Doenças infecciosas emergentes se caracterizam como enfermidades cujos patógenos evoluíram para uma nova cepa ou genótipo capaz de infectar tanto o mesmo hospedeiro quanto uma nova espécie. A ocorrência de doenças emergentes tem sido correlacionada à destruição de habitats e à perda de biodiversidade. As aves marinhas têm sido consideradas bons indicadores e sentinelas do ecossistema aquático, e uma ampla variedade de enfermidades virais têm sido investigadas e descritas em aves no mundo todo. A caracterização e o entendimento das enfermidades virais que acometem as aves marinhas que habitam a costa brasileira são de fundamental importância para a compreensão de possíveis surtos de mortalidade dentre outros fatores que interferem na conservação das aves em geral. O objetivo desta pesquisa foi investigar a ocorrência de herpesvírus, avipoxvírus e coronavírus nas espécies de aves marinhas que foram reabilitadas em três centros localizados ao longo da costa brasileira e nas colônias reprodutivas de Sula sp. e Phaeton sp. localizadas no arquipélago de Abrolhos, Bahia, Brasil, e em quatro colônias de Spheniscus magellanicus localizadas na Patagônia argentina. As análises virais foram realizadas pela técnica de PCR e RT-PCR e confirmadas pela reação de sequenciamento do amplicon identificado. Nos casos de óbito, as alterações histopatológicas foram identificadas por meio de análise microscópica. O estudo revelou a ocorrência dos três agentes virais identificados em centros de reabilitação no Brasil, além da ocorrência de herpesvírus nas populações de vida livre e ativas em seus sítios reprodutivos. Foram identificados quatro novos herpesvírus denominados: Magellanic penguin herpesvirus 1 (MagHV -1) causador de um surto de mortalidade associado a traqueíte necrótico-hemorrágica em pinguins de Magalhães em reabilitação; Magellanic penguin herpesvirus 2 (MagHV-2), identificado em pinguins de Magalhães aparentemente saudáveis nas colônias reprodutivas da Patagônia argentina; Sulid herpesvirus 1 (SuHV -1), identificado em atobás (Sula sp.) e grazinas (Phaeton sp.) nas colônias reprodutivas de Abrolhos e Thalassarchid herpesvirus 1 (ThHV -1), identificados em um albatroz de nariz amarelo (Thalassarche chlororhynchos) nas praias de Rio Grande, RS, Brasil. Também foram identificados: um novo avipox, denominado Brazilian penguinpox, causador de lesões cutâneas, esofágicas e respiratórias nos pinguins de Magalhães cutâneas, esofágicas e respiratórias nos pinguins de Magalhães em reabilitação em Santa Catarina e a identificação de dois Gammacoronavirus em três diferentes espécies assintomáticas que estavam em reabilitação em Santa Catarina e no Rio Grande do Sul. Os dados obtidos constituem uma base de informação útil para estudos futuros no campo da patologia, virologia, epidemiologia e dos impactos antrópicos na saúde das aves marinhas do cone sul. / Emerging infectious diseases are characterized as disease whose pathogens progressed to a new strain ar genotype capable of infecting the same host or a new species. The occurrence of emerging diseases has been correlated to the destruction of habitats and loss of biodiversity. Seabirds have been considered as good indicators and sentinels of aquatic ecosystem, and a wide variety of viral diseases have been investigated and described in birds worldwide. The characterization and understanding of viral diseases that affect seabirds that inhabit the Brazilian coast are of fundamental importance for the understanding of possible mortality outbreaks among other factors that influence the conservation of birds in general. The objective of this research was to investigate the occurrence of herpesvirus, coronavirus and avipoxvirus in seabird species that were rehabilitated in three centres located along the Brazilian coast and in breeding colonies of Sula sp. and Phaeton sp. located at the Abrolhos’s archipelago, Bahia, Brazil and four Spheniscus magellanicus's colonies located at Argentina's Patagonia. Viral analyzes were performed by PCR and RT-PCR and confirmed by sequencing the identified amplicon. In cases of death, the histopathological alterations were identified through optical microscopic analysis. The study revealed the occurrence of the three investigated viral agents in the Brazilian rehabilitation centres, besides the occurrence of herpesvirus in the freeliving and reproductive active seabird’s populations. Four new herpesvirus were identified and called: Magellanic penguin herpesvirus 1 (MagHV -I), causing a mortality outbreak associated with necrotic-hemorrhagic tracheitis in Magellanic penguins in rehabilitation process; Magellanic penguin herpesvirus 2 (MagHV-2), identified in apparently healthy breeding Magellanic penguins at the Argentinean Patagonia’s colonies; Sulid herpesvirus 1 (SuHV-l), identified in boobies (Sula sp.) and tropicalseabirds (Phaeton sp.) breeding colonies at Abrolhos Archipelago, and Thalassarchid herpesvirus 1 (ThHV -1), identified in a yellow nose albatross (Thalassarche chlororhynchos) that appeared on the beaches of Rio Grande, RS, Brazil. Were. also identified: a new avipox named Brazilian penguinpox causing cutaneous, esophagus and respiratory lesions in rehabilitation penguins at Santa Catarina and the identification of two Santa Catarina and the identification of two Gammacoronavirus in three different asymptomatic seabirds species that were undergoing rehabilitation in Santa Catarina and Rio Grande do Sul. The data provi de a useful information basis for further studies related to pathology, virology, epidemiology and human impacts on southern hemispheres seabirds’ health.

Doenças infecciosas emergentes se caracterizam como enfermidades cujos patógenos evoluíram para uma nova cepa ou genótipo capaz de infectar tanto o mesmo hospedeiro quanto uma nova espécie. A ocorrência de doenças emergentes tem sido correlacionada à destruição de habitats e à perda de biodiversidade. As aves marinhas têm sido consideradas bons indicadores e sentinelas do ecossistema aquático, e uma ampla variedade de enfermidades virais têm sido investigadas e descritas em aves no mundo todo. A caracterização e o entendimento das enfermidades virais que acometem as aves marinhas que habitam a costa brasileira são de fundamental importância para a compreensão de possíveis surtos de mortalidade dentre outros fatores que interferem na conservação das aves em geral. O objetivo desta pesquisa foi investigar a ocorrência de herpesvírus, avipoxvírus e coronavírus nas espécies de aves marinhas que foram reabilitadas em três centros localizados ao longo da costa brasileira e nas colônias reprodutivas de Sula sp. e Phaeton sp. localizadas no arquipélago de Abrolhos, Bahia, Brasil, e em quatro colônias de Spheniscus magellanicus localizadas na Patagônia argentina. As análises virais foram realizadas pela técnica de PCR e RT-PCR e confirmadas pela reação de sequenciamento do amplicon identificado. Nos casos de óbito, as alterações histopatológicas foram identificadas por meio de análise microscópica. O estudo revelou a ocorrência dos três agentes virais identificados em centros de reabilitação no Brasil, além da ocorrência de herpesvírus nas populações de vida livre e ativas em seus sítios reprodutivos. Foram identificados quatro novos herpesvírus denominados: Magellanic penguin herpesvirus 1 (MagHV -1) causador de um surto de mortalidade associado a traqueíte necrótico-hemorrágica em pinguins de Magalhães em reabilitação; Magellanic penguin herpesvirus 2 (MagHV-2), identificado em pinguins de Magalhães aparentemente saudáveis nas colônias reprodutivas da Patagônia argentina; Sulid herpesvirus 1 (SuHV -1), identificado em atobás (Sula sp.) e grazinas (Phaeton sp.) nas colônias reprodutivas de Abrolhos e Thalassarchid herpesvirus 1 (ThHV -1), identificados em um albatroz de nariz amarelo (Thalassarche chlororhynchos) nas praias de Rio Grande, RS, Brasil. Também foram identificados: um novo avipox, denominado Brazilian penguinpox, causador de lesões cutâneas, esofágicas e respiratórias nos pinguins de Magalhães cutâneas, esofágicas e respiratórias nos pinguins de Magalhães em reabilitação em Santa Catarina e a identificação de dois Gammacoronavirus em três diferentes espécies assintomáticas que estavam em reabilitação em Santa Catarina e no Rio Grande do Sul. Os dados obtidos constituem uma base de informação útil para estudos futuros no campo da patologia, virologia, epidemiologia e dos impactos antrópicos na saúde das aves marinhas do cone sul. / Emerging infectious diseases are characterized as disease whose pathogens progressed to a new strain ar genotype capable of infecting the same host or a new species. The occurrence of emerging diseases has been correlated to the destruction of habitats and loss of biodiversity. Seabirds have been considered as good indicators and sentinels of aquatic ecosystem, and a wide variety of viral diseases have been investigated and described in birds worldwide. The characterization and understanding of viral diseases that affect seabirds that inhabit the Brazilian coast are of fundamental importance for the understanding of possible mortality outbreaks among other factors that influence the conservation of birds in general. The objective of this research was to investigate the occurrence of herpesvirus, coronavirus and avipoxvirus in seabird species that were rehabilitated in three centres located along the Brazilian coast and in breeding colonies of Sula sp. and Phaeton sp. located at the Abrolhos’s archipelago, Bahia, Brazil and four Spheniscus magellanicus's colonies located at Argentina's Patagonia. Viral analyzes were performed by PCR and RT-PCR and confirmed by sequencing the identified amplicon. In cases of death, the histopathological alterations were identified through optical microscopic analysis. The study revealed the occurrence of the three investigated viral agents in the Brazilian rehabilitation centres, besides the occurrence of herpesvirus in the freeliving and reproductive active seabird’s populations. Four new herpesvirus were identified and called: Magellanic penguin herpesvirus 1 (MagHV -I), causing a mortality outbreak associated with necrotic-hemorrhagic tracheitis in Magellanic penguins in rehabilitation process; Magellanic penguin herpesvirus 2 (MagHV-2), identified in apparently healthy breeding Magellanic penguins at the Argentinean Patagonia’s colonies; Sulid herpesvirus 1 (SuHV-l), identified in boobies (Sula sp.) and tropicalseabirds (Phaeton sp.) breeding colonies at Abrolhos Archipelago, and Thalassarchid herpesvirus 1 (ThHV -1), identified in a yellow nose albatross (Thalassarche chlororhynchos) that appeared on the beaches of Rio Grande, RS, Brazil. Were. also identified: a new avipox named Brazilian penguinpox causing cutaneous, esophagus and respiratory lesions in rehabilitation penguins at Santa Catarina and the identification of two Santa Catarina and the identification of two Gammacoronavirus in three different asymptomatic seabirds species that were undergoing rehabilitation in Santa Catarina and Rio Grande do Sul. The data provi de a useful information basis for further studies related to pathology, virology, epidemiology and human impacts on southern hemispheres seabirds’ health.

Les zoonoses émergentes constituent un problème de santé publique majeur. A l'image des virus de l'immunodéficience humaine (VIH), influenza, ou encore Ebola, la plupart des pathogènes zoonotiques prennent leur origine chez la faune sauvage. Les chiroptères sont des réservoirs de virus zoonotiques qui peuvent provoquer des pathologies graves chez l'Homme, comme le virus de la rage ou le coronavirus responsable de la pandémie du syndrome respiratoire aigu sévère (SRAS) en 2003-2004. En Asie du Sud-Est, reconnue comme un point chaud d'émergence, les chiroptères sont régulièrement en contact avec l'Homme du fait de l'exploitation des mêmes environnements et des activités de chasse et de consommation de ces animaux sauvages. Le risque de transmission de potentiels virus des chiroptères à l'Homme reste encore très peu étudié, notamment au Cambodge et au Laos. C’est dans ce contexte que s’inscrit ce travail de thèse, qui a pour but de détecter et de caractériser des coronavirus et des astrovirus chez les chiroptères de ces deux pays, et d'explorer les environnements où le risque de transmission à l'Homme serait plus élevé.Un premier axe de travail a porté sur la détection et la caractérisation de ces deux familles virales chez des chiroptères échantillonnés de 2010 à 2013. Une forte diversité de coronavirus et d'astrovirus a été détectée chez de nombreux genres de chiroptères insectivores et frugivores. De nouveaux hôtes réservoirs et de nouvelles souches virales ont été mis en évidence, dont certaines sont relativement proches de souches pathogènes chez l'Homme ou chez d'autres espèces animales. Le deuxième axe d'étude visait une caractérisation plus approfondie des virus. L'étude des protéines impliquées dans l'entrée cellulaire (protéines de capside et de spicule pour les astrovirus et coronaivrus respectivement), permet d'évaluer le potentiel de passage de la barrière d'espèce de ces virus. Plusieurs techniques de séquençage ont été tentées, en particulier au niveau des gènes d'intérêt. Les résultats ont été très limités, et n'ont pas permis une caractérisation approfondie des souches. Néanmoins, ce travail a mis en évidence les points critiques et les approches à envisager dans l'optique d'un futur séquençage de ces virus.Enfin, le troisième axe de recherche a porté sur l'étude des facteurs environnementaux qui pourraient impacter les chiroptères et les potentiels virus zoonotiques qu'ils peuvent porter. Bien que les données aient été limitées, l'approche méthodologique et les pistes d'étude sont à retenir pour des études épidémiologiques futures. De plus les caractéristiques liées à la transformation des paysages naturels par l'Homme est un aspect important à prendre en compte. / Zoonoses are important public health issues, and represent 60% of emerging infectious diseases. Most of zoonotic pathogens originate from wildlife, such as the Human Immunodeficiency Virus, Influenza Virus or Ebola Virus. Chiroptera have been recognized as an important reservoir of zoonotic viruses, such as the lyssavirus or the coronavirus responsible for the pandemic of severe acute respiratory syndrome (SARS) in 2003-2004.Southeast Asia is a hotspot for emerging diseases. Bats represent 30% of the biodiversity and are in close contact with human populations, due to the exploitation of the same environment and the use of bats as food in subsistence hunting. So far, there has been a lack of knowledge and understanding concerning the viruses circulating in the bat population in this region, especially in Cambodia and Lao P.D.R. The work presented in this thesis is dedicated to this problematic, with a special focus on the detection and molecular characterization of coronaviruses and astroviruses in bat populations in these two countries. The aim was also to depict environmental aspects which increase the risk of potential transmission from bats to humans.The first part of this work was dedicated to the detection and typing of astroviruses and coronaviruses in bats collected over a three-year period throughout Cambodia and Lao P.D.R. A high diversity of these viruses was found in various insectivorous and frugivorous bats. New bat reservoirs and new potential virus strains were detected, including some related to strains known to be highly pathogenic for humans or livestock species.The second part of this work therefore concentrates on a deeper characterization of the strains of interest, targeting genomic regions involved in cell host entry, and thus in ability to cross species barriers .Several isolation and sequencing methods were implemented in order to characterize the regions of interest, i.e. capsid and spike proteins. Results were limited and did not permit a deeper characterization. Nevertheless, this work highlights the aspects which need to be improved in order to sequence the viruses more effectively.The final part of this thesis examined environmental factors impacting the distribution pattern of bats, as well as the potential risk for virus transmission to humans. Transformation of landscape by humans from natural to cultivated lands, appeared to be important factors to take into account when investigating bat distribution, and the viruses they can harbor. Despite the weakness of the dataset, the methodological approach is worth being considered in further epidemiological studies on bat-associated viruses.

A fragmentação e a invasão de florestas tropicais e a crescente concentração de assentamentos humanos aumentaram exponencialmente as chances de exposição a vírus emergentes e emergentes. Dado o grande potencial de espalhamento de patógenos em população humanas, a identificação e caracterização de agentes patogênicos circulantes podem melhorar a atenção primária e as capacidades de diagnóstico para um agente emergente futuro. As abordagens moleculares e metagenômicas que utilizam as tecnologias de sequenciação da próxima geração levaram a descoberta e caracterização de muitos vírus emergentes na última década. Além disso, as abordagens in silico também podem ajudar a identificar vírus emergentes usando apenas dados de sequenciamento publicamente disponíveis. Além disso, estimar a ascendência filogenética e até mesmo analisar as mudanças no uso de codons são ferramentas adicionais que podem melhorar a nossa compreensão de vírus emergentes ou reemergentes. Este projeto visou aplicar essas ferramentas em ambos os vírus que poderiam estar circulando no Brasil: Parvovírus B19 e vírus da Febre Amarela. Também exploramos as aplicações de modelos ocultos de Markov e índice de adaptação de codons usando dados publicamente disponíveis. Esperamos que este trabalho forneça uma prova de conceito para futuros projetos metagenômicos e demonstre a utilidade das várias técnicas moleculares e bioinformáticas no estudo de vírus emergentes. / Fragmentation and encroachment of tropical rainforests and the growing concentration of human settlements have exponentially increased chances of exposure to re-emerging and emerging viruses. Given the large potential for pathogens to spillover and spread in a population, identifying and characterizing circulating human pathogens could improve the readiness and diagnostic capabilities for a future emergence. Molecular and metagenomic approaches using next-generation sequencing technologies have led to the discovery and characterization of many emerging viruses over the last decade. In complement, in silico approaches can also help identify emerging viruses using only publicly available sequencing data. Moreover, estimating the phylogenetic ancestry and even analyzing changes in codon usage are additional tools that can improve our understanding of an emerging or re-emerging virus. This project aimed to apply these tools to two viruses that could be circulating in Brazil: Parvovirus B19 and Yellow Fever virus. We also explored the applications of Hidden Markov models and codon adaptation index using publicly available data. We expect this work to provide a proof-of-concept for future metagenomic projects, and demonstrate the utility for several molecular and bioinformatics techniques in the study of emerging viruses.