, 26, 27, 31, 39 e 40; ETR A; ETR B; QUB 4156) showed low discriminatory power (h = 0.02 - 0.27). Four loci (MIRU2, MIRU10, MIRU20 and Mtub30) did not present allelic diversity. Twenty-eight genotypes (V1-V28) were observed in the M. bovis isolates obtained from 35 rural properties. Among these, 30 (85.71%) presented only 1 genotype type. Only 19 samples (38.77%) presented a single MIRU-VNTR profile revealing the existence of isolates with the same MIRU-VNTR profile among different geographic regions in the State. Isolation, followed by molecular identification and genotypic discrimination by MIRU-VNTR in M. bovis isolates were sources of relevant auxiliary information in the development of strategies to eradicate TB in the study region.

Background & Objectives: This dissertation is comprised of two independent projects that seek to answer the research questions outlined in Aims 1 and 2. The first project is focused on measuring exposure to polybrominated diphenyl ethers (PBDE) throughout the early lifecourse, as well as investigating how exposure at different developmental periods relates to neuroendocrine endpoints. PBDEs are flame retardant chemicals that were used extensively in furniture and furnishings sold throughout the United States until their phase-out in 2004. Human exposure occurs primarily through incidental ingestion of PBDE-contaminated dust present in the indoor environment. The second project aimed to characterize telomere dynamics in maternal-child pairs and to evaluate associations between telomere dynamics and indicators of stress and stressful conditions. Telomeres are non-coding nucleotide repeats located at chromosome ends; they serve several functions, such as buffering against loss of important protein coding DNA regions during cell division. Both projects are focused on exposure-response relationships during early life and a central theme throughout this dissertation relates to the intersection of date, time and age in longitudinal cohort studies. Finally, the third aim seeks to integrate findings from Projects I and II and is focused on investigating whether telomere dynamics can be used as a biological indictor of stress in epidemiological research examining associations between low-level environmental chemical exposures and neurodevelopmental endpoints. Methods: Both projects were conducted using data and samples collected as part of the Columbia Center for Children’s Environmental Health (CCCEH) Mothers and Newborns study. In Project I, PBDEs were measured by the Centers for Disease Control and Prevention (CDC) using gas chromatography-mass spectrometry (GC-MS) in plasma samples collected repeatedly between birth and age 9 years. We examined determinants of 1) prenatal exposure to PBDEs (Chapter 2), and 2) trajectories of PBDE exposure over childhood, which we estimated using latent class growth analysis (LCGA) (Chapter 3). We also examined PBDE trajectories in relation to performance on tests of visual, verbal and working memory among early adolescents (Chapter 4) and investigated associations between prenatal exposure to PBDEs and thyroid hormone parameters, which were measured by radioimmunoassay in plasma samples collected at multiple ages (Chapter 5). In Project II, we used monochrome multiplex quantitative polymerase chain reaction (MMqPCR) to measure relative leukocyte telomere length (rLTL) in samples collected from mothers and newborns (umbilical cord blood) at the child’s delivery and from children at ages 2, 3, 5, 7 and 9-years (Chapter 6). We aimed to characterize rLTL dynamics over early life, examine the correlation between paired maternal-newborn rLTL, and examine associations between rLTL with measures of financial strain, perceived stress and maternal distress. Results: In Project I, we detected PBDEs in over 80% of cord blood samples and in multivariable models, sociodemographic and lifestyle factors explained 12% of cord blood PBDE variability. The largest determinant of exposure was ethnicity, with Dominican newborns having lower exposure compared to African American newborns, likely due to the reduced amount of time Dominican mothers had spent in the United States when they gave birth to the study child. Across postnatal life (2000 to 2013), PBDE concentrations in child blood decreased by approximately 12% per year, suggesting that exposure has continually declined since the PBDE phase-out in 2004. Trajectory analyses revealed several unique patterns of PBDE exposure over the early lifecourse, with the majority of children characterized by exposure that was persistently low or that peaked during toddler years. Smaller groups of children were characterized by exposure that was highest during the prenatal period and decreased after birth or by a pattern of high exposure during toddler years that remained elevated into middle childhood. We identified several important predictors of childhood PBDE exposure patterns, including modifiable factors, such as cleaning behaviors. In relation to neurodevelopmental outcomes, we found that children with sustained high exposure to PBDEs scored approximately 5-8 points lower on tests of visual memory. Associations between prenatal exposure and working memory significantly varied by sex, with inverse associations (approximately 8 points lower) observed only among girls. Children with PBDE plasma concentrations that peaked during toddler years performed better on verbal domains, however, these associations were significant only among children breastfed for more than 12 weeks. Finally, in relation to thyroid hormone levels, children with BDE-47 concentrations in the third and fourth quartiles of the exposure distribution (versus first quartile) had significantly lower TSH and free T4 levels, respectively. We did not detect associations between BDE-47 and total T4 levels; likewise, we did not detect associations between other pentaBDE congeners and any thyroid parameter. In Project II, we found that maternal-newborn rLTL in paired samples was moderately correlated and that maternal rLTL at delivery explained 8% of the variability (R2) in newborn rLTL. In relation to measures of hardship, perceived stress and demoralization, we found an inverse, albeit not statistically significant, association between maternal perceived stress and newborn rLTL. We did not detect an association with maternal rLTL, nor did we detect associations between material hardship or demoralization and maternal or newborn rLTL. When examining rLTL in child blood samples collected between birth and age 9 years, we observed a U-shaped pattern characterized by rapid shortening of rLTL between birth and 2 years, followed by gradual lengthening between ages 3 and 9 years. It remains unresolved whether this pattern reflects a true biological phenomenon or if it is an artifact of measurement error introduced by analytic or pre-analytic conditions. Conclusions: Despite the phase-out of PBDEs in 2004, exposure among children residing in New York City remained nearly ubiquitous through 2013, however, concentrations did decline over time. Our finding of several PBDE trajectories suggests that, despite the relatively long half-lives of PBDEs, a single measure may not accurately reflect exposure throughout childhood. Our findings of reduced scores on tests of working and visual memory during the prenatal and postnatal periods, respectively, support a growing body of literature linking early life PBDE exposure to disrupted neurodevelopment. The results of our analysis examining thyroid hormone disruption during childhood revealed a pattern consistent with hypothalamic or pituitary-level disruption during prenatal programming of the thyroid regulatory system. This is the first study to examine prenatal PBDE exposure in relation to childhood thyroid hormone levels, therefore, it is important that this finding is replicated by future research. Our finding of an inverse association between newborn rLTL and maternal perceived stress is consistent with results from previous research and suggests that the developing fetus may be sensitive to maternal stress perception during pregnancy, however, additional research is needed to more fully understand the mechanisms through which this transmission occurs. Our finding of increasing telomere length between toddler years and middle childhood is unexpected and raises questions about the suitability of the qPCR assay for analyzing telomere length in archived samples. Additional analyses are needed to determine whether the observed patterns reflect true biological changes or relate to measurement error introduced during sample processing, storage or analysis. Given these outstanding issues, we were ultimately unable to draw conclusions about the usefulness of telomere dynamics as a stress-sensitive biomarker.

A raiva é uma antropozoonose com alta letalidade, acomete todos os animais de sangue quente, essa doença causa enormes prejuízos econômicos ao rebanho pecuário nacional, é impossível estimar os custos reais com controle dessa doença, em decorrência do grande número de subnotificações. O uso de ferramentas moleculares permite identificar as linhagens virais circulantes, facilitando desse modo à compreensão da epidemiologia da raiva. A técnica de RT-PCR para amplificação parcial dos genes N e G, foi aplicada em 60 amostras positivas para o vírus da raiva pelas provas de imunofluorescência direta e prova biológica, procedentes dos Estados do Pará, Tocantins, Rondônia e Acre das espécies bovina, equídea, bubalina e suína. As sequências nucleotídicas obtidas para os genes N (41 amostras) e G (17 amostras) foram analisadas pelo algoritmo Neighbor-Joining e modelo evolutivo Kimura 2-parâmetros. Essa análise permitiu identificar distintas linhagens circulantes nas regiões estudadas, foi evidenciado ainda, um padrão de distribuição geográfico dessas linhagens. Além disso, este estudo possibilitou identificar marcadores moleculares para diferentes regiões geográficas, promovendo um melhor entendimento da epidemiologia molecular da raiva das linhagens circulantes da região em estudo. / Rabies is an anthropozoonosis with high mortality, affects all warm-blooded animals, this disease causes major economic losses to livestock. It is difficult to estimate the actual costs of disease control, due to sub notification of cases. Molecular techniques allow identification of genetic viral strains circulating, improving rabies epidemiology comprehension. Sixty rabies virus isolates from bovines, equines, swine and buffaloes coming from the states of Pará, Tocantins, Rondônia and Acre were analyzed in the present study. All samples were previously submitted to direct immunofluorescence test and inoculation in mice, afterwards were submitted to RT-PCR for amplification of partial Nucleoprotein and Glycoprotein genes. Nucleotide sequences from nucleoprotein (41 samples) and glycoprotein G (17 samples) genes were analyzed by Neighbor-joining algorithm and Kimura two-parameter model. This analysis allowed to identify different genetic strains circulating and its geographic distribution patterns. Moreover this study revealed molecular markers for different geographic regions, promoting a better understanding of rabies molecular epidemiology of circulating strains of study area.

Gastroenterites são uma das causas mais comuns e importantes de morbidade e mortalidade entre animais neonatos e juvenis, em muitos casos, ocasionadas por uma infecção intestinal múltipla, sendo os principais agentes virais entéricos em bovinos o rotavírus e o coronavírus bovino (BCoV). O BCoV tem distribuição mundial e causa gastroenterites em bezerros, disenteria de inverno em bovinos adultos e processos patológicos respiratórios, enquanto que nos equinos os coronavírus causam enterocolite neonatal em potros. Considerando-se que o coronavírus bovino é mais estudado do que os coronavírus equinos, havendo possibilidade de transmissão interespécies, o presente trabalho teve por objetivo a comparação multigênica do coronavírus em bovinos adultos com disenteria de inverno e bezerros com diarréia neonatal e em equinos do Brasil, com base em sequências parciais dos genes codificadores das proteínas hemagluninina-esterase (HE), espícula (S) e nucleoproteína (N). Foram utilizadas amostras fecais de 11 vacas leiteiras de um surto de disenteria de inverno e de 27 equinos testadas quanto a presença de Betacoronavirus com uma RT-PCR dirigida ao gene RdRp; em seguida, as amostras positivas foram submetidas as reações parciais de PCR para os genes N, HE e S, e posterior sequenciamento e análise genealógica. Além destas amostras, foram utilizadas 15 amostras fecais de bezerros, já estudadas parcialmente quanto ao gene S, submetidas as reações de RT-PCR para N e HE, e posterior sequenciamento e análise genealógica. Sequências representativas da população em estudo foram obtidas para todos os genes. Pode-se concluir que a genealogia de amostras entéricas de BCoV detectadas em bovinos jovens e adultos é diretamente associada a padrões geográficos quando se consideram os genes S e HE, sendo a genealogia de menor resolução para os genes HE e nucleoproteína N, para a qual há uma tendência a segregação por faixa etária do hospedeiro e que equinos podem apresentar Betacoronavirus indistinguíveis daqueles encontrados em bovinos. / Gastroenteritis is one of the leading causes of morbidity and mortality amongst young and newborn animals, often caused by multiple intestinal infections, being rotavirus and Bovine coronavirus (BCoV) the main viral causes in cattle. BCoV has a worldwide distribution and caused diarrhea in calves, winter dysentery in adult cattle and respiratory disease, while in horses coronaviruses lead to neonatal enterocolitis in foals. Taking into account that BCoV is more largely studied than equine coronaviruses and the possibility of interspecies transmission of these viruses, this research aimed to assess a multigenic comparison of coronaviruses from adult cattle with winter dysentery and calves with neonatal diarrhea as well as from equines, all from Brazil, based on partial sequences of the hemagglutinin-esterase (HE), spike (S) and nucleoprotein (N) genes. To this end, 11 samples from dairy cows with winter dysentery and 27 from horses were tested for Betacoronavirus using an RT-PCR targeted to the RdRp gene and the positive samples were next submitted to RT-PCRs to the partial amplification and sequencing of N, HE and S genes for genealogic analysis. Besides, 15 calves samples previously studied for the same S gene region were also submitted to the N and HE genes RT-PCRs and sequencing for genealogic analysis. Sequences representative of the population under study were obtained for all genes. It could be concluded that enteric BCoV genealogy from newborn and adult cattle is directly associated to geographic patterns when S and HE genes are taken into account, with a less-resolved genealogy for the HE and N genes, with a trend for an age-related segregation pattern for the last and also that horses might present Betacoronavirus undistinguishable from those found in cattle, a fact previously unknown.

Staphylococcus aureus é um patógeno versátil, capaz de causar uma grande variedade de infecções. Nos últimos anos, ocorreu um aumento da proporção de infecções causadas por S. aureus resistentes a meticilina (MRSA). A resistência a meticilina deve-se à presença do gene mecA, carreado no cassete cromossômico estafilocócico (SCCmec). Pacientes infectados ou colonizados por MRSA são reservatórios e fontes de disseminação deste microorganismo, em instituições de cuidado à saúde, principalmente através de profissionais transitoriamente colonizados. Freqüentemente, a infecção por MRSA é precedida por um período de colonização. Em 2003 foi observado um aumento das taxas de infecções hospitalares por S. aureus na Enfermaria de Dermatologia do Hospital das Clínicas (EDER), em relação aos cinco anos anteriores. Os objetivos do presente estudo foram avaliar a transmissão hospitalar de MRSA, entre os pacientes da EDER e caracterizar os isolados de MRSA, obtidos de pacientes e funcionários colonizados, presentes nessa unidade. Foi realizada a detecção dos pacientes colonizados por MRSA, através de culturas de vigilância das narinas e, quando possível, culturas de vigilância das lesões de pele, num período de seis meses. A identificação fenotípica foi confirmada por reação em cadeia da polimerase (PCR) multiplex para detecção dos genes mecA e coa. Posteriormente, os isolados de MRSA foram submetidos ao teste de sensibilidade aos antimicrobianos pelo método de microdiluição em caldo, PCR multiplex para determinação do tipo de SCCmec e tipagem molecular por eletroforese em campo pulsado (PFGE). Quarenta e cinco por cento dos pacientes eram portadores de MRSA. No início do estudo, 14% dos funcionários eram portadores de MRSA, no fim eram 18%. Foram obtidas 105 amostras de MRSA, sendo que 11 foram isoladas de funcionários da EDER e 94 isoladas de 64 pacientes que eram portadores deste microorganismo.Sessenta e um por cento dos pacientes classificados como portadores de MRSA, eram positivos na primeira coleta realizada e 39% foram identificados durante o seguimento, nas coletas posteriores. O gene da coagulase foi detectado em todas as 105 amostras e o gene mecA em 101. Todos os isolados foram sensíveis a vancomicina e resistentes a oxacilina e penicilina. Trinta e três por cento dos isolados eram multirresistentes, apresentaram SCCmec tipo IIIA e um perfil PFGE predominante. SCCmec tipo IV foi observado em 59% dos isolados. Não foi possível determinar o tipo de SCCmec de quatro isolados. Na PFGE, o perfil B1 foi o mais prevalente, apresentado por isolados de MRSA SCCmec tipo IV, obtidos de nove pacientes e de três funcionários. A transmissão hospitalar foi caracterizada em 39% dos pacientes portadores. Foi possível observar a participação dos funcionários, na transmissão cruzada de MRSA, na EDER. A colonização por MRSA, dos profissionais de cuidado à saúde, foi transitória. Além da transmissão hospitalar de MRSA, foi possível detectar pacientes que eram portadores de MRSA na admissão / Staphylococcus aureus is a versatile pathogen capable of causing a wide variety of infections. The proportion of nosocomial and community-acquired methicillinresistant Staphylococcus aureus (MRSA) infections has increased in the last years. Methicillin resistance is mediated by the mecA gene which is carried on the Staphylococcal Cassette Chromosome mec (SCCmec). In heath care settings, patients who are colonized or infected with MRSA constitute a reservoir and a source of spread of this microorganism, mainly through transiently colonized health care workers (HCWs). MRSA infections are usually preceded by a period of colonization. In 2003, an increase in the rates of MRSA nosocomial infection in the Dermatology ward of Hospital das Clínicas was observed, in comparison with the five previous years. The aims of this study were to evaluate the nosocomial transmission of MRSA in the Dermatology ward and to characterize MRSA isolates obtained from patients and HCWs. Surveillance cultures of the anterior nares and skin lesions were performed to identify patients who were MRSA carriers, during a period of six months. The phenotypic identification was confirmed by multiplex polymerase chain reaction (PCR), to detect mecA and coa genes. Subsequently, MRSA isolates were submitted to antimicrobial susceptibility testing by microdilution method, multiplex PCR for SCCmec typing and molecular typing by pulsed-field gel electrophoresis (PFGE). Forty-five percent of the patients were MRSA carriers. 14% of the HCWs were MRSA carriers at the beginning of the study and 18% at the end. One hundred and five MRSA isolates were obtained, 11 from HCWs and 94 from 64 patients who were MRSA carriers. Sixty-one percent of the patients, classified as MRSA carriers, were positive on the first culture and 39% were identified during the follow up period in the subsequent cultures. The coagulase gene was detected in all 105 isolates and the mecA gene in 101. All MRSA isolates were susceptible to vancomycin and resistant to oxacillin and penicillin. Thirty-three percent of the isolates were multiresistant, presented SCCmec Type IIIA and showed a predominant PFGE type. The SCCmec type IV was found in 59% of the isolates. It was not possible to determine the SCCmec type of four isolates. The B1 PFGE pattern was the most prevalent, presented by MRSA SCCmec type IV isolates, obtained from nine patients and three HCWs. Nosocomial transmission occurred in 39% of the MRSA carriers. It was possible to observe HCWs MRSA cross- transmission in the Dermatology ward. HCWs were transiently colonized. In addition to nosocomial transmission of MRSA, it was possible to detect patients who were MRSA carriers on admission

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / O presente estudo foi realizado, com o objetivo de aplicar a tÃcnica de PCR em seqÃÃncias palindrÃmicas extragÃnicas repetidas (REP-PCR) no monitoramento da qualidade do leite de cabra, atravÃs da detecÃÃo de Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa e Streptococcus spp., em amostras de mÃos de ordenhadores, tetos das cabras, leite, ordenhadeira e Ãgua, para o futuro estabelecimento e implantaÃÃo do sistema de AnÃlise de Perigos e Pontos CrÃticos de Controle (APPCC). Verificou-se vÃrios fingerprints de todos os isolados coletados das diferentes fontes estudadas (mÃos de ordenhadores, tetos das cabras, leite, ordenhadeira e Ãgua). Observou-se comportamentos muito similares das bandas indicando que os isolados podem ser relatados como clones epidemiolÃgicos. A Ãgua sem tratamento, utilizada para a lavagem das mÃos dos ordenhadores, caracterizou-se como um ponto crÃtico de controle (PCC), pois se destaca como iniciador de contaminaÃÃo nas amostras Streptococcus spp., Escherichia coli e Pseudomonas aeruginosa,. Outro PCC seria as mÃos do ordenhador, pois nas amostras de Staphylococcus aureus, aparece tambÃm como indicador de contaminaÃÃo. A tÃcnica demonstrou ser eficiente para a anÃlise da similaridade entre indivÃduos da mesma espÃcie, no caso, do Staphylococcus aureus, Streptococcus spp., Escherichia coli e Pseudomonas aeruginosa, sendo, portanto, uma ferramenta Ãtil para investigaÃÃo de falhas no manejo e consequentemente, na busca de um controle mais eficiente para evitar ou minimizar a disseminaÃÃo de microrganismos patogÃnicos causadores de sÃrias enfermidades em humanos e animais, que muitas vezes podem ser transmitidas atravÃs de produtos como o leite e seus derivados. / The present study was carried out, with the objective of applying the PCR technique in repetitive extragenic palindromic (REP-PCR) sequences in the monitoring of the quality of goat milk, through the detection of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Streptococcus spp., in samples of milking handlers, goats teats, milk, milk machine and water, for the future establishment and implantation of the system of Hazard Analysis Critical Control Points (HACCP). Several fingerprints was verified of all the isolates collected of the different studied sources (milking handlers, goats teats, milk, milk machine and water). It was observed very similar behaviors of the bands indicating that the isolates can be related as epidemic clones. The water without treatment, used for the wash milking handlers, it was characterized as a critical point of control (PCC), because stands out as starter contamination in the Streptococcus spp., Escherichia coli and Pseudomonas aeruginosa samples. Another PCC would be the hands of the milking handlers, because in the Staphylococcus aureus samples, it is also appears as initial point of contamination. The technique demonstrated to be efficient for the similarity analysis among individuals of the same species, in case, of the Staphylococcus aureus, Streptococcus spp., Escherichia coli and Pseudomonas aeruginosa, being, therefore, an useful tool for investigation of fails on management and consequently, in the search of more efficient control to avoid or to minimize the spread of pathogenic microorganisms that cause serious illnesses in humans and animals, and can be transmitted through products as the milk and your products.

As doenças entéricas associadas com diarreia, desidratação e perda de peso constituem um dos principais problemas da bovinocultura mundial, contribuindo para expressivos índices de morbidade e mortalidade, principalmente entre neonatos. Nesse contexto, exigências para o aprimoramento do diagnóstico laboratorial de doenças entéricas de natureza infectocontagiosa, tornaram-se constantes, face às perdas econômicas vinculadas. Entre os principais enteropatógenos virais, de distribuição mundial e história recente, destaca-se o astrovírus bovino (BoAstV), cuja primeira identificação data de 1978. BoAstV entérico induz diarreia principalmente entre neonatos e imunocomprometidos, tendo uma prevalência acima de 60% nas 5 primeiras semanas de vida dos animais. Devido à carência de dados a respeito da prevalência desse vírus no Brasil, o presente estudo foi realizado objetivando a detecção e caracterização moleculares de cepas de BoAstV em amostras fecais de bovinos com e sem diarreia de diferentes idades. O estudo foi conduzido a partir de 272 animais em diferentes estados do Brasil, obtendo-se 14,3% de positividade através de RT-PCR, sendo que 11 amostras, provenientes dos estados de São Paulo, Minas Gerais e Rio Grande do Sul, foram submetidas ao sequenciamento nucleotídico. A similaridade entre as sequências deduzidas de aminoácidos das amostras obtidas foi maior do que 86,8%, quando comparadas umas com as outras, e situou-se entre 86,2 a 94,8% quando comparadas com sequências de outros BoAstV descritos. Nas reconstruções filogenéticas, 9 amostras agruparam-se conjuntamente em clado distinto de outros BoAstV, uma amostra (BoAstV-155-BRA) formou ramo parafilético a clado que agrupa tanto outros BoAstV como astrovírus de cervídeos e a amostra restante (BoAstV-267-BRA) formou ramo basal aos astrovírus bovinos e suínos. No entanto, o posicionamento das 2 amostras divergentes (BoAstV-155-BRA e BoAstV-267-BRA) não derivou de episódios de seleção positiva ou recombinação. Em síntese, os resultados obtidos indicam, de maneira inédita, a circulação de variantes de BoAstV entérico em rebanhos de estados da região centro-sul do Brasil. / Enteric diseases associated with diarrhea, dehydration and weight loss is one of the major problems of cattle worldwide, contributing to significant morbidity and mortality, especially among newborns. In this context, demands for improving the laboratory diagnosis of infectious enteric diseases, became constant, given the economic losses involved. Among the major viral enteropathogens of worldwide distribution and recent history, highlight the bovine astrovirus (BoAstV), whose first mention dates from 1978. Enteric BoAstV induce diarrhea especially among newborns and immunocompromised animals, having a prevalence above 60% in the first 5 weeks of life. Due to lack of data concerning the occurrence of this virus in Brazil, the present study was aimed at molecular detection and characterization of BoAstV strains in fecal samples from cattle with and without diarrhea of different ages. The study was conducted on 272 animals from different states of Brazil, obtaining positivity of 14.3% by RT-PCR, and 11 samples from the states of São Paulo, Minas Gerais and Rio Grande do Sul were subjected to nucleotide sequencing. The similarity between the deduced amino acid sequences of the samples was greater than 86.8% when compared with each other and was between 86.2 to 94.8% compared with sequences of other BoAstV described. In phylogenetic reconstructions, 9 samples were grouped together in a separate clade from other BoAstV, a sample (BoAstV-155-BRA) formed a paraphyletic branch to a clade that groups both other BoAstV and deer astrovirus and the remaining sample (267-BRA-BoAstV ) formed a basal branch to bovine and porcine astrovirus. However, the positioning of the two different samples (BoAstV-155-BRA and BoAstV-267-BRA) did not derive from episodes of positive selection or recombination. In summary, the results indicate, in an unprecedented manner, the circulation of enteric BoAstV variants in herds of cattle form states of the south-central region of Brazil.

As doenças entéricas associadas com diarreia, desidratação e perda de peso constituem um dos principais problemas da bovinocultura mundial, contribuindo para expressivos índices de morbidade e mortalidade, principalmente entre neonatos. Nesse contexto, exigências para o aprimoramento do diagnóstico laboratorial de doenças entéricas de natureza infectocontagiosa, tornaram-se constantes, face às perdas econômicas vinculadas. Entre os principais enteropatógenos virais, de distribuição mundial e história recente, destaca-se o astrovírus bovino (BoAstV), cuja primeira identificação data de 1978. BoAstV entérico induz diarreia principalmente entre neonatos e imunocomprometidos, tendo uma prevalência acima de 60% nas 5 primeiras semanas de vida dos animais. Devido à carência de dados a respeito da prevalência desse vírus no Brasil, o presente estudo foi realizado objetivando a detecção e caracterização moleculares de cepas de BoAstV em amostras fecais de bovinos com e sem diarreia de diferentes idades. O estudo foi conduzido a partir de 272 animais em diferentes estados do Brasil, obtendo-se 14,3% de positividade através de RT-PCR, sendo que 11 amostras, provenientes dos estados de São Paulo, Minas Gerais e Rio Grande do Sul, foram submetidas ao sequenciamento nucleotídico. A similaridade entre as sequências deduzidas de aminoácidos das amostras obtidas foi maior do que 86,8%, quando comparadas umas com as outras, e situou-se entre 86,2 a 94,8% quando comparadas com sequências de outros BoAstV descritos. Nas reconstruções filogenéticas, 9 amostras agruparam-se conjuntamente em clado distinto de outros BoAstV, uma amostra (BoAstV-155-BRA) formou ramo parafilético a clado que agrupa tanto outros BoAstV como astrovírus de cervídeos e a amostra restante (BoAstV-267-BRA) formou ramo basal aos astrovírus bovinos e suínos. No entanto, o posicionamento das 2 amostras divergentes (BoAstV-155-BRA e BoAstV-267-BRA) não derivou de episódios de seleção positiva ou recombinação. Em síntese, os resultados obtidos indicam, de maneira inédita, a circulação de variantes de BoAstV entérico em rebanhos de estados da região centro-sul do Brasil. / Enteric diseases associated with diarrhea, dehydration and weight loss is one of the major problems of cattle worldwide, contributing to significant morbidity and mortality, especially among newborns. In this context, demands for improving the laboratory diagnosis of infectious enteric diseases, became constant, given the economic losses involved. Among the major viral enteropathogens of worldwide distribution and recent history, highlight the bovine astrovirus (BoAstV), whose first mention dates from 1978. Enteric BoAstV induce diarrhea especially among newborns and immunocompromised animals, having a prevalence above 60% in the first 5 weeks of life. Due to lack of data concerning the occurrence of this virus in Brazil, the present study was aimed at molecular detection and characterization of BoAstV strains in fecal samples from cattle with and without diarrhea of different ages. The study was conducted on 272 animals from different states of Brazil, obtaining positivity of 14.3% by RT-PCR, and 11 samples from the states of São Paulo, Minas Gerais and Rio Grande do Sul were subjected to nucleotide sequencing. The similarity between the deduced amino acid sequences of the samples was greater than 86.8% when compared with each other and was between 86.2 to 94.8% compared with sequences of other BoAstV described. In phylogenetic reconstructions, 9 samples were grouped together in a separate clade from other BoAstV, a sample (BoAstV-155-BRA) formed a paraphyletic branch to a clade that groups both other BoAstV and deer astrovirus and the remaining sample (267-BRA-BoAstV ) formed a basal branch to bovine and porcine astrovirus. However, the positioning of the two different samples (BoAstV-155-BRA and BoAstV-267-BRA) did not derive from episodes of positive selection or recombination. In summary, the results indicate, in an unprecedented manner, the circulation of enteric BoAstV variants in herds of cattle form states of the south-central region of Brazil.

With over 35 million people currently infected, the World Health Organization considers HIV a global pandemic. HIV is characterized by a high mutation rate, which allows it to evade the host immune system and develop resistance to drugs. However, this extraordinary adaptive ability may also be the key to HIV’s demise. Through the field of phylodynamics, the evolutionary behavior of the virus is being studied in an attempt to control the epidemic. In this thesis, three papers are presented in which we analyze sequences generated through the Canadian HIV Strain and Drug Resistance Surveillance program. In chapter 2 we validate a classifier which distinguishes between recent and established infections based on the proportion of mixed bases observed in population-based pol sequences. Our results will help identify recent infections and improve incidence calculations. In chapter 3, we investigate immune-induced patterns in HIV that are shared by patients of the same ethnicity. An understanding of the forces shaping HIV evolution is instrumental to the development of a vaccine relevant to the Canadian epidemic. In chapter 4, we present preliminary results of a historical reconstruction of HIV across the provinces of Canada. This analysis will highlight strategies that have succeeded or failed in controlling the epidemic. Furthermore, our work will establish whether non-B subtypes of HIV are an increasing threat to Canadian public health. Overall, this thesis provides the first country-wide evolutionary and phylogenetic analysis of the HIV epidemic.

With over 35 million people currently infected, the World Health Organization considers HIV a global pandemic. HIV is characterized by a high mutation rate, which allows it to evade the host immune system and develop resistance to drugs. However, this extraordinary adaptive ability may also be the key to HIV’s demise. Through the field of phylodynamics, the evolutionary behavior of the virus is being studied in an attempt to control the epidemic. In this thesis, three papers are presented in which we analyze sequences generated through the Canadian HIV Strain and Drug Resistance Surveillance program. In chapter 2 we validate a classifier which distinguishes between recent and established infections based on the proportion of mixed bases observed in population-based pol sequences. Our results will help identify recent infections and improve incidence calculations. In chapter 3, we investigate immune-induced patterns in HIV that are shared by patients of the same ethnicity. An understanding of the forces shaping HIV evolution is instrumental to the development of a vaccine relevant to the Canadian epidemic. In chapter 4, we present preliminary results of a historical reconstruction of HIV across the provinces of Canada. This analysis will highlight strategies that have succeeded or failed in controlling the epidemic. Furthermore, our work will establish whether non-B subtypes of HIV are an increasing threat to Canadian public health. Overall, this thesis provides the first country-wide evolutionary and phylogenetic analysis of the HIV epidemic.