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Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Stephen Higgs / The genetic composition of arboviruses is a critical determinant of viral infectivity and the capacity for virus dissemination in arthropod vectors. Due to concerns related to a hypothetical potential for loss of attenuation, the supression of vector infection and dissemination is a critical component for the rationale-based design of live-attenuated flavivirus vaccine candidates. The yellow fever virus (YFV) 17D vaccine virus is not only attenuated in vertebrates, but also has low infectivity for Aedes agypti mosquitoes and since it does not disseminate, it is not transmissible. Using a reverse genetics system, the mutations present in the envelope protein YFV 17D virus were characterized in Ae. aegypti to determine the role of mutations in limiting the viral infectivity and dissemination capacity. This knowledge would contribute to the rational design of live attenuated vaccines with the desirable phenotype of being nontransmissible by arthropod vectors. The upper lateral portion of the YFV 17D envelope (E) protein domain III (EDIII) habors the T380R mutation in the FG loop. Experiments demonstrated that the T380R mutation was associated with the viral infectivity phenotype for mosquitoes, but did not influence dissemination into the secondary tissues. The G52R mutation in the molecular hinge region that is located between E protein domains I (EDI) and II, significantly reduced viral infectivity for mosquitoes. In contrast, when cloned into the Asibi wildtype virus genetic backbone, the T173I mutation in the loop structure between the G0 and H0 β- strands did not attenuate viral infection and dissemination. The double mutant virus containing both the G52R and T173I mutations in the E protein, showed a similar attenuated reduced infectivity to the single G52R mutant. The M299I mutation in the linker region between EDI and EDIII resulted in a significantly lower viral infectivity at the initial phase of viral infection at 7 days post-infection in Ae. aegypti. In conclusion, the characterization on four mutations in the YFV 17D vaccine E protein have demonstrated three genetic loci, that can influence the process of YFV infection in Ae. aegypti. These results provide new knowledge and understanding which may have broad applications for the rationale design of safe flavivirus vaccines, via targeting genetic loci and introducing specific mutations that preclude infection of, and transmission by arthropod vectors.

Made available in DSpace on 2014-06-11T19:32:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-08-10Bitstream added on 2014-06-13T19:22:41Z : No. of bitstreams: 1 morais_ats_dr_sjrp.pdf: 1276143 bytes, checksum: 62a89d8b555ac92b5faf4baa19e4db2f (MD5) / O vírus da Febre Amarela (YFV) pertence ao gênero Flavivirus e causa uma importante doença. Nos últimos anos, uma alarmante ressurgência da circulação viral e expansão do vírus em áreas endêmicas têm sido detectadas na África e América do Sul. NS5 é uma proteína viral não estrutural com duas atividades essenciais para a replicação viral, uma de metiltransferase e outra de RNA Polimerase dependente de RNA (RdRp). Para o melhor entendimento dos mecanismos de replicação viral, interações entre NS5 e proteínas celulares têm sido amplamente estudadas. Assim, os objetivos desse estudo foram caracterizar a interação da proteína NS5 e eIF3L, avaliar a função de eIF3L na replicação do vírus da febre amarela, e caracterizar estruturalmente a proteína eIF3L. Métodos. Para identificar a interação de NS5 YFV com eIF3L, foi realizado ensaios em sistema duplo-híbrido usando RdRp NS5 YFV contra eIF3L. Para o mapeamento da interação, foram construídos mutantes deletantes de RNApol e analisados em sistema duplo-híbrido. A região de interação de RNApol foi segmentada em três fragmentos e analisada na presença de eIF3L. Para mapear os resíduos de NS5 críticos para a interação, foi realizada mutagênese sítio-dirigida no segmento 3 de ID. A interação foi analisada em ensaios in vitro e em cultura de células de mamíferos. A significância de eIF3L para a replicação do YFV foi investigada usando superexpressão de eIF3L em células BHK21-RepYF17D LucNeoIres. A proteína eIF3L foi purificada usando uma combinação de cromatografia de afinidade e de exclusão molecular para subsequente caracterização estrutural. Resultados. Nesse estudo, foi caracterizada a interação de NS5 com o fator eucariótico de início de tradução... / Yellow fever virus (YFV) belongs to the Flavivirus genus and causes an important disease. An alarming resurgence of viral circulation and expansion of the YFV endemic zones have been detected in Africa and South America in recent years. NS5 is a viral protein that contains the methyltransferase and RNA-dependent RNA polymerase domains, which are essential during viral replication. Interactions among NS5 and cellular proteins have been studied for the understanding of viral replication. The aim of this study was to characterize the interaction of NS5 protein with EIF3L and evaluate the role of EIF3L in yellow fever replication. Methods. To identify the interaction of YFV NS5 with cellular proteins, we performed a two-hybrid screen using YFV NS5 RdRp domain as bait and a human cDNA library. For mapping the interaction, RNApol deletions mutants were performed and analyses in two-hybrid system. The RNApol region of interaction was segmented in three fragments and analyses into yeast containing eIF3L. To map residues of NS5 that are critical for its interaction, we performed a site-direct mutagenesis in segment 3 of ID. The interaction was confirmed in vitro assays and by in vivo coimmunoprecipitations. The significance of eIF3L for replication of YFV was investigated using overexpression of eIF3L in BHK21-RepYF17D LucNeoIres cells. eIF3L was purified using a combination of affinity and subsequent size exclusion chromatography for subsequent structural characterization. Results. In this work we describe and characterize the interaction of NS5 with the translation factor eIF3L. The interaction between NS5 and eIF3L was confirmed by in vitro binding and in vivo coimmunoprecipitation assays. This interaction occurs in a region (Interaction Domain of RNApol domain) that is conserved in several... (Complete abstract click electronic access below)

Orientador: Maurício Lacerda Nogueira / Banca: Fátima Pereira de Souza / Banca: Cleslei Fernando Zanelli / Banca: Eurico de Arruda Neto / Banca: Luciana Barros de Arruda / Resumo: O vírus da Febre Amarela (YFV) pertence ao gênero Flavivirus e causa uma importante doença. Nos últimos anos, uma alarmante ressurgência da circulação viral e expansão do vírus em áreas endêmicas têm sido detectadas na África e América do Sul. NS5 é uma proteína viral não estrutural com duas atividades essenciais para a replicação viral, uma de metiltransferase e outra de RNA Polimerase dependente de RNA (RdRp). Para o melhor entendimento dos mecanismos de replicação viral, interações entre NS5 e proteínas celulares têm sido amplamente estudadas. Assim, os objetivos desse estudo foram caracterizar a interação da proteína NS5 e eIF3L, avaliar a função de eIF3L na replicação do vírus da febre amarela, e caracterizar estruturalmente a proteína eIF3L. Métodos. Para identificar a interação de NS5 YFV com eIF3L, foi realizado ensaios em sistema duplo-híbrido usando RdRp NS5 YFV contra eIF3L. Para o mapeamento da interação, foram construídos mutantes deletantes de RNApol e analisados em sistema duplo-híbrido. A região de interação de RNApol foi segmentada em três fragmentos e analisada na presença de eIF3L. Para mapear os resíduos de NS5 críticos para a interação, foi realizada mutagênese sítio-dirigida no segmento 3 de ID. A interação foi analisada em ensaios in vitro e em cultura de células de mamíferos. A significância de eIF3L para a replicação do YFV foi investigada usando superexpressão de eIF3L em células BHK21-RepYF17D LucNeoIres. A proteína eIF3L foi purificada usando uma combinação de cromatografia de afinidade e de exclusão molecular para subsequente caracterização estrutural. Resultados. Nesse estudo, foi caracterizada a interação de NS5 com o fator eucariótico de início de tradução... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Yellow fever virus (YFV) belongs to the Flavivirus genus and causes an important disease. An alarming resurgence of viral circulation and expansion of the YFV endemic zones have been detected in Africa and South America in recent years. NS5 is a viral protein that contains the methyltransferase and RNA-dependent RNA polymerase domains, which are essential during viral replication. Interactions among NS5 and cellular proteins have been studied for the understanding of viral replication. The aim of this study was to characterize the interaction of NS5 protein with EIF3L and evaluate the role of EIF3L in yellow fever replication. Methods. To identify the interaction of YFV NS5 with cellular proteins, we performed a two-hybrid screen using YFV NS5 RdRp domain as bait and a human cDNA library. For mapping the interaction, RNApol deletions mutants were performed and analyses in two-hybrid system. The RNApol region of interaction was segmented in three fragments and analyses into yeast containing eIF3L. To map residues of NS5 that are critical for its interaction, we performed a site-direct mutagenesis in segment 3 of ID. The interaction was confirmed in vitro assays and by in vivo coimmunoprecipitations. The significance of eIF3L for replication of YFV was investigated using overexpression of eIF3L in BHK21-RepYF17D LucNeoIres cells. eIF3L was purified using a combination of affinity and subsequent size exclusion chromatography for subsequent structural characterization. Results. In this work we describe and characterize the interaction of NS5 with the translation factor eIF3L. The interaction between NS5 and eIF3L was confirmed by in vitro binding and in vivo coimmunoprecipitation assays. This interaction occurs in a region (Interaction Domain of RNApol domain) that is conserved in several... (Complete abstract click electronic access below) / Doutor

Avec plus de 20% de morts annuels dus aux maladies infectieuses, celles-ci restent un sujet majeur de santé publique. Des maladies d’origine virale (ré)émergent suite aux changements environnementaux, climatiques et sociétaux : le virus Ebola, la Dengue ou, plus récemment, le virus Zika. Dans ce contexte, il est donc aujourd’hui crucial de développer des vaccins efficaces et sûrs contre les infections virales émergentes. Ce projet de thèse vise à mettre en place une nouvelle stratégie de production de vaccins vivants atténués ciblant les virus à ARN en travaillant sur le virus de la fièvre jaune (genre Flavivirus). Après une analyse génomique qui a permis d’approfondir une technique de modification des virus appelée « ré-encodage », des mutants de la fièvre jaune ont été produits puis caractérisés in vitro et in vivo. En parallèle, un modèle rongeur de la fièvre jaune a été développé et a permis de tester in vivo à la fois l’innocuité et l’efficacité vaccinale des virus ré-encodés. / Despite recent considerable improvements, infectious diseases remain a major issue for public health, with an estimated 20% of annual deaths caused by infections. Among them, viral diseases (re)emerge following environmental, climatic and societal changes: Ebola, Dengue and Zika viruses have recently been the object of special attention. The development of safe and efficient vaccines against emerging viruses is a major challenge for global public health. This thesis work is in line with this issue. Using the yellow fever virus (YFV, genus Flavivirus) as a model, we tried to define new strategies for the design of live-attenuated vaccines for viral infections prevention. After a genomic analysis that allowed to go further into a procedure for virus modification named “re-encoding”, we generated and characterised both in vitro and in vivo mutant strains of YFV. In parallel, a rodent model was set up to test in vivo both the safety and the protective efficiency of the re-encoded viruses.

Made available in DSpace on 2014-11-10T11:09:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-05-23Bitstream added on 2014-11-10T11:57:42Z : No. of bitstreams: 1 000790896.pdf: 1624782 bytes, checksum: 86f691c9d97bad42fa2588df159f183a (MD5) / O Vírus da Febre amarela (YFV) causa doença com considerável morbidade e mortalidade nas regiões tropicais. Diversos vírus possuem estratégias para a alteração dos processos celulares. Mecanismos de splicing celulares são essenciais para diversificar a expressão dos genes e podem aumentar seu potencial de gerar proteínas. A replicação de YFV e as interações entre proteínas virais e celulares não são totalmente conhecidas. A proteína celular hSlu7 possui sinal de localização nuclear e tem um papel importante nas reações catalíticas do segundo passo do splicing. Estudos demonstram que sob infecção de YFV hSlu7 transloca para o citoplasma. A translocação de proteínas entre o citoplasma e o núcleo pode representar um mecanismo viral da regulação da expressão gênica. Este estudo teve como objetivo a caracterização da interação entre a proteína hSlu7 e NS5 viral, bem como estudar os efeitos de interações sobre os mecanismos de splicing alternativo após a infecção de YFV. Para identificar interação de NS5 de YFV com hSlu7 foi realizado ensaio de co-imunoprecipitação. Para verificar alteração de splicing celular foram utilizados replicons pEGFP-ADAR, pI12-IL7R, pEFGP-FGFR2, bem como a alteração de isoformas de XBP-1 endógenos. Os resultados indicam que NS5 de YFV interage com proteína hSlu7 e que sua interação pode influenciar no metabolismo RNA celular. YFV demonstrou exercer modulação no splicing celular, a avaliação de replicons sugerem que em splicing dependente de hSlu7, bem como a independente ocorre uma regulação viral atuando sobre sítios de splicing fraco e que a interação hSlu7-NS5 pode alterar direta e indiretamente a regulação trans-acting / Yellow fever virus (YFV) causes disease with significant morbidity and mortality in tropical regions. Several viral strategies are avail for recruitment and alteration of the biochemical cellular processes. Cellular splicing mechanisms are essential to diversify the gene expression and increase it’s proteomic potential. Replication of YFV and the interactions between viral and cellular proteins are unknown. The cellular protein hSlu7 has an nuclear localization and an important role in the second catalytic reaction step of the alternative splicing. In our study group demonstrated that under YFV infection hSlu7 translocates to the cytoplasm. The translocation of proteins between nucleus and cytoplasm may represent a viral mechanism of cellular gene expression regulation, interference in the protein availability of the alternative splicing and viral replication control. This study aimed to characterize the interaction between the viral protein hSlu7 and NS5, as well as studying the effects of interactions on the mechanisms of alternative splicing after YFV infection. To identify interaction with YFV NS5 hSlu7 was conducted co-immunoprecipitation assay. To verify changes in cellular splicing replicons were used pEGFP-ADAR, PI12-IL7R, pEFGP-FGFR2 as well as the change of isoforms of XBP-1 endogenous.The results indicated that YFV NS5 protein interacts with hSlu7 and that their interaction may influence cellular metabolism RNA. YFV perform modulation on cellular splicing, the evaluation of replicons suggest that in hSlu7 splicing dependent and independent regulation occurs viral acting on weak splice sites and that the interaction hSlu7-NS5 can change directly or indirectly to regulate trans- acting

abstract: Despite the approval of a Dengue virus (DV) vaccine in five endemic countries, dengue prevention would benefit from an immunization strategy highly immunogenic in young infants and not curtailed by viral interference. Problematically, infants younger than 9 year of age, whom are particularly prone to Dengue severe infection and death, cannot be immunized using current approved DV vaccine. The most important issues documented so far are the lack of efficiency and enhancement of the disease in young seronegative recipients, as well as uneven protection against the four DV serotypes. Based on data from clinical trials that showed enhanced performance of dengue vaccines when the host has previous anti-flaviviral immunity, I proposed here an attractive solution to complement the current vaccine: a recombinant measles vaccine vectoring dengue protective antigens to be administered to young infants. I hypothesized that recombinant measles virus expressing Dengue 2 and 4 antigens would successfully induce neutralizing responses against DV2 and 4 and the vaccine cocktail of this recombinant measles can prime anti-flaviviral neutralizing immunity. For this dissertation, I generated and performed preclinical immune assessment for four novel Measles-Dengue (MV-DV) vaccine candidates. I generated four MVs expressing the pre membrane (prM) and full length or truncated (90%) forms of the major envelope (E) from DV2 and DV4. Two virus, MVvac2-DV2(prME)N and MVvac2-DV4(prME), expressed high levels of membrane associated full-length E, while the other two viruses, MVvac2-DV2(prMEsol)N and MVvac2-DV4(prMEsol)N, expressed and secreted truncated, soluble E protein to its extracellular environment. The last two vectored vaccines proved superior anti-dengue neutralizing responses comparing to its corresponding full length vectors. Remarkably, when MVvac2-DV2/4(prMEsol)N recombinant vaccines were combined, the vaccine cocktail was able to prime cross-neutralizing responses against DV 1 and the relatively distant 17D yellow fever virus attenuated strain. Thus, I identify a promising DV vaccination strategy, MVvac2-DV2/4(prMEsol)N, which can prime broad neutralizing immune responses by using only two of the four available DV serotypes. The current MV immunization scheme can be advantageus to prime broad anti-flaviviral neutralizing immunity status, which will be majorly boosted by subsequent chimeric Dengue vaccine approaches. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2016

Orientador: Maurício Lacerda Nogueira / Banca: Carlos Eduardo Calzavara Silva / Banca: Fátima Pereira de Souza / Resumo: O Vírus da Febre amarela (YFV) causa doença com considerável morbidade e mortalidade nas regiões tropicais. Diversos vírus possuem estratégias para a alteração dos processos celulares. Mecanismos de splicing celulares são essenciais para diversificar a expressão dos genes e podem aumentar seu potencial de gerar proteínas. A replicação de YFV e as interações entre proteínas virais e celulares não são totalmente conhecidas. A proteína celular hSlu7 possui sinal de localização nuclear e tem um papel importante nas reações catalíticas do segundo passo do splicing. Estudos demonstram que sob infecção de YFV hSlu7 transloca para o citoplasma. A translocação de proteínas entre o citoplasma e o núcleo pode representar um mecanismo viral da regulação da expressão gênica. Este estudo teve como objetivo a caracterização da interação entre a proteína hSlu7 e NS5 viral, bem como estudar os efeitos de interações sobre os mecanismos de splicing alternativo após a infecção de YFV. Para identificar interação de NS5 de YFV com hSlu7 foi realizado ensaio de co-imunoprecipitação. Para verificar alteração de splicing celular foram utilizados replicons pEGFP-ADAR, pI12-IL7R, pEFGP-FGFR2, bem como a alteração de isoformas de XBP-1 endógenos. Os resultados indicam que NS5 de YFV interage com proteína hSlu7 e que sua interação pode influenciar no metabolismo RNA celular. YFV demonstrou exercer modulação no splicing celular, a avaliação de replicons sugerem que em splicing dependente de hSlu7, bem como a independente ocorre uma regulação viral atuando sobre sítios de splicing fraco e que a interação hSlu7-NS5 pode alterar direta e indiretamente a regulação trans-acting / Abstract: Yellow fever virus (YFV) causes disease with significant morbidity and mortality in tropical regions. Several viral strategies are avail for recruitment and alteration of the biochemical cellular processes. Cellular splicing mechanisms are essential to diversify the gene expression and increase it's proteomic potential. Replication of YFV and the interactions between viral and cellular proteins are unknown. The cellular protein hSlu7 has an nuclear localization and an important role in the second catalytic reaction step of the alternative splicing. In our study group demonstrated that under YFV infection hSlu7 translocates to the cytoplasm. The translocation of proteins between nucleus and cytoplasm may represent a viral mechanism of cellular gene expression regulation, interference in the protein availability of the alternative splicing and viral replication control. This study aimed to characterize the interaction between the viral protein hSlu7 and NS5, as well as studying the effects of interactions on the mechanisms of alternative splicing after YFV infection. To identify interaction with YFV NS5 hSlu7 was conducted co-immunoprecipitation assay. To verify changes in cellular splicing replicons were used pEGFP-ADAR, PI12-IL7R, pEFGP-FGFR2 as well as the change of isoforms of XBP-1 endogenous.The results indicated that YFV NS5 protein interacts with hSlu7 and that their interaction may influence cellular metabolism RNA. YFV perform modulation on cellular splicing, the evaluation of replicons suggest that in hSlu7 splicing dependent and independent regulation occurs viral acting on weak splice sites and that the interaction hSlu7-NS5 can change directly or indirectly to regulate trans- acting / Mestre

Arbovirus infections are widespread, and their disease burden has increased in the past decade. In Africa, arbovirus infections and fever with unknown etiology are common. Due to the lack of well-established epidemiologic surveillance systems and accurate differential diagnosis in most African countries, little is known about the prevalence of human arbovirus infections in Africa. The aim of this review is to summarize the available epidemiological data and diagnostic laboratory tools of infections with dengue, yellow fever, Zika, and chikungunya viruses, all transmitted by Aedes mosquitoes. Studies indicate that these arboviral infections are endemic in most of Africa. Surveillance of the incidence and prevalence of the infections would enable medical doctors to improve the diagnostic accuracy in patients with typical symptoms. If possible, arboviral diagnostic tests should be added to the routine healthcare systems. Healthcare providers should be informed about the prevalent arboviral diseases to identify possible cases.

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.