In any host population, individuals may be infected with multiple pathogens concurrently or in sequence. The direction and strength of pathogen-pathogen interactions are often unknown and dependent on the mechanism of interaction. This thesis is concerned with the epidemiology of infections and coinfections in zebu cattle during their first year of life, and the consequences they have for hosts’ survival probabilities and growth rates. Specifically, the study aims to: a) identify the many different pathogen infections occurring in zebu cattle under one year old, b) identify the main causes of mortality and reduced growth rates, c) test for evidence of effects of pathogen-pathogen interactions on mortality and growth, and d) determine the risk factors for infections with pathogens associated with increased mortality and reduced growth rates in zebu calves. To achieve these aims data collected from an epidemiological follow-up study of a cohort of 548 indigenous zebu cattle, recruited at birth and followed for the entire first year of life was used. Growth rates were enormously variable (52 to 704% of birth-weight) and 88 (16%) of the calves died during the first year, most from infectious disease. In total, 25,104 calf weeks of observation and data from 5,337 individual calf visits were analysed. Over 50 different pathogens were identified in the cohort. The thesis begins by providing an overview of zebu cattle and the importance of cattle diseases relevant to Sub-Saharan Africa, emphasising the importance of epidemiological studies taking into account co-infections, which are common in the natural populations, as opposed to a single-pathogen focus. A detailed description of the study design, data collection and descriptive analysis of non-infectious factors, including management and environmental factors, and a descriptive analysis of all pathogens screened for in the study are provided. Using Cox proportional models with frailty terms, the study then identifies infectious and non-infectious risk factors associated with mortality. Further, the role co-infections play in decreasing survival probabilities are investigated, revealing that the hazard for death from East Coast Fever (ECF) - the single most important disease associated with 40% of all deaths - increases 10 times in animals co-infected with Trypanosoma species, and 1.3 times for every 1000 eggs per gram faeces increase in strongyle egg count. Mixed-effect models are used to study growth rates and the impact of coinfections, revealing both synergistic interactions (lower host growth rates) of T. parva and A. marginale co-infections, and antagonistic interactions (relatively higher host growth rates) of T. parva and T. mutans co-infections compared to single infections with T. parva. Further, this work shows that helminth infections can have a strong negative effect on the growth rates but this is burden-dependent. These findings provide baseline epidemiological data on the diseases with greatest impact on health and performance of young zebu cattle, information that is valuable in the prioritisation and control of diseases. Additionally, they provide evidence of co-infections affecting host growth and survival, and have important implications on disease control strategies, suggesting benefits of aan integrated approach to control of worm, tick and tsetse-borne diseases.

O Circovirus suíno tipo 2 (PCV2) é um vírus ubíquo que tem sido associado a um número de síndromes em suínos. Entre elas, a Síndrome Multissistêmica do Definhamento dos Suínos (SMDS) tornou-se uma das principais causas de perdas econômicas na suinocultura nacional. No entanto, existe incerteza se o PCV2 é, de fato, o único agente responsável por esse quadro, essencialmente porque a administração isolada do vírus a animais suscetíveis não tem sido capaz de reproduzir experimentalmente a síndrome. Em vista disso, um número de outros agentes infecciosos (e não infecciosos) tem sido examinados e sua potencial participação no desenvolvimento da SMDS tem sido pesquisada. No presente estudo foram realizados experimentos visando determinar se outro(s) agente(s) com genoma de DNA circular poderia(m) desempenhar algum papel no desenvolvimento da SMDS. Para tanto, a técnica denominada “amplificação por círculo rolante com múltiplos primers” (ACRMP) foi empregada. A ACRMP é baseada na atividade da DNA polimerase do fago phi29, uma enzima capaz de sintetizar novas moléculas de DNA a partir de um molde de DNA circular. Numa segunda etapa, o DNA amplificado é clivado com enzimas de restrição, ocasionando a linearização de grande quantidade de cópias do DNA alvo original. Como a ACRMP é realizada com primers aleatórios, nenhum conhecimento prévio da seqüência de nucleotídeos alvo é necessário. Portanto, pode-se teoricamente amplificar DNA circular de qualquer microorganismo, o que a torna ideal para o propósito do presente estudo. O DNA extraído de soros de 67 suínos com sinais clínicos de SMDS, assim como de 63 suínos saudáveis, foram submetidos à ACRMP. O principal achado deste estudo foi que o genoma de um (ou mais) anelovírus foi(ram) detectado(s) em 88,9% (56/63) dos suínos saudáveis, ao passo que o(s) mesmo(s) agente(s) somente foi(ram) detectado(s) em 16,4% (11/67) dos soros de suínos com sinais clínicos da SMDS. Alguns fragmentos de DNA potencialmente correspondentes a fragmentos de genomas virais foram seqüenciados, revelando que pelo menos um deles corresponde a uma seqüência de anelovírus suíno ainda não descrita. No entanto, outro genoma correspondente a um anelovírus foi encontrado na mesma amostra, sugerindo que mais de um vírus pode estar presente em amostras de soro. Estes resultados demonstraram que os anelovírus, de grande variabilidade genética, são significativamente mais prevalentes em suínos clinicamente saudáveis do que em suínos com SMDS. / Porcine circovirus type 2 (PCV2) is an ubiquitous virus that has been associated to a number of syndromes in swine. Among these, Postweaning Multisystemic Wasting Syndrome (PMWS) has become a major cause of economic losses in swine worldwide. However, there is uncertainty as to whether PCV2 is in fact the sole agent responsible for the disease, essentially because the disease has not been experimentally reproduced when PCV2 is inoculated onto susceptible animals. In view of that, a number of other infectious (and non infectious) agents have been examined and their potential role in PMWS searched for. This study was carried out to determine whether any other agent(s) with circular DNA genome might be playing some role in PMWS. In order to achieve that, a technique called “randomly primed rolling circle amplification” (RPRCA) was employed. RPRCA is based on the activity of bacteriophage phi29 DNA polymerase, an enzyme that synthesizes new DNA molecules starting from a circularized DNA template. In a second phase, the amplified DNA is cleaved with restriction enzymes, so giving rise to large amounts of linearized copies of the original target DNA. As RPRCA is performed with random priming, no previous knowledge of the target nucleotide sequence is necessary. Therefore, it is theoretically possible to amplify circular DNA of any microorganism, thus making it ideal for the purpose of the present study. DNA extracted from sera of 67 pigs with clinical signs of PMWS as well as from 63 healthy pigs was submitted to RPRCA. The major finding of this study was that the genome of one (or more) anelloviruses was detected in 88,9% (56/63) of the healthy pigs, whereas the same agent was only detected in 16,4% (11/67) of pigs with clinical signs of PMWS. Some of the DNA fragments corresponding to the putative virus genomes were sequenced and revealed at least one non-previously described anellovirus sequence. However, other anellovirus could be found on the same sample, suggesting that more than one genome are present in samples of serum. These results demonstrate that anelovírus, of great genetic variability, were significantly more prevalent in healthy pigs than in pigs with PMWS.

O Circovirus suíno tipo 2 (PCV2) é um vírus ubíquo que tem sido associado a um número de síndromes em suínos. Entre elas, a Síndrome Multissistêmica do Definhamento dos Suínos (SMDS) tornou-se uma das principais causas de perdas econômicas na suinocultura nacional. No entanto, existe incerteza se o PCV2 é, de fato, o único agente responsável por esse quadro, essencialmente porque a administração isolada do vírus a animais suscetíveis não tem sido capaz de reproduzir experimentalmente a síndrome. Em vista disso, um número de outros agentes infecciosos (e não infecciosos) tem sido examinados e sua potencial participação no desenvolvimento da SMDS tem sido pesquisada. No presente estudo foram realizados experimentos visando determinar se outro(s) agente(s) com genoma de DNA circular poderia(m) desempenhar algum papel no desenvolvimento da SMDS. Para tanto, a técnica denominada “amplificação por círculo rolante com múltiplos primers” (ACRMP) foi empregada. A ACRMP é baseada na atividade da DNA polimerase do fago phi29, uma enzima capaz de sintetizar novas moléculas de DNA a partir de um molde de DNA circular. Numa segunda etapa, o DNA amplificado é clivado com enzimas de restrição, ocasionando a linearização de grande quantidade de cópias do DNA alvo original. Como a ACRMP é realizada com primers aleatórios, nenhum conhecimento prévio da seqüência de nucleotídeos alvo é necessário. Portanto, pode-se teoricamente amplificar DNA circular de qualquer microorganismo, o que a torna ideal para o propósito do presente estudo. O DNA extraído de soros de 67 suínos com sinais clínicos de SMDS, assim como de 63 suínos saudáveis, foram submetidos à ACRMP. O principal achado deste estudo foi que o genoma de um (ou mais) anelovírus foi(ram) detectado(s) em 88,9% (56/63) dos suínos saudáveis, ao passo que o(s) mesmo(s) agente(s) somente foi(ram) detectado(s) em 16,4% (11/67) dos soros de suínos com sinais clínicos da SMDS. Alguns fragmentos de DNA potencialmente correspondentes a fragmentos de genomas virais foram seqüenciados, revelando que pelo menos um deles corresponde a uma seqüência de anelovírus suíno ainda não descrita. No entanto, outro genoma correspondente a um anelovírus foi encontrado na mesma amostra, sugerindo que mais de um vírus pode estar presente em amostras de soro. Estes resultados demonstraram que os anelovírus, de grande variabilidade genética, são significativamente mais prevalentes em suínos clinicamente saudáveis do que em suínos com SMDS. / Porcine circovirus type 2 (PCV2) is an ubiquitous virus that has been associated to a number of syndromes in swine. Among these, Postweaning Multisystemic Wasting Syndrome (PMWS) has become a major cause of economic losses in swine worldwide. However, there is uncertainty as to whether PCV2 is in fact the sole agent responsible for the disease, essentially because the disease has not been experimentally reproduced when PCV2 is inoculated onto susceptible animals. In view of that, a number of other infectious (and non infectious) agents have been examined and their potential role in PMWS searched for. This study was carried out to determine whether any other agent(s) with circular DNA genome might be playing some role in PMWS. In order to achieve that, a technique called “randomly primed rolling circle amplification” (RPRCA) was employed. RPRCA is based on the activity of bacteriophage phi29 DNA polymerase, an enzyme that synthesizes new DNA molecules starting from a circularized DNA template. In a second phase, the amplified DNA is cleaved with restriction enzymes, so giving rise to large amounts of linearized copies of the original target DNA. As RPRCA is performed with random priming, no previous knowledge of the target nucleotide sequence is necessary. Therefore, it is theoretically possible to amplify circular DNA of any microorganism, thus making it ideal for the purpose of the present study. DNA extracted from sera of 67 pigs with clinical signs of PMWS as well as from 63 healthy pigs was submitted to RPRCA. The major finding of this study was that the genome of one (or more) anelloviruses was detected in 88,9% (56/63) of the healthy pigs, whereas the same agent was only detected in 16,4% (11/67) of pigs with clinical signs of PMWS. Some of the DNA fragments corresponding to the putative virus genomes were sequenced and revealed at least one non-previously described anellovirus sequence. However, other anellovirus could be found on the same sample, suggesting that more than one genome are present in samples of serum. These results demonstrate that anelovírus, of great genetic variability, were significantly more prevalent in healthy pigs than in pigs with PMWS.

O Circovirus suíno tipo 2 (PCV2) é um vírus ubíquo que tem sido associado a um número de síndromes em suínos. Entre elas, a Síndrome Multissistêmica do Definhamento dos Suínos (SMDS) tornou-se uma das principais causas de perdas econômicas na suinocultura nacional. No entanto, existe incerteza se o PCV2 é, de fato, o único agente responsável por esse quadro, essencialmente porque a administração isolada do vírus a animais suscetíveis não tem sido capaz de reproduzir experimentalmente a síndrome. Em vista disso, um número de outros agentes infecciosos (e não infecciosos) tem sido examinados e sua potencial participação no desenvolvimento da SMDS tem sido pesquisada. No presente estudo foram realizados experimentos visando determinar se outro(s) agente(s) com genoma de DNA circular poderia(m) desempenhar algum papel no desenvolvimento da SMDS. Para tanto, a técnica denominada “amplificação por círculo rolante com múltiplos primers” (ACRMP) foi empregada. A ACRMP é baseada na atividade da DNA polimerase do fago phi29, uma enzima capaz de sintetizar novas moléculas de DNA a partir de um molde de DNA circular. Numa segunda etapa, o DNA amplificado é clivado com enzimas de restrição, ocasionando a linearização de grande quantidade de cópias do DNA alvo original. Como a ACRMP é realizada com primers aleatórios, nenhum conhecimento prévio da seqüência de nucleotídeos alvo é necessário. Portanto, pode-se teoricamente amplificar DNA circular de qualquer microorganismo, o que a torna ideal para o propósito do presente estudo. O DNA extraído de soros de 67 suínos com sinais clínicos de SMDS, assim como de 63 suínos saudáveis, foram submetidos à ACRMP. O principal achado deste estudo foi que o genoma de um (ou mais) anelovírus foi(ram) detectado(s) em 88,9% (56/63) dos suínos saudáveis, ao passo que o(s) mesmo(s) agente(s) somente foi(ram) detectado(s) em 16,4% (11/67) dos soros de suínos com sinais clínicos da SMDS. Alguns fragmentos de DNA potencialmente correspondentes a fragmentos de genomas virais foram seqüenciados, revelando que pelo menos um deles corresponde a uma seqüência de anelovírus suíno ainda não descrita. No entanto, outro genoma correspondente a um anelovírus foi encontrado na mesma amostra, sugerindo que mais de um vírus pode estar presente em amostras de soro. Estes resultados demonstraram que os anelovírus, de grande variabilidade genética, são significativamente mais prevalentes em suínos clinicamente saudáveis do que em suínos com SMDS. / Porcine circovirus type 2 (PCV2) is an ubiquitous virus that has been associated to a number of syndromes in swine. Among these, Postweaning Multisystemic Wasting Syndrome (PMWS) has become a major cause of economic losses in swine worldwide. However, there is uncertainty as to whether PCV2 is in fact the sole agent responsible for the disease, essentially because the disease has not been experimentally reproduced when PCV2 is inoculated onto susceptible animals. In view of that, a number of other infectious (and non infectious) agents have been examined and their potential role in PMWS searched for. This study was carried out to determine whether any other agent(s) with circular DNA genome might be playing some role in PMWS. In order to achieve that, a technique called “randomly primed rolling circle amplification” (RPRCA) was employed. RPRCA is based on the activity of bacteriophage phi29 DNA polymerase, an enzyme that synthesizes new DNA molecules starting from a circularized DNA template. In a second phase, the amplified DNA is cleaved with restriction enzymes, so giving rise to large amounts of linearized copies of the original target DNA. As RPRCA is performed with random priming, no previous knowledge of the target nucleotide sequence is necessary. Therefore, it is theoretically possible to amplify circular DNA of any microorganism, thus making it ideal for the purpose of the present study. DNA extracted from sera of 67 pigs with clinical signs of PMWS as well as from 63 healthy pigs was submitted to RPRCA. The major finding of this study was that the genome of one (or more) anelloviruses was detected in 88,9% (56/63) of the healthy pigs, whereas the same agent was only detected in 16,4% (11/67) of pigs with clinical signs of PMWS. Some of the DNA fragments corresponding to the putative virus genomes were sequenced and revealed at least one non-previously described anellovirus sequence. However, other anellovirus could be found on the same sample, suggesting that more than one genome are present in samples of serum. These results demonstrate that anelovírus, of great genetic variability, were significantly more prevalent in healthy pigs than in pigs with PMWS.

The Chlamydiaceae are a bacterial family that contains a single genus: Chlamydia. The genus Chlamydia consists of 9 species that are obligate, intracellular pathogens. Untreated C. trachomatis infections can lead to serious health ramifications, such as ectopic pregnancy, tubal factor infertility, pelvic inflammatory disease, and long-term pelvic pain. In this study, it was found that a primary antibody dilution of 1:400 using methanol fixed HeLA cells, as derived from Carrasco, et al. protocol, was only optimal for PMP-C staining. Pmp-A, Pmp-B, and Pmp-F were found to stain brighter with formaldehyde fixed, infected HeLa cells and using different primary antibody dilutions. The manuscript by Carrasco, et al., demonstrated that chlamydial persistence caused by penicillin-stressed conditions showed a decrease in Pmp-B and Pmp-C protein expression between 24-48 hpi, while Pmp-A and Pmp-F expression stayed the same under the stressful conditions. We hypothesized that under HSV- induced persistence the same results would occur. However, our data indicates that the chlamydial response to stressful conditions is not the same among persistence-inducers and implies that various inducers of persistence may affect PMP expression differently. Initially, we also hypothesized that PMP expression could be utilized as an indicator to determine whether an infected individual has a productive or persistent chlamydial infection. Due to the experiments’ results, PMP expression is most likely not a good marker to identify the type of chlamydial infection (ie. productive or persistent) in the host.

Os vírus entéricos causam infecções que podem ocasionar uma alta morbidade e mortalidade em cães. A diarreia se destaca como o principal sinal clínico e a subsequente desidratação pode causar a morte do animal. O Carnivore protoparvovirus 1 (CPV-2), Canine mastadenovirus A tipo 1 (CAdV-1), o Canine coronavirus (CCoV), o Canine rotavirus (CRV) e o Canine distemper virus (CDV) são considerados os principais agentes que causam gastroenterite viral aguda em cães jovens. O objetivo deste trabalho foi detectar a presença destas cinco espécies virais na população de cães do Brasil. Para isto, foram coletados 325 suabes retais de cães com ou sem diarreia, jovens (> 6 meses) e adultos (< 6 meses), com ou sem histórico de vacinação e de diversas regiões do Brasil. As amostras foram analisadas através da reação em cadeia da polimerase (PCR) ou transcrição reversa seguida de PCR (RT-PCR) utilizando iniciadores específicos para cada um dos agentes virais. Resultaram 81% (264/325) das amostras positivas para um destes vírus, das quais 30,7% (100/325) foram positivas para o CPV-2, 25,5% (83/325) para o CDV, 17,2% (56/325) para o CCoV, 4,6% (15/325) para o CRV e 2,7% (9/ 325) para o CAdV-1. Algumas amostras apresentaram co-infecções, sendo que as espécies mais predominantemente encontradas em co-infecções foram o CDV e CPV-2 em 15,4% (50/325) e 15,0% (49/325), respectivamente, seguidos do CCoV em 10,1% (33/325,), CRV em 3,0% (10/325) e CAdV-1 em 1,5% (5/325) das amostras. A associação viral mais observada foi CDV e CPV-2 em 31/325 (9,5%) amostras positivas para ambos os vírus. Em conclusão, os resultados demonstram que CPV-2, CDV e CCoV são os principais vírus entéricos patogênicos que circularam no Brasil entre os anos de 2008 e 2014, infectando mais frequentemente animais jovens. / Enteric viruses cause infections that lead to high morbidity and mortality. Diarrhea is the main clinical sign, whose subsequent dehydration can cause death of the animal. Carnivore protoparvovirus 1 (CPV-2), Canine mastadenovirus A (CAdV-1), Canine coronavirus (CCoV), Canine rotavirus (CRV) and Canine distemper virus (CDV) are considered the main agents that cause acute viral gastroenteritis in young dogs. The aim of this study was the detection of these five viral species in dogs from Brazil. Rectal swabs from 325 dogs, puppies (< six months old), adult dogs (> 6 months old), with or without a history of vaccination, were collected from various regions of the country. The samples were analyzed by polymerase chain reaction (PCR) or reverse transcription following followed by PCR (RT-PCR) using oligonucleotides specific for each one of this virus. As result, 81% (264/325) of the samples were observed to be positive for at least one virus, 30,7% (100/325) were positive for CPV-2, 25,5% (83/325) for CDV, 17,2% (56/325) for CCoV, 4,6% (14/325) for CRV and 2,7% (9/325) for CAdV-1. Some samples showed co-infection, where the species most predominantly found were CDV and CPV-2 with 15,4% (50/325) and 15,0% (49/325), respectively, followed by CCoV with 10,1% (33/325,), CRV with 3,0% (10/325) and CAdV-1 1,5% (5/325). The most observed viral association was CDV and CPV-2, with 31/325 (9,5%) positive samples for both viruses. In conclusion, the results showed that CPV-2, CDV and CCoV are the main pathogenic enteric viruses that circulated in Brazil between the years 2008 and 2014, infecting more frequently puppies.

Os vírus entéricos causam infecções que podem ocasionar uma alta morbidade e mortalidade em cães. A diarreia se destaca como o principal sinal clínico e a subsequente desidratação pode causar a morte do animal. O Carnivore protoparvovirus 1 (CPV-2), Canine mastadenovirus A tipo 1 (CAdV-1), o Canine coronavirus (CCoV), o Canine rotavirus (CRV) e o Canine distemper virus (CDV) são considerados os principais agentes que causam gastroenterite viral aguda em cães jovens. O objetivo deste trabalho foi detectar a presença destas cinco espécies virais na população de cães do Brasil. Para isto, foram coletados 325 suabes retais de cães com ou sem diarreia, jovens (> 6 meses) e adultos (< 6 meses), com ou sem histórico de vacinação e de diversas regiões do Brasil. As amostras foram analisadas através da reação em cadeia da polimerase (PCR) ou transcrição reversa seguida de PCR (RT-PCR) utilizando iniciadores específicos para cada um dos agentes virais. Resultaram 81% (264/325) das amostras positivas para um destes vírus, das quais 30,7% (100/325) foram positivas para o CPV-2, 25,5% (83/325) para o CDV, 17,2% (56/325) para o CCoV, 4,6% (15/325) para o CRV e 2,7% (9/ 325) para o CAdV-1. Algumas amostras apresentaram co-infecções, sendo que as espécies mais predominantemente encontradas em co-infecções foram o CDV e CPV-2 em 15,4% (50/325) e 15,0% (49/325), respectivamente, seguidos do CCoV em 10,1% (33/325,), CRV em 3,0% (10/325) e CAdV-1 em 1,5% (5/325) das amostras. A associação viral mais observada foi CDV e CPV-2 em 31/325 (9,5%) amostras positivas para ambos os vírus. Em conclusão, os resultados demonstram que CPV-2, CDV e CCoV são os principais vírus entéricos patogênicos que circularam no Brasil entre os anos de 2008 e 2014, infectando mais frequentemente animais jovens. / Enteric viruses cause infections that lead to high morbidity and mortality. Diarrhea is the main clinical sign, whose subsequent dehydration can cause death of the animal. Carnivore protoparvovirus 1 (CPV-2), Canine mastadenovirus A (CAdV-1), Canine coronavirus (CCoV), Canine rotavirus (CRV) and Canine distemper virus (CDV) are considered the main agents that cause acute viral gastroenteritis in young dogs. The aim of this study was the detection of these five viral species in dogs from Brazil. Rectal swabs from 325 dogs, puppies (< six months old), adult dogs (> 6 months old), with or without a history of vaccination, were collected from various regions of the country. The samples were analyzed by polymerase chain reaction (PCR) or reverse transcription following followed by PCR (RT-PCR) using oligonucleotides specific for each one of this virus. As result, 81% (264/325) of the samples were observed to be positive for at least one virus, 30,7% (100/325) were positive for CPV-2, 25,5% (83/325) for CDV, 17,2% (56/325) for CCoV, 4,6% (14/325) for CRV and 2,7% (9/325) for CAdV-1. Some samples showed co-infection, where the species most predominantly found were CDV and CPV-2 with 15,4% (50/325) and 15,0% (49/325), respectively, followed by CCoV with 10,1% (33/325,), CRV with 3,0% (10/325) and CAdV-1 1,5% (5/325). The most observed viral association was CDV and CPV-2, with 31/325 (9,5%) positive samples for both viruses. In conclusion, the results showed that CPV-2, CDV and CCoV are the main pathogenic enteric viruses that circulated in Brazil between the years 2008 and 2014, infecting more frequently puppies.

Os vírus entéricos causam infecções que podem ocasionar uma alta morbidade e mortalidade em cães. A diarreia se destaca como o principal sinal clínico e a subsequente desidratação pode causar a morte do animal. O Carnivore protoparvovirus 1 (CPV-2), Canine mastadenovirus A tipo 1 (CAdV-1), o Canine coronavirus (CCoV), o Canine rotavirus (CRV) e o Canine distemper virus (CDV) são considerados os principais agentes que causam gastroenterite viral aguda em cães jovens. O objetivo deste trabalho foi detectar a presença destas cinco espécies virais na população de cães do Brasil. Para isto, foram coletados 325 suabes retais de cães com ou sem diarreia, jovens (> 6 meses) e adultos (< 6 meses), com ou sem histórico de vacinação e de diversas regiões do Brasil. As amostras foram analisadas através da reação em cadeia da polimerase (PCR) ou transcrição reversa seguida de PCR (RT-PCR) utilizando iniciadores específicos para cada um dos agentes virais. Resultaram 81% (264/325) das amostras positivas para um destes vírus, das quais 30,7% (100/325) foram positivas para o CPV-2, 25,5% (83/325) para o CDV, 17,2% (56/325) para o CCoV, 4,6% (15/325) para o CRV e 2,7% (9/ 325) para o CAdV-1. Algumas amostras apresentaram co-infecções, sendo que as espécies mais predominantemente encontradas em co-infecções foram o CDV e CPV-2 em 15,4% (50/325) e 15,0% (49/325), respectivamente, seguidos do CCoV em 10,1% (33/325,), CRV em 3,0% (10/325) e CAdV-1 em 1,5% (5/325) das amostras. A associação viral mais observada foi CDV e CPV-2 em 31/325 (9,5%) amostras positivas para ambos os vírus. Em conclusão, os resultados demonstram que CPV-2, CDV e CCoV são os principais vírus entéricos patogênicos que circularam no Brasil entre os anos de 2008 e 2014, infectando mais frequentemente animais jovens. / Enteric viruses cause infections that lead to high morbidity and mortality. Diarrhea is the main clinical sign, whose subsequent dehydration can cause death of the animal. Carnivore protoparvovirus 1 (CPV-2), Canine mastadenovirus A (CAdV-1), Canine coronavirus (CCoV), Canine rotavirus (CRV) and Canine distemper virus (CDV) are considered the main agents that cause acute viral gastroenteritis in young dogs. The aim of this study was the detection of these five viral species in dogs from Brazil. Rectal swabs from 325 dogs, puppies (< six months old), adult dogs (> 6 months old), with or without a history of vaccination, were collected from various regions of the country. The samples were analyzed by polymerase chain reaction (PCR) or reverse transcription following followed by PCR (RT-PCR) using oligonucleotides specific for each one of this virus. As result, 81% (264/325) of the samples were observed to be positive for at least one virus, 30,7% (100/325) were positive for CPV-2, 25,5% (83/325) for CDV, 17,2% (56/325) for CCoV, 4,6% (14/325) for CRV and 2,7% (9/325) for CAdV-1. Some samples showed co-infection, where the species most predominantly found were CDV and CPV-2 with 15,4% (50/325) and 15,0% (49/325), respectively, followed by CCoV with 10,1% (33/325,), CRV with 3,0% (10/325) and CAdV-1 1,5% (5/325). The most observed viral association was CDV and CPV-2, with 31/325 (9,5%) positive samples for both viruses. In conclusion, the results showed that CPV-2, CDV and CCoV are the main pathogenic enteric viruses that circulated in Brazil between the years 2008 and 2014, infecting more frequently puppies.

Objective: The objective of this study was to describe the prevalence of sexually transmitted co-infections and assess factors associated with a single infection and co-infections. Methods: A total of 388 women were included in this study. At enrollment of the EVRI trial women were tested for five STIs: Human papilloma virus (HPV), Chlamydia trachomatis, Neisseria gonorrhoeae, Herpes simplex virus-2 (HSV-2) and Treponema pallidum. Prevalence of STI infections and proportion of women with different combinations of co-infections were calculated. Factors associated with single infection and STI co-infection were assessed using a polytomous logistic regression model and odds ratio (OR) and 95% confidence intervals (95% CI) were reported as the measure of association. Results: Prevalence of a single STI and concurrent STI co-infections were high. Prevalence of chlamydia was 33%, syphilis 6%, HSV-2 46% and HPV 71%. The most common STI co-infection pattern was HPV-HSV (32%), followed by HPV-chlamydia (17%). The odds of single STI compared to no STIs was significantly lower for women who had education level of grade 7 compared to women who had some college or technical education (OR 0.16, 95% CI: 0.03-0.79).The odds of a single STI compared to no STIs were significantly higher (OR 3.02, 95% CI: 1.05-8.64) and the odds of concurrent STIs compared to no infection were significantly higher (OR 3.86, 95% CI: 1.42-10.48) for women with three or more lifetime partners compared to one life time partner. Conclusions: STIs, single and multiple concurrent infections, are common among this cohort of South African women. These results strengthen the recommendation that STI screening and treatment needs to be a component of multiple intervention strategies among high-risk women residing in communities with high STI prevalence.

This thesis explores the evolution of avian influenza A viruses (IAV), as well as host-pathogen interactions between these viruses and their main reservoir host, the Mallard (Anas platyrhynchos). IAV is a genetically diverse, multi-host virus and wild birds, particularly dabbling ducks, are the natural reservoir. At our study site, up to 30% of migratory Mallards are infected with IAV during an autumn season, and host a large number of virus subtypes. IAV diversity is driven by two main mechanisms: mutation, driving genetic drift; and reassortment following co-infection, resulting in genetic shift.   Reassortment is pervasive within an autumn season, both across multiple subtypes and within a single subtype. It is a key genetic feature in long-term maintenance of common subtypes, as it allows for independent lineage turn-over, generating novel genetic constellations. I hypothesize that the decoupling of successful constellations and generation of novel annual constellations enables viruses to escape herd immunity; these genetic changes must confer antigenic change for the process to be favourable. Indeed, in an experiment utilizing vaccines, circulating viruses escaped homosubtypic immunity, resulting in the proliferation of infections with the same subtype as the vaccine. While the host plays an important role in shaping IAV evolutionary genetics, one must consider that Mallards are infected with a multitude of other microorganisms. Here, Mallards were infected with IAV, gamma coronaviruses, and avian paramyxovirus type 1 simultaneously, and we found a putative synergistic interaction between IAV and gamma coronaviruses.   Mallards occupy the interface between humans, poultry, and wild birds, and are the reservoir of IAV diversity. New incursions of highly pathogenic H5 viruses to both Europe and North America reaffirms the role of wild birds, particularly waterfowl, in diffusion of viruses spatially. Using European low pathogenic viruses and Mallard model, this thesis contributes to aspects of epidemiology, ecology, and evolutionary dynamics of waterfowl viruses, particularly IAV