Diseases in marine animals are emerging at an increasing rate. Disease forecasting enabled by virus surveillance presents a proactive solution for managing emerging diseases. Broad viral surveys aid in disease forecasting by providing baseline data on viral diversity associated with various hosts, including many that are not associated with disease. However, these viruses can become pathogens due to expansion in host or geographic range, as well as when changing conditions shift the balance between commensal viruses and the host immune system. Therefore, it is extremely valuable to identify and characterize viruses present in many different hosts in a variety of environments, regardless of whether the hosts are symptomatic or not. The lack of a universal gene shared by all viruses makes virus surveillance difficult, because no single assay exists that can detect the enormous diversity of viruses. Viral metagenomics circumvents this issue by purifying viral particles directly from host tissues and sequencing the nucleic acids, allowing for virus identification. However, virus identification is only the first step, which should ideally be followed by complete sequencing of the viral genome to identify genes of interest and develop assays to reveal viral prevalence, tropism, ecology, and pathogenicity. This dissertation focuses on the discovery of novel viruses in marine animals, characterization of complete viral genomes, and the development of subsequent diagnostic assays for further analysis of virus ecology. First, viral metagenomics was used to explore the viruses present in the healthy Weddell seal (Leptonychotes weddellii) population in Antarctica, which led to the discovery of highly prevalent small, circular single-stranded DNA (ssDNA) viruses. The lack of knowledge regarding the viruses of Antarctic wildlife warrants this study to determine baseline viral communities in healthy animals that can be used to survey changes over time. From the healthy Weddell seals, viral metagenomics led to the discovery of 152 novel anellovirus genomes, encompassing two anellovirus species. Characterizing these viruses is important for understanding the prevalence and diversity of ssDNA viruses, which have only recently been described in marine animals. Furthermore, since emerging diseases can be caused by changing conditions affecting host susceptibility to a virus that was previously not related to disease (opportunistic pathogen), having baseline data allows for quick identification of the pathogen. In addition to determining baseline data, viral metagenomics can explore the role of viruses in disease. A novel virus, Asterias forbesi-associated circular virus (AfaCV), was discovered in the Atlantic sea star Asterias forbesi displaying symptoms of sea star wasting disease (SSWD). AfaCV was the first circular replicase-encoding ssDNA (CRESS-DNA) virus discovered in echinoderms, but it was only present in 10% of SSWD sea stars indicating it is not involved in the development of the disease. This dissertation also focuses on elucidating the role of two previously characterized viruses, chelonid fibropapillomatosis-associated herpesvirus (CHHV5; Chelonid herpesvirus 5, ChHV5) and Zalophus californianus anellovirus (ZcAV), in animal health. PCR amplicon sequencing was used to obtain large portions of the 132 kb genome of ChHV5, the putative etiological agent of the neoplastic sea turtle disease, fibropapillomatosis. Obtaining the genome of ChHV5 from Florida green, Kemp’s ridley, and loggerhead sea turtles provides data for phylogenetic analysis across geographic locations and sea turtle species, as well as a reference for designing downstream molecular assays to examine viral latency. ZcAV was first described from the lungs of captive sea lions involved in a mortality event. PCR could not detect ZcAV in the blood of infected animals, and since sea lions are a protected species, it is not possible to obtain lung biopsies from live sea lions to determine ZcAV prevalence or its role in sea lion health. To answer these important questions, an enzyme-linked immunosorbent assay (ELISA) was developed to detect antibodies to ZcAV in serum from wild sea lion populations. This newly developed ELISA showed that sea lions mount an immune response to ZcAV, and was used to determine the prevalence of ZcAV among wild sea lion populations. This dissertation makes an important contribution to marine science through discovery and characterization of viruses present in healthy and diseased marine animals. Several different methods were used for virus whole-genome sequencing including viral metagenomics, PCR amplicon sequencing, and target enrichment. These findings were expanded upon by developing and using PCR assays and a serological assay to screen for virus prevalence. These methods have implications for viral surveillance and understanding the role of novel viruses in animal health.

Submitted by biblioteca unifenas (biblioteca@unifenas.br) on 2018-03-02T18:56:27Z No. of bitstreams: 1 Rodrigo Felippin dissertação.pdf: 1035260 bytes, checksum: 2e8140a60a20265593d1c98c27337277 (MD5) / Made available in DSpace on 2018-03-02T18:56:27Z (GMT). No. of bitstreams: 1 Rodrigo Felippin dissertação.pdf: 1035260 bytes, checksum: 2e8140a60a20265593d1c98c27337277 (MD5) Previous issue date: 2016-12-08 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Fundação de Amparo à Pesquisa do Estado de Minas Gerais - FAPEMIG / The experiment was conducted with the objective of evaluating the behavior of endemic diseases, which affect the sanity of dairy herds, directly influencing the productive and reproductive results of the animals. Blood samples of 216 animals were evaluated for BoHV-1 Ac, BVD Ac, BVD Ag and Neospora Caninum Ac, from 3 properties of the southern Minas Gerais, which belonged to the Dutch, Jersey and Girolando breeds. The animals were separated and distributed into groups according to the category, age, open days and test titration result. In order to identify the prevalence of these pathogens in the studied properties, the activity of these agents was monitored by the individual serology of the animals. For the BVD virus, 38.4% of the animals were positive, showing a significant effect (P <0.0001), with variation in viral activity ranging from 58% and 44.8% to 9.7%. Searching for viral fragments (antigen), which demonstrates the presence of the BVD virus, only 1 animal from the property with a higher incidence of positive serologies was diagnosed positive. This animal was later confirmed as permanently infected (PI), a condition in which the immune system identifies the virus as a particle of the organism itself, serving as a source of transmission for the herd. For the protozoan Neospora Caninum, 27.3% of the animals were seropositive, and again the property effect (P <0.01) showed higher prevalences (35% and 40%) in the same properties with high BVD indexes. The interpretation of the results obtained for IBR, however, should consider the behavior of a herpes virus, where, once infected, the animal remains infected for life. The indexes found (P <0.001) of positive prevalence ranged from 85.0% to 51.6%. We conclude that these infectious agents act on the reproduction of each property, varying according to the flow of the animals, animal concentration and sanitary aspects. And that the implementation of a health program based on the serological diagnosis is feasible and possible to be incorporated into the routine of the properties. For the BVD to identify the presence of PI animals is fundamental to maintain the health of the herd. / O experimento foi conduzido com objetivo de avaliar o comportamento de doenças endêmicas, que afetam a sanidade dos rebanhos leiteiros, influenciando diretamente nos resultados produtivos e reprodutivos dos animais. Foram avaliadas amostras sanguíneas de 216 animais para BoHV-1 Ac, BVD Ac, BVD Ag e Neospora Caninum Ac, oriundos de 3 propriedades do Sul de Minas Gerais, que pertenciam as raças: Holandês, Jersey e Girolando. Os animais foram separados e distribuídos em grupos de acordo com a categoria, idade, dias em aberto e resultado da titulação dos testes. Com intuito de identificar a prevalência desses patógenos nas propriedades estudadas, a atividade destes agentes foi monitorada pela sorologia individual dos animais. Para o vírus da BVD 38,4% dos animais foram positivos, demonstrando efeito significativo (P<0,0001) de propriedade, com variação da atividade viral desde valores altos como 58% e 44,8% até 9,7%. Pesquisando por fragmentos virais (antígeno), o que demonstra a presença do vírus da BVD, apenas um animal proveniente da propriedade com maior incidência de sorologias positivas foi diagnosticado positivo. Este foi posteriormente confirmado como permanentemente infectado (PI), condição em que o sistema imunológico identifica o vírus como partícula do próprio organismo, servindo de fonte de transmissão para o rebanho. Para o protozoário Neospora Caninum, 27,3% dos animais foram soropositivos e, novamente o efeito de propriedade (P<0,01) revelou maiores prevalências (35% e 40%) nas mesmas propriedades com altos índices para BVD. A interpretação dos resultados obtidos para IBR, no entanto, deve ser considerada a partir do comportamento de um herpes vírus, onde, uma vez infectado, o animal permanece assim por toda a vida. Os índices encontrados (P<0,001) de prevalências positivas variaram com resultados entre 85,0% a 51,6%. Concluímos que esses agentes infecciosos atuam na reprodução de cada propriedade, variando de acordo com o fluxo dos animais, concentração de animais e aspectos sanitários. E que a implantação de um programa sanitário baseado no diagnóstico sorológico, é viável e possível de ser incorporada na rotina das propriedades. Para a BVD identificar a presença de animais PI é fundamental para manter a saúde do rebanho.

As infecções pneumocócicas são uma importante causa de morbi-mortalidade entre as crianças. Até 2000, era disponível apenas a vacina pneumocócica polissacarídica 23valente, de uso a partir dos 2 anos de idade. Essa vacina era recomendada para crianças com fibrose cística (FC) e para as asmáticas em uso de corticóide oral, dentre outras recomendações. A partir de 2000, licenciou-se a vacina pneumocócica conjugada 7valente, com grande impacto contra infecções causadas pelos sorotipos vacinais. Nos países onde as crianças não são universalmente vacinadas com essa vacina, as recomendações permanecem as mesmas. Atualmente, os adultos asmáticos estão incluídos nas recomendações para vacinação pneumocócica nos EUA. Há poucos estudos sobre o risco de doença pneumocócica em crianças asmáticas per si e naquelas com fibrose cística e sobre a resposta à vacina pneumocócica conjugada. Salienta-se que ainda não há um critério estabelecido para avaliar a resposta sorológica a essa vacina. Recentemente, foi sugerido o critério de 0,35mcg/ml por Elisa para se correlacionar com proteção para doença invasiva pneumocócica. Objetivou-se determinar a concentração dos anticorpos contra os sorotipos vacinais contidos na vacina pneumocócica conjugada 7valente em crianças com asma moderada em uso de corticóide inalatório e em crianças com fibrose cística; avaliando-as pelos critérios de 0,35mcg/ml, 1,3mcg/ml e aumento de 4 vezes o título pós em relação ao pré-vacinal, para cada sorotipo e para a vacina, considerando-se a positividade para 5 sorotipos. Foram avaliadas 18 crianças em cada grupo. A mediana da idade foi de 82,5m nas asmáticas e 69,5m naquelas com FC. Foi colhida amostra para sorologia pré-vacinação e outra após 2 doses da vacina conjugada. As concentrações de anticorpos para os sorotipos vacinais foram quantificadas pelo Elisa. Para 0,35mcg/ml de corte, a grande maioria nos dois grupos já era positiva à inclusão para os sorotipos vacinais e à vacina. Considerando-se o valor de 1,3mcg/ml, entre os que eram negativos, as crianças asmáticas responderam entre 66,7% (9V) e 100% (14), e as com FC, entre 50% (19F) e 100% (6B e 14); e, em relação à resposta vacinal para esse nível, as asmáticas apresentaram 81,8% de resposta, enquanto as com FC, 91,7%. Avaliando-se pelo aumento de 4 vezes o título pós em relação ao pré-vacinal, a melhor resposta aos sorotipos, nos asmáticos, foi de 33,3% (4, 6B, 14 e 18C), e a nos com FC, 61,1% para o 6B; em termos de resposta vacinal, obteve-se 16,7% e 44,4%, para as asmáticas e aquelas com FC, respectivamente. Não houve interferência da vacinação prévia com a vacina pneumocócica polissacarídica. As medianas dos títulos pós em relação aos pré-vacinais, para os sorotipos, nos dois grupos, apresentaram um aumento significante. Apesar de boa parte das crianças apresentarem uma positividade elevada à inclusão, aquelas que eram negativas tenderam a apresentar uma boa resposta à vacina. / Pneumococcal infections are an important morbi-mortality cause among children. Until 2000, it was only available the 23-valent polysaccharide pneumococcal vaccine for children over two years old. This vaccine was recommended for cystic fibrosis (CF) children and to asthmatics children in use of oral corticosteroids, among other recommendations. From 2000, it was licensed the 7-valent conjugated pneumococcal vaccine, with a great impact against the infections caused by the vaccine serotypes. In the countries that dont make a universally use of this vaccine for children, the recommendations remain the same. At the present time, asthmatic adults are included for the pneumococcal vaccine recommendations in the United States. There are few studies about pneumococcal disease risk with cystic fibrosis children and asthmatics, per si, and about the conjugated pneumococcal vaccine response. It points out that there are no a definitive criteria or evaluation established for the serology response for this vaccine. It was suggested, recently, that the level of 0,35mcg/ml, measured by ELISA, is adequate to correlate with the invasive pneumococcal disease protection. The goal of this study was to determine the antibodies concentration of the seven vaccine serotypes from 7-valent conjugated pneumococcal vaccine among children with moderate asthma in use of inhaled corticosteroids and with cystic fibrosis. It was considered the dosage 0,35mcg/ml and 1,3mcg/ml levels and the four-fold increase between pre- and post-immunization concentrations levels, to each serotype and to the vaccine (positivity for five serotypes or more) for positivity. Eighteen children were included in each study group. The age median was 82,5 months for the asthmatics and 69,5 months for the CF children. A blood sample was taken for pre-immunization serology and a second one after the second vaccine dose was given. The antibodies concentrations for the vaccine serotypes were measured by ELISA. Considering the 0,35mcg/ml levels, the majority of children, in both groups, was positive for vaccine serotypes and for the vaccine as well in the beginning. At the 1,3mcg/ml level, among the children with negative serology, asthmatic children responded between 66,7% (9V) and 100% (14), and those with CF, between 50% (19F) and 100% (6B e 14). Related to the vaccine response for this level, the asthmatics had a 81,8% response, while the CF childrens response was 91,7%. Evaluating for the four-fold increase between pre- and post-immunization concentrations, the best response observed for the vaccine serotypes was 33,3% (4, 6B, 14 e 18C) for the asthmatics. In the CF group the best result was 61,1% (6B). In terms of the vaccine response, it was observed that 16,7% and 44,4% were the results for both the asthmatics and CF group, respectively. The polysaccharide vaccine didnt interfere in the results. The medians of the pre- and post-immunization antibodies concentrations for the vaccine serotypes, in both groups, were significantly increased. Despite those children that were already positive for the criteria evaluated, at the first moment of the study, for those children that were negative, the majority had a positive serology towards the vaccination response.

Einführung Die Prävalenz der alveolären (AE) und zystischen Echinokokkose (CE) in Deutschland nimmt zu, aber die Gesamtzahl der Fälle in den nördlichen und östlichen Bundesländern ist noch immer gering. Betroffene Patienten werden überwiegend in wenigen spezialisierten Zentren in Süddeutschland behandelt, sodass in anderen Regionen Deutschlands bislang nur relativ wenig klinische Erfahrung mit AE und CE vorhanden ist. Ziele Ziel unserer Studie war es, das derzeitige Management von Patienten mit Verdacht auf oder bestätigter Echinokokkose an einem Zentrum der tertiären Versorgungsstufe in einer Niedrigprävalenzregion zu bewerten, um eine Verbesserung des Vorgehens bei Verdacht auf AE/CE bzw. bereits gesicherter Diagnose zu erreichen. Methodik Alle Patienten, die am Universitätsklinikum Leipzig zwischen dem 01.01.2004 und dem 30.09.2018 infektionsserologisch auf Echinokokken untersucht wurden oder die Diagnose „AE“ bzw. „CE“ erhalten hatten, wurden in eine retrospektive Kohortenstudie eingeschlossen. Klinischer Verlauf, bildgebende sowie histopathologische Befunde, Therapiecharakteristika, relevante Begleiterkrankungen und mögliche Risikofaktoren für AE bzw. CE wurden bewertet. Die Datenanalyse umfasste weiter eine zeitlich gestaffelte Prävalenzabschätzung für unser Zentrum sowie Sensitivitäts- und Spezifitätsberechnungen für die durchgeführten serologischen Tests. Ergebnisse Insgesamt wurden 382 Patienten in die Analyse einbezogen. 11 AE- und 7 CE-Fälle wurden identifiziert. Die mittlere Prävalenzrate der AE in dieser Kohorte lag bei 2,9 % und die der CE bei 1,8 %. Bei 4 Patienten war die Diagnose bereits auswärtig gesichert worden und eine gezielte Überweisung zur spezialisierten Behandlung erfolgt. 56 % der Patienten wiesen bekannte Risikofaktoren für CE bzw. AE auf. Mit Ausnahme eines Falls waren alle CE-Fälle Migranten mit ausländischer Herkunft. Die durchgeführten serologischen Tests zeigten für beide Erkrankungen eine Sensitivität von 86 % und eine Spezifität von 91 %. 2 Patienten mit zunächst falsch negativer Diagnose (einer mit AE und einer mit CE) wurden durch ultraschallgestützte Biopsie korrekt diagnostiziert. Alle CE-Fälle und 5 AE-Fälle (45 %) wurden unter Albendazolschutz chirurgisch versorgt. Die restlichen 6 AE-Fälle erhielten eine Langzeitbehandlung mit Albendazol. Es wurden keine Todesfälle infolge Echinokokkose beobachtet. Schlussfolgerungen Sowohl AE als auch CE sind im Großraum Leipzig seltene Erkrankungen, wenngleich ein Anstieg der Fallzahlen an unserem Zentrum zu verzeichnen ist. Aufgrund unterschiedlicher begünstigender Faktoren wie z. B. Zunahme der Migration ist in Zukunftmit einemweiteren Anstieg zu rechnen. Diagnosestellung und Therapiemanagement stellen sowohl für die AE als auch für die CE eine Herausforderung dar und sollten von einem Expertenteam begleitet werden, darunter erfahrene Infektiologen, Bildgebungsspezialisten und versierte hepatobiliäre Chirurgen. Der Aufbau eines deutschen Echinokokkosenetzwerks wäre sinnvoll.

Orientador: Carlos Roberto Teixeira / Resumo: A leptospirose é uma zoonose potencialmente fatal causada por bactérias do gênero Leptospira. Espécies animais hospedeiras adaptadas a sorovares específicos podem ser portadoras e dispersoras ambientais da bactéria. De 2009 a 2011, 45 mamíferos silvestres (39 gambás Didelphis albiventris, quatro ouriços Sphiggurus villosus, um ratão-do-banhado Myocastor coypus e uma capivara Hidrochoerus hidrochaeris) encontrados por munícipes em áreas antrópicas de Monte Mor, SP, foram capturados, contidos e tiveram amostras de soro coletadas para detecção de anticorpos para Leptospira. As amostras foram tituladas pela técnica de soroaglutinação microscópica (MAT) para diferentes sorogrupos. Um total de 35,56% (16/45) animais foram reagentes para presença de anticorpos para Leptospira para um total de 11 sorogrupos diferentes. O sorovar dominante mais frequente, dentre os 12 identificados, foi o Icterohaemorrhagiae (6/16), seguido de Gryppotyphosa (4/16) e Pyrogenes (2/16). Didelphis albiventris, espécie mais abundante no estudo, apresentou uma prevalência de 35,9% (14/39) de anticorpos para Leptospira, enquanto S. villosus teve 0% (0/4) e M. coypus (1/1) e H. hidrochaeris (1/1) 100%. Dentre os Didelphis albiventris avaliados, houve maior frequência de reatividade sorológica à Leptospira interrogans, sorogrupos Icterohaemorrhagiae, com 35,71% (5/14) e Gryppotyphosa com 28,57% (4/14), indicando contaminação ambiental por tais leptospiras e a possibilidade de exposição e infecção de humanos e ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Leptospirosis is a potentially fatal zoonosis caused by Leptospira bacteria. Some animal host species are adapted to specific serovars being potential carriers and environmental dispersers. From 2009 to 2011, 45 wild mammals (39 opossums Didelphis albiventris, four porcupines Sphiggurus villosus, one coypu Myocastor coypus and one capybara Hidrochoerus hidrochaeris) found by citizens in anthropic areas of Monte Mor municipality were captured, contained and had sera samples collected for Leptospira antibody detection. The samples were titrated by the microagglutination technique (MAT) for different serogroups. A total of 35.56% (16/45) animals were reactive for Leptospira antibodies for 11 different serogroups. The most frequent serovar, among the 12 identified, was Icterohaemorrhagiae (6/16), followed by Gryppotyphosa (4/16) and Pyrogenes (2/16). Didelphis albiventris, the most abundant species in the study, had a prevalence of 35.9% (14/39) for Leptospira antibodies, while S. villosus had 0% (0/4), M. coypus (1/1) and H. hydrochaeris (1/1) 100%. Among the seropositive D. albiventris, 35.71% (5/14) and 28.57% (4/14) seroreacted for Leptospira interrogans species, serogroups Icterohaemorrhagiae and Gryppotyphosa respectively, indicating environmental contamination by these bacteria and the possibility of exposure and infection of humans and domestic animals in the studied area. / Mestre

The prevalence of Brucella canis in South Africa is unknown and suspected to be under-detected. The majority of dogs in South Africa are not tested for Brucella canis, not only because of the level of awareness of Brucella canis in South Africa, but also because of the lack of clinical suspicion. It is not known how the infection entered South Africa. Brucella canis, a zoonotic organism that causes canine brucellosis in dogs, is a significant cause of reproductive failure in dogs worldwide. Canine brucellosis is a chronic infectious zoonotic disease whose main etiological agent, the Brucella canis bacterium, are rough, intracellular proteobacteria in the Brucellaceae family. Clinical signs in bitches are mainly infertility and abortion, while in males, epididymitis and orchitis occur. However, discospondylitis may develop in both sexes. A serological survey was conducted to determine the prevalence of Brucella canis infection in dogs from the Nelson Mandela Bay Metropolitan (NMBM) Port Elizabeth (PE) area. A total of 400 samples were collected, 350 of which were collected in seven different townships and 50 were collected in the three different welfare organisations in the study area. Of the 400 serum samples collected, 39 (9.75%) tested serologically positive by using the Tube Agglutination Test (TAT), the 2-Mercaptoethanol-TAT (2ME-TAT) or the Compliment Fixation Test (CFT). The results of the CFT showed that nine of the 39 positive samples had a maximum antibody titre of 784 IU/ml. The prevalence rate varied tremendously between the samples from the townships and those from the welfare organisations. The prevalence rate of seropositive animals in PE ranged between 5% and 16% in the study area. No positive cases were found in KwaMagxaki and the Animal Welfare Society of PE, but both were surrounded by areas that had positive cases of Brucella canis infection. The female dogs in the study area had a higher sero-prevalence of only 0.0169 (95% CI, 0.0631 to 0.1489) differences in proportion, and were thus not significant (p > 0.05). However, the female spayed dogs had a much higher significant difference of 0.1898 (95% iv CI, 0.1058 to 0.2738) in proportion to the male neutered dogs and were thus statistically significant (p < 0.05). Despite those results, out of all the dogs positive for Brucella canis only two were neutered males and five were spayed females, and the rest were all intact. In conclusion, according to the results, Brucella canis antibodies were detected in sera of dogs mostly from the townships surveyed. Preventive measures against this contagion should be taken into consideration to eliminate Brucella canis infection from the entire dog population. Reservoir dogs and actively infected dogs either should be kept in quarantine or should be euthanized, because not only can they spread the disease and end the reproductive life of any breeding animal, but they are also a risk to human health. Even though this is the first survey conducted in the Eastern Cape, the results are still high dogs in the study area had a higher sero-prevalence of only 0.0169 (95% CI, 0.0631 to 0.1489) differences in proportion, and were thus not significant (p > 0.05). However, the female spayed dogs had a much higher significant difference of 0.1898 (95% iv CI, 0.1058 to 0.2738) in proportion to the male neutered dogs and were thus statistically significant (p < 0.05). Despite those results, out of all the dogs positive for Brucella canis only two were neutered males and five were spayed females, and the rest were all intact. In conclusion, according to the results, Brucella canis antibodies were detected in sera of dogs mostly from the townships surveyed. Preventive measures against this contagion should be taken into consideration to eliminate Brucella canis infection from the entire dog population. Reservoir dogs and actively infected dogs either should be kept in quarantine or should be euthanized, because not only can they spread the disease and end the reproductive life of any breeding animal, but they are also a risk to human health. Even though this is the first survey conducted in the Eastern Cape, the results are still high / College of Agriculture and Environmental Sciences / M. Sc. (Agriculture)

Les virus géants d'amibes( Acanthamoeba) sont des virus à ADN double brin . Ces virus géants ont été isolés depuis 2008 essentiellement à partir de prélèvements d'eaux et sols) collectés dans diverses régions géographiques à travers le monde, ou à partir de prélèvements humains (selle, liquide broncho-alvéolaire et sang). Ils sont repartis en 4 familles virales dont les plus représentées sont les familles Mimiviridae et Marseilleviridae avec pour membres fondateurs respectifs Mimivirus et Marseillevirus et comptent à ce jour respectivement 44 et 20 isolats. Les virus géants d'amibes sont ubiquitaires dans notre biosphère, et les êtres humains y sont potentiellement exposés. Au cours de cette Thèse, nous avons premièrement écrit une revue de la littérature décrivant les outils de mise en évidence des virus géants d'amibes chez l'homme incluant la sérologie, la culture, la PCR ou l'hybridation de sondes fluorescentes in situ. Deuxièmement, nous avons conçu et évalué 5 systèmes de PCR en temps réel détectant les membres des groupes de mimivirus d'amibes, leurs virophages et les marseillevirus. Nous avons participé à un 3ème travail décrivant les différentes procédures d'isolement sur amibes utilisées jusqu'à présent dans notre laboratoire . Enfin, dans un 4ème travail préliminaire, nous avons recherché par PCR la présence des mimivirus et marseillevirus dans 701 plasmas de patients infectés par HIV-1.Au total, nos travaux ont décrit les mises au point, performances et limites des tests de PCR pour l'étude des virus géants, et ont contribué aux outils et fourni des éléments pour l'étude de l'implication des virus géants d'amibes en pathologie humaine. / The giant viruses of amoebas( Acanthamoeba) are double stranded DNA viruses. These giant viruses have been isolated essentially from water and soil samples collected in various geographic regions around the world or from human samples (stool, blood and bronchoalveolar fluid). These giant viruses are divided into four viral families among which those comprising the largest number of representatives are the Mimiviridae and Marseilleviridae families, whose respective founders are Mimivirus and Marseillevirus and comprise 44 and 20 representative members, respectively. Giant viruses of amoeba are ubiquitous in our biosphere, which means that humans can be exposed to them. In this Thesis, we initially wrote a review of the literature describing the tools to detect the present of these giant viruses in humans, including serology, culture isolation, PCR and fluorescence in situ hybridization (FISH). Secondly, we designed and evaluated the performance of five real-time PCR systems targeting the members of the 3 groups of mimiviruses of amoeba, their virophages and the marseilleviruses. We were involved in a third work that described the different isolation procedures on amoebae used so far in our laboratory for giant viruses. Finally, in a fourth preliminary work, we looked by PCR for the presence of mimiviruses and marseilleviruses DNA in 701 plasma from patients infected with HIV-1. In summary, our work described the developed PCR assays for the study of giant viruses, and their performance and limitations, and it contributed to the tools and evidence for the study of the involvement of the giant amoeba virus in human pathology.

L'objectif de cette thèse est le développement d'un vaccin recombinant capripoxvirus protégeant contre la variole des ruminants, la Fièvre de la Vallée du Rift (FVR) et la Peste des Petits Ruminants (PPR) comme modèle vaccinal destiné aux pays atteints par ces infections. Une première partie de ce travail a consisté en une enquête sérologique en Tunisie pour évaluer les prévalences PPR et FVR. L'enquête menée a montré une séroprévalence PPR de 7,6% et l'absence de FVR. Le risque lié à une infection par le virus de la fièvre de la vallée du Rift n'est pas nul en raison de l'identification des vecteurs compétents Culex theileri et Culex pipiens dans les zones échantillonnées. L'élaboration du vaccin capripoxvirus FVR-PPR porte sur l'expression des gènes NSmGN-FVR et H-PPR où chacune des valences est insérée dans le site de la thymidine kinase et le site d'un analogue du récepteur à l'interleukine 8 respectivement. Le vecteur choisi pour la souche vaccinale Kenya Sheeppox-1. Bien que nos travaux aient conduit à l'obtention du capripoxvirus double recombinant, ce dernier n'a pu être purifié. L'alternative a donc été d'évaluer l'effet protecteur et l'immunogénicité induits par le simple recombinant capripoxvirus- NSmGN-FVR, qui est un produit de l'étape intermédiaire dans l'élaboration du double recombinant FVR-PPR. L'effet protecteur de notre construction a été validé par deux expérimentations chez des souris Mus m. musculus MBT/Pas, avec épreuve infectieuse. Le nombre de doses administrées, les voies d'administration ont été déterminants dans cette protection justifiée par l'obtention d'anticorps neutralisants anti-FVR. L'étude de l'immunogénicité a été réalisée sur un modèle caprin sans épreuve infectieuse, une séroconversion FVR a été observée. La lymphoprolifération et le typage des sous populations lymphocytaires ont été analysés. / The aim of this thesis was to develop a capripoxvirus based recombinant vaccine against ruminant pox, Rift Valley fever (RVF) and peste des petits ruminants (PPR) considered as a vaccine model for countries affected by these infections. The first part of the work consisted in a serological survey conducted in Tunisia to detect the PPR and RVF presence. A PPR seroprevalence of 7.6% has been found and no antibodies against RVF were detected. However, the risk of infection with rift valley fever virus persists since competent vectors such as Culex pipiens and Culex theileri has been identified in the sampled areas. The development of the RVF-PPR vaccine candidate is based on the NSmGN-FVR and H-PPR gene expression - where each of the genes is inserted into the thymidine kinase and the Interleukin 8 receptor analogue genes, respectively. The vector chosen is the vaccine strain Sheeppox Kenya-1. Although the double recombinant RVF-PPR has been produced, it could not be purified. The alternative was to evaluate the protection and the immunogenicity of the single recombinant capripoxvirus NSmGN-FVR, which is a product of an intermediate step of the process of the double recombinant preparation. The protection of our vaccine candidate has been performed by two mice experiments in Mus m. musculus MBT/Pas, with challenge. The number of doses, the route of administration played a key role in the protection confirmed by the presence of neutralizing anti-RVF antibodies. The study of the immunogenicity of the vaccine candidate was conducted in goats without challenge, RVF seroconversion has been shown. Lymphoproliferation studies and lymphocytes subpopulations typing have been analysed.

Introdução e Objetivos: A Hepatite pelo Vírus E (HEV) é uma infecção conhecida mundialmente por ter seu curso assintomático e autolimitado na maioria dos casos. Nos últimos anos, casos de evolução para cronicidade têm sido descritos envolvendo população de pacientes imunocomprometidos, particularmente os transplantados de órgãos sólidos. A prevalência da infecção pelo HEV na população de transplantados de fígado é ainda desconhecida em nosso meio. Pacientes e Métodos: Nós avaliamos parâmetros de infecção pelo HEV (HEV RNA, anti-HEV IgM e anti-HEV IgG) em uma coorte de 294 adultos transplantados de fígado seguidos no HCFMUSP. Para pesquisa dos anticorpos foi utilizada a metodologia ELISA (RecomWell HEV IgM/ IgG da Mikrogen®), sendo os resultados indeterminados e com IgM isoladamente positivo confirmados por Immunoblotting (RecomLine IgM/ IgG da Mikrogen®). Para pesquisa do HEV RNA utilizou-se a metodologia de PCR em tempo real One-Step com primers e sondas que amplificam um fragmento da ORF3 do genoma viral. Foram avaliados dados demográficos e laboratoriais de toda população de transplantados. Posteriormente, foram analisadas apenas as biópsias hepáticas de 122 pacientes transplantados devido à Hepatite pelo Vírus C (VHC) possuidores ou não de marcadores sorológicos ou moleculares do HEV de acordo com a classificação METAVIR. Resultados: Amostras de 8,2% (24/294) dos pacientes foram positivas para anti-HEV IgG, 2% (6/294%) positivas para anti-HEV IgM e 5,8% (17/274) mostraram positividade para o HEV RNA. Apenas um paciente mostrou positividade tanto para anti-HEV IgM quanto para o anti-HEV IgG. Setenta e sete vírgula oito por cento (95/122) dos pacientes transplantados pelo VHC foram tratados com esquema que incluía ribavirina por um período mínimo de 6 meses antes da coleta do sangue. Dentre os transplantados pela cirrose por VHC que apresentaram positividade para o anti-HEV IgG apenas 37,5% (3/122) mostraram níveis de fibrose maior que 2, enquanto que 41,7% (5/122) dos positivos para o HEV RNA demonstraram níveis de fibrose maior que 2. Em geral, a prevalência do HEV no cenário pós transplante hepático parece ser baixa podendo não trazer um dano histológico significativo no cenário pós transplante. Conclusão: Nós concluímos que apesar de alguns estudos demonstrarem riscos de cronificação pelo HEV, esse vírus tem baixa prevalência em nosso meio e os pacientes transplantados de fígado pelo VHC que apresentaram marcadores sorológicos ou moleculares para o HEV não tiveram níveis mais acentuados de fibrose quando comparados com os pacientes que não apresentaram indícios de infecção pelo HEV no momento da análise / Background and Aims: Hepatitis E Virus (HEV) is an infection known worldwide for its asymptomatic and self-limited course in most of the cases. In the last five years, cases evolving to chronicity have been described involving immunosuppressed patients, especially in recipients of solid organs transplants. The HEV infection prevalence in liver transplanted patients has yet to be fully assessed by our community. Patients and Methods: We evaluated laboratory parameters for the HEV infection (HEV RNA, anti-HEV IgM and anti-HEV IgG) in a cohort of 294 adult patients who had liver transplants on the HCFMUSP (Clinical Hospital of University of São Paulo School of Medicine). In order to investigate the antibodies, we used Elisa methodology (RecomWell HEV IgM/ IgG by Mikrogen®) and the indeterminate results and isolates positive anti-HEV IgM were confirmed by immunoblotting (RecomLine IgM/ IgG by Mikrogen®). For screening of HEV RNA, One-Step PCR in real time was used with primers and probes that amplify a fragment of the ORF3 from the viral genome. Laboratory and demographic data were collected in the entirety of the transplanted population. Following that, the hepatic biopsies of 122 patients transplanted due to Hepatitis C (HCV) were analysed with or without serological or molecular markers of HEV according to METAVIR score. Results: Serological samples of 24 (8.2%) of the patients tested positive for anti-HEV IgG, 06 (2%) were positive for anti-HEV IgM and 17 (5.8%) showed positive results for HEV RNA. Only one patient showed positive results for both anti- HEV IgM and anti-HEV IgG. Also, 95 (77.8%) of the patients transplanted because of the HCV infection received treatment including Ribavirin for at least 6 months before the blood sample collection. Among the transplanted patients due to HCV cirrhosis who presented positive results for anti-HEV IgG, only 3 (37.5%) showed fibrosis beyond stage 2, while 5 (41.7%) of the HEV RNA positive patients had liver fibrosis higher than 2. Conclusion: Overall, the prevalence of HEV in the post-hepatic transplant scenario appears to be low, seemingly not harmful histologically in the post-transplant cases. We have concluded that although some studies showed risks of HEV chronification, patients who had their livers transplanted due to HCV who showed serological or molecular markers for HEV did not have higher levels of fibrosis when compared to patients who showed no indications of HEV infection at the time of the analysis

Com o objetivo de avaliar os equinos alojados no Jóquei Clube de São Paulo, Brasil, quanto a presença de anticorpos contra Theileria equi e Babesia caballi, foram testadas 180 amostras de soro sanguíneo por meio da técnica de C-ELISA (Competitive Enzyme-Linked Immunosorbent Assay), metodologia atualmente recomendada pela OIE (Organização Internacional de Epizootíases) por ter alta sensibilidade e especificidade. A frequência de animais com sorologia positiva para Theileria equi foi de 6,66% (12/180), para Babesia caballi foi de 22,3% (40/180) e para infecção concomitante foi de 6,66% (12/180). Os resultados sorológicos obtidos por este estudo revelam que 35,5% (64/180) dos animais possuem anticorpos contra a babesiose equina sendo que a maioria dos animais acometidos tem dois e três anos de idade e portanto estão há menos tempo no hipódromo. Fatores como a ausência de carrapatos vetores, o uso de terapias babesicidas repetidas e o longo tempo de permanência dos animais no Jóquei após o tratamento, favorecem a diminuição dos títulos de anticorpos sem que ocorra reinfecção. Esses fatores podem justificar o menor número de animais com sorologia positiva para a doença nos cavalos com idade acima de quatro anos. Considerando-se esses resultados sugere-se que os animais sejam avaliados sorologicamente ao ingressarem no Jóquei Clube de São Paulo para que o uso de medicamentos contra a doença seja feito de forma adequada e para que os sinais clínicos compatíveis com babesiose equina em animais sorologicamente negativos sejam melhor avaliados e considerados em diagnósticos diferenciais. / In order to evaluate the presence of antibodies against Theileria equi and Babesia caballi in horses kept at the Jockey Club in São Paulo city, Brazil, a total of 180 samples of blood serum was tested using the Competitive Enzyme-Linked Immunosorbent Assay (C-ELISA test). This methodology has been recommended by the International Organization of Epizooties (IOE) due to its high sensitivity and specificity. The frequency of seropositive animals for Theileria equi, Babesia caballi and for both was 6.66% (12/180), 22.3% (40/180) and 6.66% (12/180), respectively. Serological results showed that 35.5% of the animals (64/180) had antibodies against equine piroplasmosis; they were from two to three years old and were at the Jockey Club for a shorter period of time. Factors such as absence of thick vectors, repeated therapy using babesicidal drugs and the long period of time that the animals stayed in the Jockey Club after treatment favoured the lowering of antibody titers with no reinfection. These factors might be responsible for the fewer number of animals with positive serology for the disease in horses over four years of age. Based on these findings, animals should be serologically evaluated at the time of entrance into the Jockey Club so that the use of drugs against the disease be performed properly and clinical signs suggestive of equine babesiosis in serologically negative animals be better evaluated and considered for differential diagnosis.