[pt] Zika Vírus (ZIKV) é um vírus transmitido pelos mosquitos Aedes aegypti (mesmo transmissor da dengue e da febre chikungunya) e o Aedes albopictus. O contágio principal pelo ZIKV se dá pela picada do mosquito que, após se alimentar do sangue de alguém contaminado, pode transportar o ZIKV durante toda a sua vida, transmitindo a doença para uma população que não possui anticorpos contra ele. Também pode ser transmitido através de relação sexual de uma pessoa com Zika para os seus parceiros ou parceiras, mesmo que a pessoa infectada não apresente os sintomas da doença.Neste trabalho, apresentamos dois modelos matemáticos para a epidemia do ZIKV usando (1) equações diferenciais ordinárias e (2) equações diferenciais ordinárias com atraso temporal, que é o tempo que os mosquitos levam para desenvolver o vírus. Fazemos uma comparação entre as duas variantes de modelagem e, para facilitar o trabalho com os modelos, fornecemos uma interface gráfica com o usuário. Simulações computacionais são realizadas para o Suriname e El Salvador, que são países propensos a desenvolver a epidemia de maneira endêmica. Para estudar a difusão espacial do ZIKV, propomos um modelo baseado em equações de advecção-difusão e criamos um esquema numérico com elementos finitos e diferenças finitas para resolvê-lo. / [en] The Zika Virus (ZIKV) is a virus transmitted by Aedes aegypti mosquitoes (same as the one transmitting dengue and chikungunya fever) and Aedes albopictus. The main way of contagion by the ZIKV is caused by the bite of a mosquito that, after feeding from someone contaminated, can transport the ZIKV throughout its life, transmitting the disease to a population that does not have the immunity. It can also be transmitted through a person s sexual relationship with ZIKV to their partners, even if the infected person does not have the symptoms of the disease. In this work, we present two mathematical models for the ZIKV epidemic by using (1) ordinary differential equations and, (2) ordinary differential equations with temporal delay, which is the time it takes mosquitoes to develop the virus. We make a comparison between the two modeling variants and, to facilitate the work with the models, we provide a graphical user interface. Computational simulations are performed for Suriname and El Salvador, which are countries that are prone to develop the epidemic in an endemic manner. In order to study the spatial diffusion of ZIKV, we propose a model based on advection-diffusion equations and create a numerical scheme with finite elements and finite differences to resolve it.

Os Flavivirus são transmitidos por mosquitos (Diptera: Culicidae) que se refugiam em remanesctentes de Mata Atlântica. Essas áreas verdes correspondem às Unidades de Conservação e parques urbanos, que estão espalhados pela região metropolitana de São Paulo. Este estudo foi realizado com o intuito de conhecer as espécies de culicídeos que circulam na Área de Proteção Ambiental (APA) Capivari-Monos, na zona Sul do município de São Paulo, e no Parque Estadual da Cantareira (PEC), na zona Norte do mesmo município, e de investigar infecção natural por Flavivirus na fauna de culicídeos amostrada. Também foi proposto relacionar a variedade, a quantidade e identidade dos Flavivirus detectados com os padrões de riqueza, abundância e diversidade das assembleias de mosquitos. Foram realizadas 14 coletas, mensalmente, em quatro pontos de coleta na APA e três no PEC, todos com diferentes níveis de intervenção antrópica, no período de março de 2016 a abril de 2017. Armadilhas automáticas luminosastipo CDC (com atração de CO2 e ácido lático) foram instaladas na copa das árvores e no nível do solo. O esforço amostral foi equivalente para os todos os pontos, sendo que foram instaladas duas armadilhas em cada ponto (uma na copa e outra no solo), com 18 horas de coleta, permitindo amostragem de culicídeos de hábitos diurnos, crepusculares e noturnos. Os espécimes foram transportados com vida para o Laboratório de Saúde Pública da Faculdade de Saúde Pública da Universidade de São Paulo, criopreservados a temperatura -70ºC, identificados morfologicamente e agrupados em pools (com até 10 indivíduos). Os pools foram submetidos à técnica de isolamento viral em cultura de células (C6/36), seguida do teste de imunofluorescência indireta. Os pools positivos foram submetidos à reação de RT-qPCR e, posteriormente, sequenciados. Duas árvores de similaridade foram construídas para confirmação dos Flavivirus. No total, 1216 exemplares de culicídeos foram amostrados (13 gêneros), cuja riqueza foi de 42 táxons. A APA registrou a maior abundância (878 espécimes) e maior riqueza (37 táxons). A Cachoeira foi o ponto de coleta na APA que amostrou a maior riqueza e abundância, contudo, com a mais baixa diversidade. Entretanto, a Borracharia obteve alta riqueza, baixa abundância e a maior diversidade. O PEC amostrou 338 indivíduos e a riqueza foi de 23 táxons. Dentre os pontos do PEC, a Trilha do Pinheirinho amostrou a maior riqueza e abundância. An. (Ker.) cruzii, Cx. (Cux.) sp, Cx. (Mel.) vaxus, Li. durhami, Wy. (Prl.) confusa e Wy. (Pho.) theobaldi foram detectadas com infecção natural por Flavivirus. O sequenciamento revelou infecção por ZIKV em An. (Ker.) cruzii, Li. durhami e Wy. (Prl.) confusa, e infecção por DENV-2 em Cx. (Cux.) sp e Cx. (Mel.) vaxus. Concluiu-se que a riqueza, abundância e diversidade estão relacionadas entre si e, juntas, influenciaram na detecção de espécies de culicídeos naturalmente infectadas por Flavivirus, sendo que estes foram detectados em espécies provenientes de pontos de coleta cuja riqueza e abundância foram altas, e a diversidade baixa. A quantidade e a variedade dos Flavivirus também foram influenciadas por esses três fatores, para ocorrer na natureza. Não foi possível correlacionar a identidade dos Flavivirus com os três fatores uma vez que as espécies detectadas com infecção natural por esses vírus não são apontadas como potenciais vetoras. Além disso, a abundância e a diversidade pareceram ter uma relação inversa entre si. / Flaviviruses are transmitted by mosquitoes (Diptera: Culicidae) that take refuge in remnants of the Atlantic Forest. These green areas correspond to Conservation Units and urban parks which are spread throughout the metropolitan region of São Paulo. This study was carried out in order to identify the Culicidae fauna that circulate in Capivari-Monos Environmental Protection Area (APA), located in the South area of the city of São Paulo, and in Cantareira State Park (PEC), North area of the same municipality and to investigate natural Flaviviruses infection in this sampled Culicidae fauna. It was also proposed to relate the variety, quantity and identity of the Flaviviruses detected with patterns of richness, abundance and diversity of mosquito assemblages. Fourteen collections were carried out monthly at four collection sites in the APA and three in the PEC, all sites with different levels of anthropogenic intervention, during March 2016 to April 2017. CDC automatic traps (with attraction of CO2 and lactic acid) were installed in the canopy and on ground. The sampling effort was equivalent for all the points, and two traps were installed at each point (one in the canopy and the other on ground), with 18 hours of sampling, allowing sampling culicidae of daytime, morning and evening twilight, and nightlyl habits. The specimens were carried alive to the Public Health Laboratory of the School of Public Health of the University of São Paulo, were cryopreserved at a -70ºC temperature, identified morphologically and grouped in pools (with up to 10 individuals). The pools were submitted to the virus isolation technique in cell culture tissue (C6 / 36), followed by the indirect immunofluorescence test. The positive pools were submitted to the RT-qPCR reaction and, subsequently, sequenced. Two similarity trees were made only to confirm Flaviviruses infection. In total, 1216 specimens of culicidae were sampled (13 genera), and the richness was 42 taxa. In addition to APA recorded the highest abundance (878 specimens) and also highest richness (37 taxa). Cachoeira was the collection site in APA that showed the greatest richness and abundance as well, however, with the lowest diversity. In addition, Borracharia obtained high richness, low abundance and highest diversity. PEC sampled 338 specimens and the richness was 23 taxa. Among the collection sites of the PEC, Pinheirinho Trail showed the highest richness and also abundance. An. (Ker.) cruzii, Cx. (Cux.) sp, Cx. (Mel.) vaxus, Li. durhami, Wy. (Prl.) confusa and Wy. (Pho.) theobaldi were detected with natural Flaviviruses infection. The sequencing analyzes revealed ZIKV infection in An. (Ker.) cruzii, Li. durhami and Wy. (Prl.) confusa, and DENV-2 infection in Cx. (Cux.) sp and Cx. (Mel.) vaxus. It has concluded that the richness, abundance and also diversity are related to each other and, together, influenced the detection of species of culicidae naturally infected by Flaviviruses, which were detected in species from collection sites whose richness and abundance were high. About quantity and variety of Flaviviruses, these were also influenced by the three factors on nature. It was not possible to correlate the identity of the Flaviviruses with the three factors since the species detected with natural infection by these viruses are not indicated as potential vectors. Moreover, abundance and diversity appeared to have an inverse relation.

abstract: Zika virus (ZIKV) outbreaks have been linked to several neurological pathologies in the developing fetus, which can progress to spontaneous abortion and microcephaly in newborns whose mothers were infected with the virus during pregnancy. ZIKV has also been correlated with neurological complications in adults such as Guillain-Barré Syndrome (GBS). ZIKV outbreaks often occur in low income areas with limited access to healthcare. Therefore, there is a need to create a low-cost preventative vaccine against the virus. Mature ZIKV particles contain a lipid bilayer, a positive sense single stranded RNA genome and three structural proteins: the envelope (E), membrane (M) and capsid (C) proteins. Congruently, to other members of the Flaviviridae family, ZIKV proteins are synthesized as a polyprotein precursor which needs to be processed to release the mature structural and non-structural viral proteins. Past studies have determined the ZIKV precursor protein is cleaved by a host furin protease which separates the Pr peptide and the M protein, while the host signal peptidase separates the M and E protein. Processing is important for correct folding of the E protein. In turn, the most important neutralizing antibodies upon infection are directed against epitopes of the E protein. In this work, we used a Bean Yellow Dwarf Viral vector system to transiently express, in Nicotiana benthamiana plants, a portion of the ZIKV polyprotein encoding the Pr, M and E proteins. I further demonstrate that plants can proteolytically process the polyprotein to yield the two integral membrane proteins M and E. These proteins can be shown to co-partition into a soluble membrane-particulate fraction, consistent with formation of enveloped virus-like particles (VLPs). This work provides the first step in creating a low-cost sustainable plant-based production system of ZIKV VLPs that can be explored as a potential component 0f a low-cost prophylactic vaccine against ZIKV. / Dissertation/Thesis / Masters Thesis Molecular and Cellular Biology 2018

Zikaviruset är ett virus som fått stor uppmärksamhet i framför allt Sydamerika från 2015 och framåt då allt fler fall uppmärksammats. Detta arbete har utförts som en litteraturstudie med mål att sammanfatta kunskapsläget kring Zikavirusets morfologi, spridning, historia, komplikationer, diagnostik samt rådande behandlingsmöjligheter. Som källor används information från Folkhälsomyndigheten, CDC, PAHO och WHO samt MeSH-sökningar via PubMed. Viruset tillhör familjen Flaviviridae. Liknande andra virus i samma grupp kan infektionen ge feber, makulopapulösa hudutslag, konjunktivit, ledvärk, huvudvärk och myalgi. Det beskrevs först redan på slutet av 1940-talet i Afrika och har sedan rapporterats ha spridit sig till Asien, Oceanien, Stilla havsöarna och nu senast med utbrott i Sydamerika. Virusinfektionen har blivit mycket omdiskuterad då allt mer bevis kunnat läggas fram för att den kan leda till Guillain-Barrés syndrom samt även utöva teratogena effekter med mikrocefali som följd. Man har kartlagt spridning framför allt via myggarten Aedes men bevis finns även för att sexuell spridning kan ske samt att sjukdomen förefaller även kunna spridas från mor till foster. Diagnostiken baseras på RT-PCR och serologiska tester. I nuläget finns ingen aktiv behandling. Sammanfattningsvis har Zikavirus spridit sig snabbt genom Syd- och latinamerika sista åren och visat sig utgöra ett hot mot folkhälsan i dessa områden varför ett framtagande av ett fungerande vaccin är önskvärt.

Expanding urbanization, climate change, and population growth contribute to increased transmission and spread of arthropod-borne viruses (arboviruses), many of which cause severe disease in humans. Pathogenic arboviruses include dengue, Zika, tick-borne encephalitis, and sindbis viruses, which together threaten more than half the global population. Thus, there is a constant need for safe, specific, and sensitive molecular tests to identify early-stage infections for accurate diagnosis and molecular epidemiological data for disease prevention and control. The study tested the biosafety of using FTA™ cards when working with pathogenic arboviruses by conducting an infectivity assay using sindbis virus. Conditions for RNA extraction and storage of arboviruses on FTA were analyzed by measuring viral RNA (vRNA) stability using a SYBR-Green, Pan-Flavi RT-qPCR method composed of degenerate primers able to detect a variety of flaviviruses. Data from a Pan-Flavi RT-qPCR study comprising of 222 clinical blood and serum samples collected from a 2018 dengue virus outbreak in Hanoi (Vietnam) was analyzed to establish applicability of FTA for molecular epidemiology and diagnosis. Results showed that sindbis virus infectivity was inhibited by FTA-adsorption. FTA-adsorbed arboviruses were extracted with the highest yield using Trizol extraction and were preserved at storage at 4-20ºC for up to 30 days. The results showed that clinical blood samples acquired higher yields of vRNA for molecular testing than serum samples and that it may be possible to perform sequencing for genomic analysis. The study suggests that FTA cards may facilitate the storage and transportation of adsorbed arboviruses for downstream molecular epidemiological and diagnostic tests.

Dans le monde entier, les infections virales causent des problèmes de santé majeurs et récurrents, engendrant de sérieux problèmes socio-économiques. Notamment, les virus de la famille Flaviviridae qui représentent un fardeau considérable sur la santé mondiale et font partie des domaines prioritaires de la virologie médicale selon le rapport 2016 du ‘Global Virus Network’. Bien que le traitement actuel contre le virus de l’hépatite C (VHC) ait un taux de guérison dépassant 98%, d’autres comme le virus de la dengue (DENV) et le virus zika (ZIKV) n’ont pas encore de traitement spécifique autorisé. En prenant avantage de la grande expertise de notre laboratoire dans l’étude du VHC, nous avons utilisé des données d’une étude de biologie des systèmes visant à identifier l’interactome des différentes protéines virales. Les techniques utilisées ont combiné l’immunoprécipitation des protéines virales suivie de l’identification des protéines interacteurs humaines par spectrométrie de masse. Des études de génomique fonctionnelle par ARN interférent (ARNi) ont permis d’étudier l’effet de la diminution de l’expression des protéines identifiées sur la réplication du VHC. Cette étude a conduit à la découverte de l’interactant spécifique 17-bêta-hydroxystéroïde déshydrogénase de type 12 (HSD17B12 ou DHB12) de la protéine virale Core comme facteur cellulaire requis à la réplication du VHC. HSD17B12 est une enzyme cellulaire dont l’activité catalytique est requise pour l’élongation des acides gras à très longue chaîne (VLCFA) lors de la deuxième des quatre réactions du cycle d’élongation. Dans cette étude, nous avons déterminé que les cycles de réplication du VHC, ZIKV et DENV dépendent de l’expression et de l’activité métabolique du facteur cellulaire HSD17B12. Ainsi, nous avons étudié les effets de l’inhibition de l’expression génique par ARNi et de façon pharmacologique sur la réplication de plusieurs flavivirus dans une approche antivirale à large spectre. Nous avons démontré que le silençage de HSD17B12 diminue significativement la réplication virale, l’expression des protéines virales et la production de particules infectieuses de cellules Huh7.5 infectées par la souche JFH1 du VHC. L'analyse de la localisation cellulaire de HSD17B12 dans des ii cellules infectées suggère une colocalisation avec l'ARN double brin (ARNdb) aux sites de réplication virale, ainsi qu’avec la protéine Core (et les gouttelettes lipidiques) aux des sites d’assemblage du virus. Nous avons également observé que le silençage de HSD17B12 réduit considérablement le nombre et la taille des gouttelettes lipidiques. En accord avec ces données, la diminution de l’expression de HSD17B12 par ARNi réduit significativement l’acide oléique et les espèces lipidiques telles que triglycérides et phosphatidyl-éthanolamine dans l'extrait cellulaire total. Ces travaux suggèrent une contribution de la capacité métabolique de HSD17B12 lors de la réplication du VHC. De même, nous avons démontré que le silençage de HSD17B12 réduit significativement les particules infectieuses de cellules infectées par DENV et ZIKV. Ces études supportent le rôle de HSD17B12 dans l’efficacité des processus de la réplication de l'ARN viral et de l’assemblage de particules virales. De plus, l'inhibiteur spécifique de HSD17B12, INH-12, réduit la réplication du VHC à des concentrations pour lesquelles aucune cytotoxicité notable n'est observée. Le traitement avec 20 μM d'INH-12 réduit jusqu'à 1,000 fois les particules infectieuses produite par des cellules Huh-7.5 infectées par DENV et ZIKV lors de plusieurs cycles de réplication, et bloque complètement l'expression des protéines virales. En conclusion, ces travaux ont conduit à une meilleure compréhension du rôle de HSD17B12 lors de la synthèse de VLCFA et de lipides requise à la réplication du VHC, permettant d’explorer l’inhibition de HSD17B12 et de l’élongation d’acides gras à très longue chaîne comme nouvelle approche thérapeutique pour le traitement à large spectre des infections par les virus de la famille Flaviviridae. / Infections with viruses are major recurrent socio-economical and health problems worldwide. These include infections by viruses of the Flaviviridae family, which present a substantial global health burden and are among the priority areas of medical virology according to the Global Virus Network 2016 report. While the current treatment regimens for hepatitis C virus (HCV) infection have cure rates of more than 98%, other important members of Flaviviridae like dengue virus (DENV) and zika virus (ZIKV) have no specific licensed treatments. By taking advantage of the most-studied HCV, which our lab has developed a vast expertise in the last 20 years, we used proteomics data of an HCV interactome study, combining viral protein immunoprecipitation (IP) coupled to tandem mass spectrometry identification (IP-MS/MS) and functional genomics RNAi screening. The study uncovered the 17-beta-hydroxysteroid dehydrogenase type 12 (HSD17B12, also named DHB12), as a specific host interactor of core that promotes HCV replication. HSD17B12 catalytic activity is involved in the synthesis of very-long-chain fatty acids (VLCFA) upon the second step of the elongation cycle. In this study, taking HCV as a virus model, we elucidated the dependency of HCV, dengue virus (DENV) and zika virus (ZIKV) replication on expression and metabolic capacity of the host factor HSD17B12. We investigated the effects of the inhibition of gene expression by RNAi and of its pharmacological enzymatic inhibition on flavivirus replication in a broad-spectrum antiviral approach. We showed that silencing expression of HSD17B12 decreases viral replication, viral proteins and iv infectious particle production of the JFH1 strain of HCV in Huh7.5 cells. The cellular localization analysis of HSD17B12 showed a co-staining with double-stranded RNA (dsRNA) at viral replication sites and with core protein (and lipid droplets) at virus assembly sites. Furthermore, HSD17B12 gene silencing drastically reduced the number and size of lipid droplets. In association, the reduced expression of HSD17B12 by RNAi decreases oleic acid levels and lipids such as triglycerides (TG) and phosphatidylethanolamine (PE) in whole-cell extract. The data suggested the requirement of the metabolic capacity of HSD17B12 for HCV replication. Similarly, we provide evidence that HSD17B12 silencing significantly reduces DENV and ZIKV infectious particles. The studies support a role of HSD17B12 for effective viral RNA replication and particle assembly processes. Moreover, the specific HSD17B12 inhibitor, INH-12, reduces HCV replication at concentrations for which no appreciable cytotoxicity is observed. The treatment of DENV- and ZIKV-infected Huh- 7.5 cells with 20 μM of INH-12 dramatically reduces production of infectious particles by up to 3-log10 in infection assays, and completely block viral protein expression. In conclusion, these studies extends our understanding of the role of HSD17B12 in VLCFA synthesis required for the replication of HCV, allowing to explore the inhibition of HSD17B12 and elongation of VLCFA as a novel therapeutic approach for the treatment of a broad-spectrum of viruses of the Flaviviridae family.