Estudos preliminares visando a identificação de possíveis agentes virais associados à síndrome multissistêmica do definhamento dos suínos (SMDS) revelaram uma possível associação inversa entre a presença de TTSuV1 e a ocorrência da SMDS. Com base neste achado, foi formulada a hipótese de que o TTSuV1 poderia ser capaz de inibir a multiplicação do PCV2, impedindo assim o desenvolvimento da SMDS. Buscando esclarecer esta questão, seria necessário desenvolver um sistema eficiente de replicação para este vírus, até o presente ainda não disponível. Em vista disso, foi desenvolvido um método de detecção de infecções por TTSuV em cultivos celulares para a avaliação de possíveis linhagens a serem potencialmente utilizadas para isolamento e multiplicação destes vírus. Genomas de TTSuVs foram detectados em células de linhagem de origem suína e não suína assim como em um dos lotes de tripsina. Os soros utilizados como suplemento para o meio de cultivo não apresentaram genomas de TTSuV. Desta forma, o lote de tripsina contaminado pode ser considerado uma importante fonte de contaminação, principalmente em células de origem não suína. Com o objetivo de avaliar uma possível associação entre os TTSuVs e a ocorrência da SMDS, a frequência de detecção e quantificação de genomas de TTSuV1 e TTSuV2 em tecidos e soros de suínos com e sem SMDS foram determinadas. A análise feita nos diferentes tecidos de suínos revelou uma aparente correlação inversa entre a presença do genoma de TTSuV1 e a ocorrência da SMDS. Quanto ao TTSuV2 em tecidos de suínos com e sem a SMDS, nenhuma diferença estatística foi observada. A distribuição do genoma de TTSuV1 e TTSuV2 nos diferentes tecidos examinados não revelou um órgão alvo específico. A frequência de detecção e a carga viral de TTSuV1 e 2 nas amostras de soro de suínos com e sem a SMDS não apresentaram diferença significativa. No entanto, a carga viral de TTSuV2 foi mais alta do que a carga viral de TTSuV1 nos soros de todos os grupos de animais estudados. Estes resultados indicam uma alta frequência de detecção de ambas as espécies de TTSuV em amostras de tecidos e soros de suínos com e sem a SMDS. / Preliminary studies aiming the identification of possible viral agents associated with the postweaning multisystemic wasting syndrome (PMWS) revealed a possible negative association between TTSuV1 and occurrence of PMWS. Based on this finding was hypothesized that TTSuV1 might be able to inhibit the PCV2 multiplication, preventing the development of PMWS. To better clarify this, would be require an efficient system of replication for this virus, which has not been reported in the literature. In view of this, a method for detection of TTSuV infections in cell culture was developed to assess possible cell lineages to be potentially used for virus isolation and multiplication. TTSuV genomes were detected in cell lineages of porcine and nonporcine origin as well as a batch of trypsin. Sera used as media supplement was not found to contain TTSuV genomes. Thus, the contaminated batch of trypsin can be considered an important source of contamination, especially in cells of non-porcine origin. In order to evaluate a possible association between the TTSuVs and the occurrence of PMWS, the frequency of detection and quantification of TTSuV1 and TTSuV2 genomes in tissues and sera from pigs with and without PMWS were determined. The analysis in the different tissues of pigs reveal an apparent inverse correlation between the frequency of detection of TTSuV1 genomes and the occurrence of PMWS. Regarding TTSuV2 in tissues of PMWS and non-PMWS-affected animals no significant differences was observed. The distribution of TTSuV1 and TTSuV2 genomes in tissues did not reveal any particular target organ. The frequency of detection and viral load of TTSuV1 and TTSuV2 in sera samples were no significant statistically among animals PMWS-affected and healthy pig. The mean of TTSuV2 viral load was significantly highest than TTSuV1 in sera of all groups studied. These results indicate a high frequency of detection of both TTSuV species in tissues and sera samples from PMWS-affected and healthy pig.

Geólogo / En este informe se presentan antecedentes obtenidos en geología de campo y geocronología, junto con un modelo de evolución paleogeográfica de las rocas estratificadas cenozoicas localizadas en la quebrada La Jaula, en la cuenca del Río Teno, en el flanco occidental de la Cordillera Principal de Chile central (35°S). Se realizó una caracterización de la estratigrafía y geología estructural, junto con la obtención de edades para dos unidades litológicas a través de dataciones radiométricas por el método U-Pb en circones detríticos. Los depósitos estratificados que afloran en el cerro Corona del Fraile y en la quebrada La Jaula corresponden a (1): facies sedimentarias fluvio-lacustres provenientes del retrabajo de unidades de edad Eoceno-Oligoceno y (2) una posterior acumulación de volcanitas provenientes del arco volcánico del Mioceno Inferior. Basado en los datos obtenidos en este trabajo es posible acotar la edad máxima de depositación de las secuencias volcánicas de la Unidad Corona del Fraile (González y Vergara, 1962) al Mioceno inferior (Burdigaliano) y correlacionarlas con la serie volcánica del Mioceno, la cual, al norte de los 35°S, ha sido asignada a la Formación Farellones. Se adjunta un mapa geológico a escala 1:25.000 y un perfil estructural de la zona.

To protect public health, drinking water systems are monitored for indicator organisms that correlate with fecal contamination and suggest the presence of human pathogens. Total coliforms, fecal coliforms, and E. coli are the most commonly used indicator organisms. These bacteria generally colocate with fecal pollution, but some limitations exist. In particular, the ability of indicator bacteria to predict the presence of enteric viruses is questionable because of distinct transport and survival characteristics of bacteria and viruses. Although viral indicators of enteric viruses have been proposed, none have been implemented into the current regulatory framework. In this thesis, the correlation of bacteria and viruses in drinking water sources and treatment systems is reviewed, and the potential of Torque Teno virus (TTV) to qualify as an indicator virus is discussed. TTV is unique among enteric viruses as it infects approximately 80% of healthy individuals worldwide, is transmitted by the fecal-oral route, causes no observable illness, and lacks seasonal fluctuations.

Some viral metagenomic serum samples contain a huge amount of Anellovirus, which is a genetically diverse family with a few conserved regions making it hard to efficiently characterize. Multiple sequence alignment of the Anelloviruses found in the sample must be constructed to get a clear picture of Anellovirus diversity and to identify stable regions. Using available multiple sequence alignment software directly on these fragments results in an MSA of a very poor quality due to their diversity, misaligned regions and low-quality regions present in the sequence. An efficient MSA must be constructed in order to characterize these Anellovirus present in the samples. Pairwise alignment is used to align one fragment to the database sequences at a time. The fragments are then aligned to the database sequences using the start and end position from the pairwise alignment results. The algorithm will also exclude non-aligned portions of the fragments, as these are very hard to handle properly and are often products of misassembly or chimeric sequenced fragments. Other tools to aid further analysis were developed, such as finding a non-overlapping window that contains the most fragments, find consensus of the alignment and extract any regions from the MSA for further analysis. An MSA was constructed with a high percent of correctly aligned bases compared to an MSA constructed using MSA softwares. The minimal number of genomes found in the sampled sequence was found as well as a distribution of the fragments along the database sequence. Moreover, highly conserved region and the window containing most fragments were extracted from the MSA and phylogenetic trees were constructed for these regions.

Made available in DSpace on 2016-12-08T16:24:07Z (GMT). No. of bitstreams: 1 PGCA09MA052.pdf: 726948 bytes, checksum: 2a141d4d92b1c5ac552655f7c9ad3c1a (MD5) Previous issue date: 2009-11-06 / Many infectious agents have been associated with reproductive failure in swine, representing significantly economic losses for production. Recently, Porcine Circovirus Type 2 (PCV2), etiologic agent of PCVAD or PCV2 associated diseases, was associated with reproductive failure in swine around the world. To confirm the pathogenic potential of PCV2 inducing reproductive failure in sows, it s necessary the viral isolation and antigen and nucleic acid demonstration in fetuses. Other viral agent, Torque Teno Vírus (TTV), also have been recently associated with infections caused by PCV2. TTV alone has not showed pathogenic signals in swine, but, its role in co-infections with other pathogens has been investigated. The present study aimed the diagnostic of PCV2 in natural infections where there was reproductive failure, as well as to establish and apply the Polimerase Chain Reaction (PCR) technique for TTV from organs. Samples from field cases, as aborted fetuses, mummified, stillborn, fragile piglets and material from abattoir sows were collected and processed to diagnostic infection in order to detect PCV2 by PCR and immunohistochemistry (IHC). Samples were collected from 21 farms; and a total of 169 fetuses were necropsied. Moreover, reproductive samples from 83 abattoir sows were collected in 4 slaughterhouses of Santa Catarina State. In the present study was possible detect viral DNA by PCR in 29 (17,1%) of 169 analyzed fetuses, where heart and lymphoid tissues showed virus DNA more frequently, 41,4% and 37,8%, respectively. Viral presence was confirmed by IHC in tissues, which detected viral antigens in 17 PCV2 positives fetuses by PCR. Samples of reproductive tissues from sows also were tested by PCR and PCV2 was identified in 4 sows (4,8%). PCR technique aimed to detect TTV was established for viral DNA from organs. Samples of reproductive tissues from sows were tested, and were found both genogroups of TTV (TTV1 and TTV2), in 25 (30,1%) and 41 (49,3%) sows, respectively. Fetuses samples that resulted positive to PCV2 by PCR were also tested to TTV, and it was observed the occurrence of co-infection between these agents. The results obtained here suggest the involvement of PCV2 in reproductive failure in sows, besides show that TTV was present in analyzed samples, corroboring the association with PCV2 / Muitos agentes infecciosos têm sido associados às falhas reprodutivas na produção de suínos, representando significativas perdas econômicas para os suinocultores. Recentemente o Circovirus Suíno tipo 2 (PCV2), agente etiológico da circovirose suína, foi associado a falhas reprodutivas em suínos em diversas partes do mundo. Para confirmar o potencial patogênico do PCV2 causando falhas reprodutivas em porcas, é necessário o isolamento do vírus e demonstração de antígeno e ácido nucléico viral em fetos. Outro agente viral, o Torque Teno Vírus (TTV), também foi recentemente associado às infecções causadas pelo PCV2. O TTV sozinho ainda não tem se mostrado patogênico em suínos, porém, seu papel em co-infecções com outros patógenos vem sendo investigado. O presente trabalho teve por objetivos diagnosticar o PCV2 em infecções naturais onde existiam falhas reprodutivas, assim como padronizar e aplicar a técnica de Reação em Cadeia da Polimerase (PCR) para TTV a partir de órgãos. Amostras provenientes de casos clínicos de campo, como fetos abortados, mumificados, natimortos, leitões inviáveis e material de fêmeas descartadas foram coletadas e processadas para diagnóstico da infecção pelo PCV2 através de PCR e imunoistoquímica (IHQ). Foram colhidas amostras de 21 granjas produtoras de suínos, totalizando 169 fetos, que foram necropsiados para coleta de órgãos. Além disso, amostras de órgãos reprodutivos de 83 fêmeas descartadas foram colhidas em 4 abatedouros da região oeste catarinense. No presente estudo foi possível detectar DNA viral por PCR em 29 (17,1%) dos 169 fetos analisados, sendo coração e tecidos linfóides os órgãos onde o vírus foi identificado com maior freqüência, 41,4% e 37,8%, respectivamente. A presença do vírus foi confirmada por teste de IHQ dos tecidos, sendo encontrado antígeno viral em 17 fetos positivos para PCV2 por PCR. As amostras de tecido reprodutivo das fêmeas também foram testadas por PCR e o PCV2 foi identificado em 4 porcas (4,8%). Visando a detecção de TTV foram testadas por PCR amostras de órgãos reprodutivos de fêmeas suínas, sendo diagnosticados os dois genogrupos de TTV, TTV1 e TTV2 em 25 (30,1%) e 41 (49,3%) fêmeas, respectivamente. As amostras de fetos que resultaram positivas para PCV2 pela técnica de PCR também foram testadas para TTV, observando-se a ocorrência de coinfecção entre estes agentes. Os resultados obtidos evidenciam o provável envolvimento do PCV2 em falhas reprodutivas em fêmeas suínas, bem como mostram que o TTV está presente nas amostras analisadas, confirmando a associação com o PCV2

Submitted by Anderson Silva (avargas@icict.fiocruz.br) on 2012-10-23T13:30:15Z No. of bitstreams: 1 carlos_a_p_nascimento_ioc_bcm_0045_2011.pdf: 1006058 bytes, checksum: e670c764b773d1d5bd9fa107d877a76b (MD5) / Made available in DSpace on 2012-10-23T13:30:15Z (GMT). No. of bitstreams: 1 carlos_a_p_nascimento_ioc_bcm_0045_2011.pdf: 1006058 bytes, checksum: e670c764b773d1d5bd9fa107d877a76b (MD5) Previous issue date: 2011 / CNPq FAPERJ / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil. / O Torque teno virus (TTV) é um vírus de DNA do gênero Alphatorquevirus da família Anelloviridae. O TTV é altamente prevalente em populações de todo o mundo. Isolados foram classificados em cinco grupos filogenéticos (1-5) com grande distância genética entre eles. A presença do TTV já foi detectada nas fezes, porém, não se sabe se todos os cinco genogrupos do TTV são excretados nas fezes, e qual a distribuição do TTV entre os genogrupos. A fim de avaliar a presença, a diversidade genômica e a carga viral do TTV em fezes, 135 amostras de pacientes com gastroenterite foram analisadas. O DNA do TTV foi extraído de suspensão fecal e três diferentes métodos de reação em cadeia da polimerase (PCR), dois qualitativos e um quantitativo, foram avaliados. Nas amostras de fezes estudadas, 123 (91,1%) foram positivas em pelo menos um dos três métodos. O DNA do TTV pertencente aos genogrupos de 1 a 5 foi detectado em 37 (27,4%), 27 (20,0%), 57 (42,2%), 29 (21,5%) e 33 (24,4%) amostras, respectivamente. Co-infecções com dois, três, quatro e cinco genogrupos do TTV foram encontradas em 23 (17,0%), 15 (11,1%), 7 (5,2%) e 7 (5,2%) amostras fecais, respectivamente. Assim, 52 (38,5%) amostras continham mais de um genogrupo de TTV. A carga viral variou de 2,6 a 6,5 log de genoma equivalentes por grama de fezes. No entanto, variações de carga viral foram observadas em função do genogrupo detectado e do número de genogrupos presentes simultaneamente. Os resultados encontrados são os primeiros a mostrar a alta prevalência e a diversidade de TTV nas fezes humanas. / Torque teno virus (TTV) is a DNA virus of the genus Alphatorquevirus of Anelloviridae family. The TTV is highly prevalent in populations from around the world. Isolates have been classified into at least five main phylogenetic groups (1-5) showing a large genetic distance between them. The presence of TTV has been detected in feces. However, are presently unknown whether all five TTV genogroups are excreted in feces and the genogroup distribution. To evaluate the presence and the genomic distribution of TTV DNA in feces, 135 samples of patients with gastroenteritis were analyzed. The DNA was extracted of fecal suspension and three different PCR methods, two qualitative and one quantitative, were used. One hundred and twenty three (91.1%) samples were positive with at least one method. The TTV DNA belonging to the genogroups 1 to 5 was detected in 37 (27.4%), 27 (20.0%), 57 (42.2%), 29 (21.5%) and 33 (24.4%) fecal samples, respectively. Coinfections with two, three, four and five TTV genogroups were found in 23 (17.0%), 15 (11.1%), 7 (5.2%) and 7 (5.2%) fecal samples, respectively. Thus, 52 (38.5%) samples contained more than one TTV genogroup. Viral loads ranged from 2.6 to 6.5 log genome equivalents per gram of feces. However, variations of viral load were noted depending on genogroup and number of coinfecting TTV genogroups. These results are the first to show high prevalence and the diversity of TTV isolates in human feces.

No description available.

Le Canada est l’un des plus grands pays exportateurs de porc du monde et le Québec à lui seul compte pour 6% de ce commerce mondial. Pour conserver sa compétitivité et l’excellence de ses produits, une connaissance approfondie des agents infectieux circulant au sein des troupeaux est primordiale. Plusieurs pathogènes sont peu étudiés et pourtant retrouvés chez les porcs à travers la planète. Cette étude avait pour but l’évaluation de la prévalence des astrovirus porcins, calicivirus, kobuvirus porcin, rotavirus, torque teno sus virus ainsi que le virus de l’hépatite E lors du suivi de porcelets dans un réseau de production porcine, de la maternité jusqu’en fin d’engraissement. Nous voulions brosser un portrait de l’excrétion de ces virus à travers les différentes étapes de production des animaux. L’échantillonnage de porcelets sains et en diarrhée en pré-sevrage a permis de déterminer lesquelles de ces infections virales constituaient des facteurs de risque pour la diarrhée à ce stade de production. Le virome intestinal, la partie virale du microbiome, a également été caractérisé permettant de connaître la diversité des virus entériques porcins aux différentes étapes de production, ainsi qu’entre les porcelets sains et en diarrhée. De plus, la dissémination du virus de l’hépatite E dans l’environnement ainsi que les sources probables de contamination ont été décrites à l’aide d’échantillons provenant des environnements intérieurs et extérieurs de fermes d’engraissement, de la cour d’un abattoir et de transporteurs d’animaux. Les résultats obtenus ont permis de décrire les dynamiques temporelles d’excrétion de ces virus entériques porcins en fonction des stades de production des porcs, démontrant une différence dans l’excrétion de ces virus en fonction de l’âge. Les calicivirus, ainsi que les astrovirus porcins groupes 3 et 5 étaient des facteurs de risque de diarrhée en maternité. Pour la première fois au Canada, la détection et la caractérisation des souches du kobuvirus porcin ont été réalisées, permettant de mieux comprendre leur diversité et leur persistance à travers les stades de production. La diversité du virome entérique porcin a été analysée avec la plateforme de séquençage MiSeq et cette diversité était différente entre les porcelets sains et en diarrhée, ainsi qu’entre les stades de production. Cependant, les traitements enzymatiques utilisés pour le prétraitement des échantillons fécaux ne permettaient pas le séquençage de certains virus à ARN simple-brin. Des souches similaires du virus de l’hépatite E étaient présentes dans l’environnement des fermes, ainsi qu’aux endroits communs à forte circulation des intervenants du réseau. Les activités dans la cour de l’abattoir pourraient donc être impliquées dans la dissémination de ce virus. Cette étude a permis de mieux connaitre la prévalence et la distribution des virus entériques infectant les porcs. De plus, certains des virus entériques étudiés ont été reconnus comme facteurs de risque de la diarrhée en co-infections et devront être étudiés en détail pour comprendre leurs mécanismes en relation avec la diarrhée néonatale. Des interventions plus spécifiques lors d’éclosion de diarrhées porcines, dont l’étiologie est inconnue, pourront donc être réalisées, ainsi que l’élaboration de mesures de biosécurité plus adaptées en fonction du stade de production des porcs. / Canada is a major pork exporter around the world and the province of Quebec alone accounts for 6% of this trade. To maintain the province’s competitiveness and the excellence of its products, a comprehensive understanding of the infectious agents circulating in herds is essential. Several pathogens have been intensively studied, while others have yet to be investigated even though they have been reported in pigs all around the world. This study evaluated the prevalence of porcine astroviruses, calicivirus, porcine kobuvirus, rotavirus, torque teno sus virus and hepatitis E virus, monitored in a pig production network, from the nursing farms to the end of the fattening farms to portray the excretion patterns of these viruses through the different life stages of pigs. The sampling of healthy piglets alongside piglets with diarrhea in the nursing farms allowed to determine which viruses, or co-infections of viruses were factors of diarrhea at this life stage. The intestinal virome, the viral part of the microbiome, was characterized and viral diversity of porcine enteric viruses at different life stages, as well as between healthy and diarrheic piglets were evaluated. Moreover, the dissemination of the hepatitis E virus in the farm environment, as well as the possible sources of contamination were described, from the indoor and outdoor environment of fattening farms, the slaughterhouse yard and animal transporters. The results obtained in this study described the temporal excretion dynamics of these porcine enteric viruses according to the life stages of the pigs, demonstrating the difference in the excretion of the studied viruses according to the life stage. The calicivirus, as well as the porcine astrovirus groups 3 and 5 were found to be risk factors for diarrhea in the nursing farms. For the first time in Canada, the detection and characterization of porcine kobuvirus strains were evaluated and provided a better understanding of their diversity and the persistence of these strains in the network. The porcine enteric virome diversity was analyzed on a MiSeq sequencing platform and this diversity was different between healthy and diarrheic piglets, as well as between the different life stages. However, the different enzymatic treatments used as pretreatments for fecal samples altered the ability to detect certain single-stranded RNA viruses. Similar strains of the hepatitis E virus were present in the indoor and outdoor environment of the fattening farms, as well as in common places of high circulation from the various stakeholders in the pig production network. The activities in the slaughterhouse yard could therefore be involved in the spread of this virus. This study shed light on enteric viruses infecting pigs. In addition, some of the infections from enteric viruses studied were risk factors for diarrhea in co-infections and will need to be studied in more details to understand their mechanisms, in relation to neonatal diarrhea. More specific interventions during outbreaks of porcine diarrhea of unknown etiology could be carried out, as well as the development of more adapted biosecurity measures according to the life stage of the pigs.