Emerging viruses represent a significant threat to human health. Understanding the drivers of emergence, such as viral evolution, is a critical avenue to combat these pathogens. One specific group of emerging pathogens of interest is flaviviruses. Flaviviruses are arthropod-borne viruses (arbovirus) in the family Flaviviridae. The medically relevant flaviviruses can be divided into two groups – tick-borne and mosquito-borne. Included within the mosquito-borne flaviviruses group are dengue viruses 1-4 (DENV 1-4), which causes 400 million infections annually, and Zika virus (ZIKV), which caused over 128 million infections from 2013-2018. These viruses, which are cocirculating, share high sequence similarity in key antigenic regions. Because of these similarities, pre-existing immunity to DENV has been correlated with altered pathogenesis of subsequent ZIKV infections. Despite this, there has been little analysis of the effects of pre-existing DENV immunity on the evolution of subsequent flavivirus infection, despite being characterized for many other viruses. Given that mutation that could arise from cross-reactive immune selection could alter pathology or transmissibility, it is critical to assess the role of cross-reactive immune selection as an evolutionary driver. However, this line of research has historically been difficult due to the inherent toxicity of flavivirus infectious clones in bacteria. To mitigate the toxic nature of flavivirus clones, we developed several entirely in vitro workflows using a combination of rolling circle amplification (RCA) and replication cycle reaction (RCR). We demonstrated that RCA was a comparable substitute to traditional plasmid propagation using an alphavirus infection clone. We further demonstrated that RCR could be used to generate infectious clones by producing infectious clones of DENV2 and SARS-CoV-2, as well as demonstrating it could be used to introduce mutations into infectious clones by producing a D614G SARS-CoV-2 mutations. With this technology in place, we used in vitro directed evolution system, where we passaged ZIKV in convalescent patient serum to assess the role of cross-reactive immune selection as an evolutionary driver. After passaging, we performed next-generation sequencing to assess the impacts of cross-reactive immune selection on the viral populations and to identify mutations that arose post-passaging. We observed that ZIKV passaged in convalescent DENV serum had reduced diversity and divergence in the premembrane region. Within the convalescent DENV passaged population, we identified two mutations of interest with the dominant antibody binding region – E-V335I and NS1-T139A. These mutations were then introduced using our in vitro workflows. The resulting mutant viruses were then assessed for their replicative fitness in mammalian cell culture and mosquito models and their sensitivity to neutralization. We observed that while both E-V355I and NS1-T139A have increased fitness in mammalian cells, they had reduced fitness in mosquitoes. These results align with the trade-off hypothesis, which states that in a multi-host system, adaptation to one host reduces fitness in the other hosts. When we assessed the neutralization sensitivity of the mutants, we observed that while NS1-T193A was resistant to neutralization, E-V355I was more sensitive to neutralization. These results indicate that neutralization escape is not necessary for enhanced post-passaging in convalescent DENV serum. Our findings demonstrate that cross-reactive immune selection can generate several mutations with altered fitness in mammalian cells and mosquitos. This research is significant for both highlighting novel technologies to facilitate molecular virology and demonstrating that cross-reactive immune selection has the potential to alter the evolutionary trajectory of flaviviruses. This work provides critical information to understand how flaviviruses are evolving and emerging, and therefore critical information to address their threat to human health. / Doctor of Philosophy / Emerging viruses represent a significant threat to human health. We must understand what drives these viruses to adapt and evolve to respond to these threats. One virus family of extreme importance is the genera flavivirus. Flaviviruses are arthropod-borne viruses (arbovirus) that can be spread by the bites of ticks and mosquitoes. Included in the mosquito-borne flavivirus are dengue virus 1-4 (DENV1-4), which accounts for 400 million new infections annually, and Zika virus (ZIKV), which caused more than 128 million infection from 2013-2018. In addition to co-circulating, DENV 1-4 and ZIKV share several key similarities in their protein structures, which results in pre-existing DENV immunity effect how subsequent infections behave. The effect of pre-existing immunity on the evolution of these viruses has not been well established, despite similar studies being performed for other viruses. Given that the mutations that could arise from immune-driven evolution could alter disease severity or transmissibility, the impacts of immune-driven evolution must be characterized. However, the current tools available to perform this research are suboptimal, as the toxicity of flavivirus genomes hampers out ability to perform bacterial cloning, which has historically been necessary to develop and modify infectious clones. To mitigate the toxicity, we developed a "bacteria-free" workflow using emerging technologies like rolling circle amplification (RCA) and replication cycle reaction (RCR). With the technology in place, we propagated several generations of ZIKV or DENV in the presence of serum from human patients with a history of DENV infections. We then sequenced the viruses and identified mutations that arose during passaging. The mutations were then inserted using our bacteria-free workflow into infectious clones. The resulting viruses were assessed for their ability to replicate in mammalian cells, their ability to infect mosquitos, and their sensitivity to patient serum. We found that exposing ZIKV to serum from patients with pre-existing immunity to DENV can result in ZIKV developing several mutations. These mutations make the virus more effective at infecting mammalian cells and less effective at infecting mosquitos. This research is significant as it highlights novel technologies to aid researchers, and it demonstrates that pre-existing immunity has the potential to alter the evolutionary trajectory of flaviviruses. This information is critical in understanding flavivirus evolution and their emergence and therefore is critical to addressing their threat to human health.

Le virus de la dengue cause une maladie de type grippal qui peut dans certains cas évoluer vers des fièvreshémorragiques mortelles. Mon projet de thèse porte sur la réplication de ce virus. Je focalise sur la compréhension du mécanisme d'action de la protéine NS5 de ce virus. La protéine contient 2 domaines : 1) domaine méthyltransférase, essentiel pour la traduction des protéines virales, 2) domaine polymérase, synthétisant le génome ARN du virus. Premièrement, nous avons démontré que la polymérase joue un rôle principal dans la conservation de l'extrémité 3' et 5' du génome et de l'anti-génome. Puis, j'ai caractérisé l'influence du domaine méthyltransférase sur l'activité polymérase de la protéine NS5. J'ai développé un système d'études mécanistiques en utilisant des techniques biochimiques de cinétique pré-stationnaire pour la protéine NS5, et obtenu des paramètres cinétiques et thermodynamiques de cette protéine envers ses substrats. Avec ce même système, j'ai pu tester des activités de la polymérase NS5 avec des ARN coiffés et triphosphates de différente longueur, mimant les séquences à l'extrémité 5' du génome du virus de la dengue. L'activité polymérase de NS5 est influencée par la présence de la coiffe de l'ARN, ce qui m'a permis de proposer une distance physique correspondant à environ 13 nucléotides entre les sites actifs domaines méthyltransférase et polymérase. Mes travaux ouvrent la voie à la détermination de la structure 3D de NS5 avec ses ARN et des nucléotides 5'-triphosphate.Elucider son mécanisme d'action, c'est être capable d'inhiber son action et donc de pouvoir proposer des molécules capables d'arrêter la prolifération virale lors d'une infection. / Dengue virus causes dengue fever, which may evolve towards life-threatening hemorrhagic fever. My research projectfocuses on dengue replication, and more precisely on the mechanism of NS5 at the molecular/atomic level. NS5 is a bifunctionalenzyme containing two domains: 1) a methyltransferase domain essential for translation of viral proteins, 2) apolymerase domain synthesizing the viral RNA genome. First, we demonstrated the main role of the polymerase in theconservation of 5' and 3' ends of dengue genome and anti-genome RNAs. Next, I showed the influence of themethyltransferase domain on the activity of the polymerase domain. I also developed a system allowing mechanistic studiesusing pre-steady state kinetics to characterize NS5 in depth. I have made use of this system to determine the catalyticparameters of NS5 towards its substrates. Using the same pre-steady state system, I was able to test the polymerase activityof NS5 with capped and uncapped 5'-triphosphate RNAs of different lengths corresponding to the 5'-end of the dengue RNAgenome. The polymerase activity of NS5 is significantly affected by the presence of the 5'-cap, which allowed me to designan experimental set-up pointing to a minimal physical distance of around 13 nucleotides between the methyltransferase andpolymerase active sites. My work will be useful to characterize the biophysics of NS5 in complex with its RNA and NTPsubstrates, and then to determine the crystal structure of such complex at play during viral RNA synthesis. Knowing thedetailed NS5 mechanism paves the way to inhibit its action and thus design drugs aiming at stopping a viral infection.

A caracterização da variabilidade genética intra-hospedeiro do vírus da dengue (DENV) é fundamental para a compreensão de sua evolução e dinâmica populacional no contexto atual como um importante patógeno viral humano. A diversidade viral acumulada em hospedeiros infectados influencia diretamente em outros aspectos como patogênese, transmissão e imunidade do hospedeiro. Contudo, apesar de existirem vários estudos sobre a diversidade genética intra-hospedeiro em dengue, nenhum tem sido relatado para DENV-4 até o presente momento. O ressurgimento e disseminação desse sorotipo foi associado com a sua co-circulação e o substituição dos sorotipos 1, 2 e 3 durante os recentes surtos no município do Guarujá-SP. Com base neste quadro epidemiológico, este estudo visou identificar a variação genética intra-hospedeiro do DENV-4 em amostras coletadas durante o surto de 2013, utilizando tecnologias de sequenciamento de nova geração. Portanto, nós caracterizamos a variabilidade genética de DENV-4 em diferentes níveis e as forcas evolutivas que afetam essa diversidade. Em adição, foram explorados os principais eventos na transmissão das variantes de DENV-4 identificadas. Nossos resultados revelaram uma baixa diversidade genética intra-hospedeiro para DENV-4. No entanto, mutação e pressões seletivas foram mecanismos importantes na variabilidade genética do vírus. A nível populacional, as variantes estão sujeitas á seleção natural negativa, não obstante identificamos seleção positiva atuando sob sítios específicos. Nenhuma evidência de recombinação foi detectada. Além disso, contra-intuitivamente, variantes de baixa frequência estão sendo transmitidas e contribuindo para diversidade genética do DENV-4 circulando em Guarujá. Nossos resultados fornecem novas evidências potencialmente úteis para futuros trabalhos focados em infecções mistas, escape imunológico, assim como o espalhamento e diversificação viral. / Characterizing intra-host genetic variability in dengue virus (DENV) virus is paramount for understanding its evolution and population dynamics in the context of its current status as a major human viral pathogen. The extent to which viral diversity accrues in infected host influences aspects such as pathogenesis, transmission, and host immunity. Although there are several studies about intra-host genetic diversity in dengue, so far nothing has been revealed about DENV-4. In the Guarujá municipality in the State of São Paulo, the reemergence and spread of this serotype was associated with its co-circulation and the displacement of serotypes 1, 2 and 3 during recent outbreaks. Based on this epidemiological framework, we seek to identify the intra-host genetic variation of DENV-4 strains from samples collected during the 2013 outbreak by using deep sequencing technologies. We characterized the genetic variability of DENV-4 at different levels, and the forces shaping this diversity. Likewise, we explored major transmission events among DENV-4 variants. Our results revealed a low intra-host genetic diversity for DENV-4. However, we found selective and mutational pressures contributing to genetic diversity, while recombination did not seem play an important role. We further identified purifying selection at population level but sites subject to potential diversifying selection. Additionally, we observed low frequency haplotypes being transmitted among hosts and contributing to the viral diversity of DENV-4 circulating in Guarujá. Our findings provide preliminary insights for future studies in mixed infections, drug resistance, virus variant spread and immune scape. This study is the first effort to investigate the intra-host diversity of DENV-4.

A imunidade inata que o mosquito apresenta tenta combater os patógenos dentro do organismo do mosquito impedindo que este seja transmitido para outros hospedeiros. A resposta celular apresenta três diferentes processos: fagocitose, encapsulamento e formação nodular, todos estes processos buscam eliminar os patógenos. Peptídeos antimicrobianos fazem parte da resposta humoral do mosquito, sendo codificados por genes e secretados por diversos tipos celulares. Um peptídeo novo pouco conhecido descoberto em Anopheles gambiae, a gambicina, demonstrou bons resultados no combate de parasitas. Na infecção por Plasmodium galleceum, não há diferença significativa na expressão deste peptídeo entre o grupo controle e infectado nos intervalos analisados. Na infecção por vírus dengue, sorotipo 2, a gambicina não apresenta diferença significativa no intervalo de 24 horas após a infecção, quando comparamos grupo controle e infectado, nos intervalos de 7 dias e 14 dias após a infecção, a expressão da gambicina é maior no grupo controle quando comparemos com o grupo infectado. / Innate immunity presents a mosquito tries to combat the pathogens inside the body of the mosquito preventing it from being transmitted to other hosts. The cellular response has three different processes: phagocytosis, encapsulation and nodule formation, all these processes seek to eliminate pathogens. Antimicrobial peptides are part of the humoral response mosquito being encoded by genes and secreted by several cell types. A little known new peptide discovered in Anopheles gambiae, the gambicina showed good results in controlling pests. In Plasmodium infection galleceum, there is no significant difference in the expression of this peptide between the control group and infected in the analyzed intervals. In infection with dengue virus serotype 2, the gambicina no significant difference within 24 hours after infection when comparing the control group and infected at intervals of 7 days and 14 days after infection, the expression is higher in gambicina control group when compare to the infected group.

A caracterização da variabilidade genética intra-hospedeiro do vírus da dengue (DENV) é fundamental para a compreensão de sua evolução e dinâmica populacional no contexto atual como um importante patógeno viral humano. A diversidade viral acumulada em hospedeiros infectados influencia diretamente em outros aspectos como patogênese, transmissão e imunidade do hospedeiro. Contudo, apesar de existirem vários estudos sobre a diversidade genética intra-hospedeiro em dengue, nenhum tem sido relatado para DENV-4 até o presente momento. O ressurgimento e disseminação desse sorotipo foi associado com a sua co-circulação e o substituição dos sorotipos 1, 2 e 3 durante os recentes surtos no município do Guarujá-SP. Com base neste quadro epidemiológico, este estudo visou identificar a variação genética intra-hospedeiro do DENV-4 em amostras coletadas durante o surto de 2013, utilizando tecnologias de sequenciamento de nova geração. Portanto, nós caracterizamos a variabilidade genética de DENV-4 em diferentes níveis e as forcas evolutivas que afetam essa diversidade. Em adição, foram explorados os principais eventos na transmissão das variantes de DENV-4 identificadas. Nossos resultados revelaram uma baixa diversidade genética intra-hospedeiro para DENV-4. No entanto, mutação e pressões seletivas foram mecanismos importantes na variabilidade genética do vírus. A nível populacional, as variantes estão sujeitas á seleção natural negativa, não obstante identificamos seleção positiva atuando sob sítios específicos. Nenhuma evidência de recombinação foi detectada. Além disso, contra-intuitivamente, variantes de baixa frequência estão sendo transmitidas e contribuindo para diversidade genética do DENV-4 circulando em Guarujá. Nossos resultados fornecem novas evidências potencialmente úteis para futuros trabalhos focados em infecções mistas, escape imunológico, assim como o espalhamento e diversificação viral. / Characterizing intra-host genetic variability in dengue virus (DENV) virus is paramount for understanding its evolution and population dynamics in the context of its current status as a major human viral pathogen. The extent to which viral diversity accrues in infected host influences aspects such as pathogenesis, transmission, and host immunity. Although there are several studies about intra-host genetic diversity in dengue, so far nothing has been revealed about DENV-4. In the Guarujá municipality in the State of São Paulo, the reemergence and spread of this serotype was associated with its co-circulation and the displacement of serotypes 1, 2 and 3 during recent outbreaks. Based on this epidemiological framework, we seek to identify the intra-host genetic variation of DENV-4 strains from samples collected during the 2013 outbreak by using deep sequencing technologies. We characterized the genetic variability of DENV-4 at different levels, and the forces shaping this diversity. Likewise, we explored major transmission events among DENV-4 variants. Our results revealed a low intra-host genetic diversity for DENV-4. However, we found selective and mutational pressures contributing to genetic diversity, while recombination did not seem play an important role. We further identified purifying selection at population level but sites subject to potential diversifying selection. Additionally, we observed low frequency haplotypes being transmitted among hosts and contributing to the viral diversity of DENV-4 circulating in Guarujá. Our findings provide preliminary insights for future studies in mixed infections, drug resistance, virus variant spread and immune scape. This study is the first effort to investigate the intra-host diversity of DENV-4.

Made available in DSpace on 2015-04-22T22:14:01Z (GMT). No. of bitstreams: 1 Ilia Gilmara Carvalho.pdf: 530450 bytes, checksum: 50f84ac4bf26a69a84cf2a4b2a031978 (MD5) Previous issue date: 2008-12-31 / Fundação de Amparo à Pesquisa do Estado do Amazonas / The study had for objective the detection and typing of the dengue virus, in the vectors Aedes aegypti and Aedes albopictus through the Polimerase Chain Reaction (PCR) using specific primers. During the period of December of 2005 to December of 2006 8984 mosquitoes were collected, of these 827 they were Aedes, being 819 Ae. aegypti (414 females and 405 males) and 8 Ae. albopictus (7 females and 1 male), in 46 neighborhoods of the city of Manaus including all of the geographical areas of the city. The females were grouped in pools from 1 to 10 mosquitoes for microtubes, in agreement with the gender, it dates from collection, neighborhood and stocked to -70C in the same day of the collection, totaling 143 pools (138 of Ae. aegypti and 5 of Ae. albopictus). Those pools were macerated in PBS containing albumin, and a bracket of the softened was removed for inoculation in cell culture, and other bracket was used to accomplish the extraction of the viral RNA. Once extracted, RNA was submitted the reaction of reverse transcription following by the chain reaction of the polimerase (RT-PCR). The positive samples in RT-PCR were submitted the reaction of semi nested PCR and the products of this reaction were resolved in agarose gel to 1,5% with etídio bromide. Of the 143 analyzed pools, 114 (111 of Ae. aegypti and 3 of Ae. albopictus) they were positive for DENV 3, just a pool was shown positive for two sorotipos, DENV 1 and DENV 3. The prevalence pools Ae. aegypti infected with DENV 3 in the city of Manaus was of 53%, being larger in the areas Center-west (70%), South (60%) and West (53%), and smaller in the area East (23%). This is the first report of the detection of DENV 3 in field-caught Ae. albopictus naturally infected in Brazil. The monitoring of the circulation viral in mosquitoes with the use of the technique of RT-PCR allows the previous knowledge of the levels of spread viral in certain areas contributing to determine the time and place to apply the prevention measures and control. / O estudo teve por objetivo a detecção e tipagem do vírus dengue, nos vetores Aedes aegypti e Aedes albopictus por meio da Reação em Cadeia da Polimerase (PCR) utilizando primers específicos. Durante o período de Dezembro de 2005 a Dezembro de 2006 foram coletados 8984 mosquitos, destes 827 eram Aedes, sendo 819 Ae. aegypti (414 fêmeas e 405 machos) e 8 Ae. albopictus (7 fêmeas e 1 macho), em 46 bairros da cidade de Manaus abrangendo todas as zonas geográficas da cidade. As fêmeas de Ae. aegypti e Ae. albopictus foram agrupadas em pools de 1 a 10 mosquitos por microtubos, de acordo com o gênero, data de coleta, bairro e estocado a -700C no mesmo dia da coleta, totalizando 143 pools (138 de Ae. aegypti e 5 de Ae. albopictus). Esses pools foram macerados em PBS contendo albumina, e uma alíquota do macerado foi retirada para inoculação em cultura de célula, e outra alíquota foi utilizada para realizar a extração do RNA viral. Uma vez extraído, o RNA foi submetido a reação de transcrição reversa seguida da reação em cadeia da polimerase (RT-PCR). As amostras positivas na RT-PCR foram submetidas a reação de Semi Nested PCR e os produtos desta reação foram resolvidos em gel de agarose a 1,5% corado com brometo de etídio. Dos 143 pools analisados, 114 (111 de Ae. aegypti e 3 de Ae. albopictus) foram positivos para DENV 3, apenas um pool mostrou-se positivo para dois sorotipos, DENV 1 e DENV 3. A prevalência de mosquitos Ae. aegypti infectados com DENV 3 na cidade de Manaus foi de 80%. Em todas as zonas a prevalência foi maior que 53%, sendo maior nas zonas Centro-oeste (70%), Sul (60%) e Oeste (53%), e menor na zona Leste (23%). Este foi o primeiro achado no Brasil da identificação do DENV 3 em amostras de Ae. albopictus , coletados em campo na forma adulta. O monitoramento da circulação viral em mosquitos com o uso da técnica de RT-PCR permite o conhecimento prévio dos níveis de disseminação viral em determinadas áreas contribuindo para determinar a época e local para aplicar as medidas de prevenção e controle.

A major obstacle to the development of dengue virus (DENV) vaccines has been the need to immunise concurrently against each of the four DENV serotypes in order to avoid sensitising recipients to developing severe DENV infections. A problem already encountered with live attenuated tetravalent DENV vaccines has been the difficulty in eliciting adequate immune responses against all four DENV serotypes in human hosts. This could have been due to variations in the antigenicity and/or the replication rates of the four DENV serotypes. Non-replicating DNA vaccines avoid the issue of different replication rates. Currently, only DENV-1 and DENV-2 DNA vaccines have been evaluated. In this study, a number of DNA vaccines for each of the four DENV serotypes were developed and their immunogenicity was evaluated in outbred mice. These vaccines included DNA vaccines encoding the DENV prM-E protein genes derived from the four DENV serotypes (pVAX-DEN1, -DEN2, -DEN3 and -DEN4), and DNA vaccines encoding DENV prM and hybrid-E protein genes derived from multiple DENV serotypes. The hybrid-E protein genes were constructed by substituting either domains I and II, domain III, and/or the stem-anchor region from the E protein of one DENV serotype with the corresponding region from another DENV serotype. A number of superior DNA vaccines against each of the four DENV serotypes were identified based on their ability to elicit high titres (≥40, FFURNT50) of neutralising antibodies against the corresponding DENV in mice. The superior DNA vaccines against DENV-1 were pVAX-DEN1, pVAX-C2M2E211, pVAX-C2M2E122 and pVAX-C2M1E122. The superior DNA vaccine against DENV-2 was pVAX-C2M1E122 and the superior DNA vaccines against DENV-3 were pVAX-DEN3 and pVAX-C2M3E344. The superior DNA vaccines against DENV-4 were pVAX-C2M3E344, pVAX-C2M4E434 and pVAX-C2M4E433. Each of these DNA vaccines could provide effective protection against infection by the corresponding DENV serotypes. This is the first study to describe the development of DNA vaccines against DENV-3 and DENV-4. However, mice immunised with a tetravalent DENV DNA vaccine, composed of a DNA vaccine encoding the prM-E protein genes from each of the four DENV serotypes (pVAX-DEN1-4), elicited high titres of neutralising antibodies against DENV-1 and DENV-3 only. Nevertheless, the results from this study suggested that a tetravalent DENV DNA vaccine, composed of pVAX-DEN1, pVAX-C2M1E122, pVAX-DEN3 and pVAX-C2M4E434, may provide effective concurrent protection against infection by each of the four DENV serotypes. In addition, mice immunised with pVAX-C2M1E122, which encoded a hybrid-E protein gene derived from DENV-1 and DENV-2, elicited high titres of anti-DENV-1 and anti-DENV-2 neutralising antibodies, and mice immunised with pVAX-C2M3E344, which encoded a hybrid-E protein gene derived from DENV-3 and DENV-4, elicited high titres of anti-DENV-3 and anti-DENV-4 neutralising antibodies. This result suggested that the co-immunisation of these two hybrid-E DNA vaccines also may provide effective concurrent protection against infection by each of the four DENV serotypes. Extracellular E proteins, believed to be in the form of recombinant subviral particles (RSPs), were recovered from the tissue culture supernatant of all DNA vaccine-transfected mammalian cells by ultracentrifugation, except for cells transfected with the pVAX-C2M2E122 hybrid-E DNA vaccine. Western blotting with the monoclonal antibody 4G2 (flavivirus cross-reactive) demonstrated that the extracellular E proteins expressed by the DNA vaccines were synthesized and cleaved in a manner similar to that of native DENV E proteins. In addition, mammalian cells transfected with pVAX-DEN1, pVAX-DEN2 or pVAX-DEN3 secreted higher amounts of extracellular E proteins than cells transfected with pVAX-DEN4. The amount of extracellular E protein secreted by pVAX-DEN4-transfected cells increased when the c-region of the prM/E signal peptidase cleavage site was made more polar. In contrast, decreasing the polarity of the c-region of the C/prM signal peptidase cleavage site of pVAX-DEN4 resulted in no detectable extracellular E proteins from pVAX-DEN4-transfected cells. This result suggested that the amount of extracellular E proteins secreted by cells transfected with DNA expressing the DENV prM-E protein genes may be dependent of the efficiency of C/prM and prM/E protein cleavages by host-derived signal peptidases. Mice immunised with the mutated pVAX-DEN4, which was capable of expressing large amounts of extracellular E proteins in vitro, produced significantly higher concentrations of Th1-type anti-DENV-4 antibodies than mice immunised with the unmodified pVAX-DEN4, but failed to produce detectable levels of anti-DENV-4 neutralising antibodies. In contrast, increasing the ratio of CpG-S to CpG-N motifs in the pVAX-DEN2 DNA vaccine by incorporating either an additional CpG-S motif, or an antibiotic resistance gene with a high ratio of CpG-S to CpG-N motifs, resulted in a significant increase in both the concentration of Th1-type anti-DENV-2 antibodies and the titres of anti-DENV-2 neutralising antibodies in immunised mice. This result suggested that increasing the amount of CpG-S motifs in DENV DNA vaccines may present an simple and effective approach to increasing the immunogenicity of the DENV DNA vaccines.

Dengue virus (DENV) is the causative agent of dengue fever (DF), the most prevalent arthropod-borne viral disease in the world and therefore is considered an emerging global health threat. The four DENV serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) that infect humans are distinguished from one another by unique antigenic determinants (epitopes) on the DENV envelope (E) protein. The E protein is the primary antigenic site of the DENV and is responsible for inducing neutralising antibody (Ab) and cell mediated immune response in DENV infected hosts. The DENV E protein also mediates attachment of virions to host cell receptors and entry of virions into host cells by membrane fusion. The study of epitopes on DENV E protein is necessary for understanding viral function and for the design of unique polyvalent vaccines capable of inducing a neutralising antibody response against each DENV serotype. Reverse genetics using infectious cDNA clones has enabled the construction of functional intertypic DENV, where the E protein of one DENV serotype is put in the genetic background of a different DENV serotype. In addition, observations from our laboratory indicate that chimeric E proteins, consisting of E protein structural domains from different DENV serotypes can fold into functional proteins. This suggests that there is potential to engineer viruses with intertypic DENV E proteins as potential DENV vaccine candidates, which is the long term goal of studies within our research group. However, if a chimeric E protein was to be constructed containing epitopes involved in antibody mediated neutralisation of each DENV serotype, then knowledge of the location of these epitopes on the E protein of each DENV serotype would be essential. Prior to this study, monoclonal antibodies (MAbs) had been used to identify epitopes involved in antibody mediated neutralisation on the E protein of all DENV serotypes, except DENV-4. The primary objective of this study was to identify epitopes on the DENV-4 E protein involved in neutralisation by antibodies. In order to achieve this objective, a panel of 14 MAbs was generated against DENV-4 in BALB/c mice and characterised using various serological and functional assays. The identification of DENV-4 specific neutralising MAbs in the panel was essential for subsequent experiments aimed at determining antigenic domains, structural domains or specific epitopes (peptides or amino acids) involved in the neutralisation of DENV-4. The majority of MAbs (11/14) generated against DENV-4 recognised the E protein. The remaining three MAbs reacted with the non-structural (NS) 1 protein. The majority of MAbs against the E protein were DENV or Flavivirus group reactive, but four MAbs were DENV-4 specific. All MAbs against the E protein recognised conformationally dependent epitopes and were able to capture DENV-4 in an enzyme linked immuno-adsorbent assay (ELISA). Eighty percent (9/11) of the anti-E MAbs produced for this study neutralised infection of cells by DENV-4 in vitro. Three of the neutralising MAbs (F1G2, 18F5 and 13H8) were DENV-4 specific and also demonstrated the strongest neutralisation activity of the panel, reducing DENV-4 infectivity by 100-1000 fold. The amount of virus neutralised by the MAbs was not related to the avidity of the MAbs. The DENV-4 specific MAbs F1G2, 18F5 and 13H8 were used to identify epitopes involved in neutralisation of DENV-4. The MAbs that effectively captured DENV-4 were used in competitive binding assays (CBAs) to determine spatial relationships between epitopes and therefore define antigenic domains on the DENV-4 E protein. The CBAs indicated that the epitopes recognised by the panel of MAbs segregated into two distinct domains (D4E1 and D4E2) and both contained epitopes involved in neutralisation. CBAs incorporating human serum from DENV-4 infected patients suggested that the MAbs recognised the same, or spatially related, epitopes in domain D4E2 as antibodies from humans who had experienced natural dengue infections, indicating the clinical relevance of such epitopes for the development of DENV vaccines. The reactivity of the capture MAbs with low pH treated DENV-4 was also evaluated in an attempt to identify epitopes that might be more accessible during low pH-mediated virus fusion. Only one of the MAbs (13H8) recognised an acid resistant epitope. Initial attempts to identify epitopes on the DENV-4 E protein involved in neutralisation followed the traditional epitope mapping approach of selecting subpopulations of DENV-4 which escaped neutralisation by MAbs. These attempts were unsuccessful so a variety of strategies for mapping epitopes were used including DENV-4 variant analysis and site directed mutagenesis of the DENV-4 E protein, MAb screening of chimeric DENV-3/4 E proteins and MAb screening of a bacterial peptide display library. DENV-4 variants including DENV-4 isolates from different geographical locations or chemically mutagenised DENV-4 were screened with neutralising MAbs to identify neutralisation escape mutant (n.e.m.) viruses. Site directed mutagenesis of the DENV-4 E protein confirmed whether amino acid changes identified in DENV-4 n.e.m.s were essential for the binding of neutralising MAbs to an epitope. The MAb screening of DENV-4 variants identified n.e.m.s with amino acid changes at residues E95, E96, E156, E157, E203, E329 and E402 of the DENV-4 E protein. Site directed mutagenesis of the DENV-4 E protein identified two epitopes recognised by the DENV-4 specific neutralising MAbs F1G2 and 18F5 at specific amino acid residues within domains II and III of the DENV-4 E protein. No specific epitopes were identified for the MAb 13H8; however this MAb did recognise domain I and II of the DENV-4 E protein, when screened against DENV-3/4 chimeric DENV E proteins. The first epitope, which was recognised by the MAb F1G2, contained residue E95 which was located in domain II of the DENV-4 E protein. The aspartate (Asp) to alanine (Ala) change at E95 prevented the binding of F1G2 to the DENV-4 E protein. The binding of F1G2 to the E95 residue was confirmed using the pFlitrX bacterial peptide display library, which demonstrated binding of F1G2 to a peptide homologous with residues E99-E104. No peptides recognised by 13H8 and 18F5 were identified by this method. The MAb F1G2 also bound to the domain III region (E300-E495) of the DENV-4 E protein when screened against DENV-3/4 chimeric DENV E proteins. This implied that F1G2 may be recognising a discontinuous epitope consisting of domains II and III. The second epitope, which was recognised by MAb 18F5, contained residue E329 which was located in domain III of the DENV-4 E protein. The alanine (Ala) to threonine (Thr) change at E329 prevented the binding of 18F5 to the DENV-4 E protein. MAb 18F5 also bound to the domain III region (E300-E495) of the DENV-4 E protein when screened against DENV-3/4 chimeric E proteins, thus confirming the E329 epitope. The potential mechanisms by which the DENV-4 specific MAbs neutralise virus infection were evaluated by the virus overlay protein binding assay (VOPBA). The binding of MAb 18F5 to a domain III (E329) epitope of the DENV-4 E protein and the binding of MAb F1G2 to domain II (E95, E99-E104) and domain III epitopes (chimeric E protein) of the DENV-4 E protein, prevented the attachment of DENV-4 to a 40 kDa C6/36 cell protein. In contrast the binding of MAb 13H8 to domains I and II of the DENV-4 E protein did not prevent attachment of DENV-4 to the same protein. This was preliminary evidence that the binding of domain III epitopes by the MAbs F1G2 and 18F5 may be important in preventing virus attachment. The binding of MAb 13H8 to domains I and II, and the ability of this MAb to recognise DENV-4 treated at low pH, suggested that MAb 13H8 may block epitopes exposed at low pH that are required for low pH mediated virus fusion to host cell membranes. Overall, the different methods used in this study identified epitopes involved in the neutralisation of DENV-4. The distribution of epitopes involved in neutralisation throughout the DENV-4 E protein were similar to the distribution of epitopes involved in neutralisation on the DENV-1, 2 and 3 E proteins. This suggested that it might be possible to elicit neutralising antibodies against multiple DENV serotypes using chimeric E-proteins derived from two or more DENV serotypes and therefore, facilitate the design of novel tetravalent DENV vaccines.

There are four serotypes of dengue virus designated dengue 1, 2, 3 and 4 (D1, D2, D3 and D4) and epidemiological studies indicate that a severe complication of dengue virus infection - dengue hemorrhagic fever (DHF) is more likely to occur following a secondary infection. DHF is hypothesized to be immunologically mediated and may be triggered by virus-specific T cells. It is also likely that dengue virus-specific cytotoxic T lymphocytes (CTLs) are important for recovery from dengue virus infections. An analysis of the immune response during acute illness and when the patient has recovered from the infection (immune state) is therefore important as it will provide insights into the immunopathological nature of the disease. This thesis initially examines the CD8+CTL responses in volunteers who have received live attenuated dengue vaccines and then investigates acute and immune T cell responses in children following natural infection with dengue. When this project was initiated, there was little available information on the human CD8+ T cell responses to dengue viruses. PBMC from one donor had generated memory CD8+CTL to the nonstructural protein NS3 of dengue virus. Memory CD8+CTL responses were therefore analyzed to determine the diversity of the T cell response to dengue virus and to identify immunodominant proteins using PBMC from eight healthy adult American volunteers who had received monovalent live-attenuated candidate vaccines of the 4 dengue serotypes. All the donors had specific T cell proliferation to dengue viruses and to other flaviviruses that we tested. CTLs were generated from the stimulated PBMC of all donors and in the seven donors tested, dengue virus-specific CD8+CTL activity was demonstrated. The nonstructural proteins NS3 and NS1.2a and the structural protein E were recognized by CD8+CTLs from six, five and three donors respectively. All donors recognized either NS3 or NS 1.2a. In a donor who received a dengue 4 vaccine, CTL killing was seen in bulk culture against the premembrane protein (prM). This is the first demonstration of a CTL response against the prM protein. The CTL responses using PBMC of two donors were serotype-specific whereas all other donors had serotype-cross reactive responses. For one donor, CTLs specific for E, NSl.2a and NS3 proteins were all HLA-B44 restricted. For the three other donors tested the potential restricting alleles for recognition of NS3 were HLA-B38, A24 and/or B62 and B35. These results indicate that the CD8+CTL responses of humans after immunization with a single serotype of dengue virus are diverse and directed against a variety of proteins. The nonstructural proteins NS3 and NSl.2a appear to be immunodominant and should be considered when designing subunit vaccines for dengue. Previously T cell responses had not been examined in people who have had natural infections with dengue. The HLA diversity between North American Caucasians and populations where dengue is a serious health problem, calls for the analysis of immune responses in people who have been infected with natural circulating strains of the virus. We examined the memory cytotoxic T lymphocytic (CTL) responses of peripheral blood mononuclear cells (PBMC) obtained from patients in Thailand 12 months after natural symptomatic secondary dengue infections. In all four patients analyzed, CTLs were detected in bulk culture PBMC against nonstructural dengue proteins. Numerous CD4+ and CD8+ CTL lines were generated from the bulk cultures of two patients, KPP94-037 and KPP94-024, which were specific for the NSl.2a and NS3 proteins respectively. All CTL lines derived from both patients were crossreactive with other serotypes of dengue virus. The CD8+ NS1.2a specific lines from patient KPP94-037 were HLA-B57 restricted and the CD8+ NS3 specific lines from patient KPP94-024 were HLA-B7 restricted. The CD4+ CTL lines from patient KPP94-037 were HLA-DR7 restricted. A majority of the CD8+CTLs isolated from patient KPP94-024 were found to recognize a.a. 221-232 on NS3. These results demonstrate that after symptomatic secondary natural dengue infections in Thai patients, CTLs are mainly directed against nonstructural proteins and are broadly crossreactive. The data correlate with our observations that nonstructural proteins are immunodominant proteins in volunteers who received dengue vaccines. We were interested in examining CTL responses in children during their acute illness and comparing them to memory CTLs obtained from the same children a year or more after the infection. A detailed analysis on samples from nine patients during their acute illness failed to generate any dengue virus-specific CTL responses. We therefore decided to determine if cell mediated responses are altered during acute dengue infection. Decreased proliferative responses to mitogens and recall antigens have been observed in PBMC obtained during several acute human viral infections. All responses of PBMC during acute illness were compared to the same patients PBMC obtained at least 6 months after their infection. Proliferative responses to PHA, anti-CD3, tetanus toxoid and dengue antigens were significantly decreased in PBMC obtained during the acute infection. The proliferative responses to PHA were restored by the addition of gamma-irradiated autologous immune or allogeneic PBMC. Cell contact with the irradiated PBMC was necessary to restore proliferation. Non-T cells from the acute PBMC of dengue patients did not support proliferation of T cells from control donors in response to PHA, but T cells from the PBMC of patients with acute dengue proliferated if accessory cells from a control donor were present. Addition of anti-CD28 antibodies restored anti-CD3-induced proliferation of the PBMC of some patients. The percentage of monocytes was reduced in the acute sample of PBMC of the dengue patients. Addition of IL-2 or IL-7, but not IL-4 or IL-12 also restored proliferation of acute PBMC stimulated with anti-CD3. The results demonstrate that both quantitative and qualitative defects in the accessory cell population during acute dengue illness result in a depression of in vitro T cell proliferation. The data generated from this project shed light on the nature of the immune responses during acute natural dengue infections. It strengthens the existing data on the human memory CD8+CTL responses to dengue viruses and validates the observations by examining memory CTL responses after natural dengue infection in patients from Thailand. In addition, we demonstrate a profound defect in lymphoproliferative responses during dengue illness.

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No. of bitstreams: 2 Tese - Angela Ferreira Lopes de Teive e Argolo - 2014.pdf: 1773502 bytes, checksum: 393b63ce506fdd2be70f95e14be99755 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2014-12-19 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / Dengue is an endemic disease in Goias state with current circulation of the four serotypes. In the last five years has been occurred a significant increase in cases, hospitalizations and deaths caused by dengue in the region. In this thesis the first manuscript analyzed data from the virological surveillance of DENV in Goias during 1994-2013. Virus isolation in C6/36 (A.albopictus) cell culture followed by indirect immunofluorescence using monoclonal antibodies were performed in LACEN-GO. During the study period the four serotypes have been identified with introduction of DENV-1 in 1994, DENV-2(1998), DENV-3(2002) and DENV-4(2011). Among 21,684 virus isolation tests performed 4,839(22.3%) were positive. DENV-1 was isolated in 3,023(62.5%), DENV-3 in 1,051 (21.7%), DENV-4 in 413(8.5%) and DENV-2 in 352(7.3%) samples respectively. There were changes in the predominance of serotypes throughout the study period with dominance of DENV-1 between 1994-2002 and 2009-2011, DENV-3 in 2003-2008 and DENV-4 in 2013. The DENV-2 was never prevalent among serotypes isolated in LACEN-GO. The time series of the virological surveillance of dengue in Goias showed the introduction and the temporal sequence of circulation of DENV in the state. This study contributes to characterize the epidemiological scenario of dengue in Goias with possible implications for epidemiological surveillance of the disease in the region. The second manuscript evaluated the presence of dengue serotype-specific neutralizing antibodies (NAb) in patients involved in a clinical dengue cohort established during epidemic of 2012-2013 in Goiania, state of Goias. Among 452 participants of the cohort we analyzed the paired samples from 60 patients classified as severe dengue (n=40) or dengue fever (n=20). The eligibility criteria were confirmation of the infection by IgM, NS1Ag and /or RT-PCR; IgG positive in at least one of the samples. Monotypic or multitypic response were defined: PRNT50≥1/20 for only one serotype or ≥1/20 for two or more serotypes simultaneously. The infecting serotype was defined by ≥4 fold increase in the title of NAb in paired samples. Overall 73.3% of patients had NAb against DENV-4, 68.3% against DENV-1, 68.3% against DENV-2 or 61.6% against DENV-3. The patients' ages ranged from 3 to 81 years. Regardless of age group 85% of patients had multitypic response while 15% had monotypic response. Patients infected with DENV-4 showed the greatest difference in NAb titers in comparison to other serotypes indicating predominance of seroconversion for serotype 4. There was no correlation among preexistent NAb and disease severity. The characterization of dengue serotype-specific immune response is important to study the relationship of preexistence of neutralizing antibodies with clinical outcomes of disease also facing the perspective of introducing of antidengue vaccines to identify protective immunity. / A dengue é uma doença endêmica em Goiás com atual circulação dos quatro sorotipos virais com aumento expressivo no número de casos, hospitalizações e óbitos pela doença de forma acentuada nos últimos cinco anos. Na presente tese o primeiro manuscrito analisou os dados da vigilância virológica dos DENV em Goiás no período de 1994-2013. Os testes de isolamento viral em cultura celular C6/36(A.albopictus) seguido de imunofluorescência indireta utilizando anticorpos monoclonais foram realizados no LACEN-GO. No período do estudo, os quatro sorotipos virais foram identificados no estado com introdução do DENV-1 em 1994, DENV-2(1998), DENV-3(2002) e DENV-4(2011). Do total de 21.684 testes de isolamento viral 4.839(22,3%) foram positivos. DENV-1 foi isolado em 3.023(62,5%), DENV-3 em 1.051(21,7%), DENV-4 em 413(8,5%) e DENV-2 em 352(7,3%) amostras. A predominância dos sorotipos virais alternou ao longo do período com DENV-1 dominante entre os anos de 1994-2002 e 2009-2011, DENV-3 entre 2003-2008 e DENV-4 em 2013. O DENV-2 nunca foi predominante entre os sorotipos isolados no LACEN-GO. A série histórica da vigilância virológica da dengue em Goiás mostrou a introdução e a sequência temporal da circulação dos DENV no estado. Este estudo contribui para a caracterização do cenário epidemiológico da dengue em Goiás com possíveis implicações nas ações de vigilância epidemiológica da doença na região. O segundo manuscrito avaliou a presença de anticorpos neutralizantes (AcN) antidengue sorotipo específico em pacientes de uma coorte clínica de dengue estabelecida durante a epidemia de 2012-2013, em Goiânia-GO. Entre os 452 participantes da coorte, analisamos amostras pareadas de 60 pacientes classificados como dengue grave (n=40) ou dengue (n=20). Os critérios de elegibilidade foram a confirmação da infecção por IgM, NS1Ag e/ou RT-PCR; IgG positivo em pelo menos uma das amostras. Resposta monotípica ou multitípica foram definidas por PRNT50≥1/20 para apenas um sorotipo viral ou ≥1/20 para dois ou mais sorotipos virais simultaneamente. O sorotipo viral infectante foi definido por um aumento ≥4 vezes no título dos AcN em amostras pareadas. No total 73,3% dos pacientes apresentaram AcN contra DENV-4, 68,3% contra DENV-1, 68,3% contra DENV-2 ou 61,6% contra DENV-3. A idade dos pacientes variou de 3 a 81 anos. Independente da faixa etária 85% dos pacientes apresentaram resposta multitípica enquanto 15% tiveram resposta monotípica. Pacientes infectados por DENV-4 apresentaram a maior diferença de títulos de AcN em comparação com outros sorotipos virais indicando predominância de soroconversão para o sorotipo 4. Não houve correlação entre preexistência de AcN com a gravidade da doença. A caracterização de resposta imune sorotipo específica é importante para estudar a relação de anticorpos neutralizantes preexistentes com a gravidade clínica da doença, bem como frente à perspectiva de introdução de vacinas antidengue para identificar a imunidade protetora.