Analysis of HCV quasispecies dynamic under selective pressure of combined therapy

Background: The quasispecies composition of Hepatitis C virus (HCV) could have important implications with regard to viral persistence and response to interferon-based therapy. The complete NS5A was analyzed to evaluate whether the composition of NS5A quasispecies of HCV 1a/1b is related to responsiveness to combined interferon pegylated (PEG-IFN) and ribavirin therapy.Methods: Viral RNA was isolated from serum samples collected before, during and after treatment from virological sustained responder (SVR), non-responder (NR) and the end-of-treatment responder patients (ETR). NS5A region was amplified, cloned and sequenced. Six hundred and ninety full-length NS5A sequences were analyzed.Results: This study provides evidence that lower nucleotide diversity of the NS5A region pre-therapy is associated with viral clearance. Analysis of samples of NRs and the ETRs time points showed that genetic diversity of populations tend to decrease over time. Post-therapy population of ETRs presented higher genetic distance from baseline probably due to the bottleneck phenomenon observed for those patients in the end of treatment. The viral effective population of those patients also showed a strong decrease after therapy. Otherwise, NRs demonstrated a continuous variation or stability of effective populations and genetic diversity over time that did not seem to be related to therapy. Phylogenetic relationships concerning complete NS5A sequences obtained from patients did not demonstrate clustering associated with specific response patterns. However, distinctive clustering of pre/post-therapy sequences was observed. In addition, the evolution of quasispecies over time was subjected to purifying or relaxed purifying selection. Codons 157 (P03), 182 and 440 (P42), 62 and 404 (P44) were found to be under positive selective pressure but it failed to be related to the therapy.Conclusion: These results confirm the hypothesis that a relationship exists between NS5A heterogeneity and response to therapy in patients infected with chronic hepatitis C. © 2013 Jardim et al.; licensee BioMed Central Ltd.

On Hepatitis C Virus Evolution: The Interaction between Virus and Host towards Treatment Outcome

Background:Hepatitis C is a disease spread throughout the world. Hepatitis C virus (HCV), the etiological agent of this disease, is a single-stranded positive RNA virus. Its genome encodes a single precursor protein that yields ten proteins after processing. NS5A, one of the non-structural viral proteins, is most associated with interferon-based therapy response, the approved treatment for hepatitis C in Brazil. HCV has a high mutation rate and therefore high variability, which may be important for evading the immune system and response to therapy. The aim of this study was to analyze the evolution of NS5A quasispecies before, during, and after treatment in patients infected with HCV genotype 3a who presented different therapy responses.Methods:Viral RNA was extracted, cDNA was synthesized, the NS5A region was amplified and cloned, and 15 clones from each time-point were sequenced. The sequences were analyzed for evolutionary history, genetic diversity and selection.Results:This analysis shows that the viral population that persists after treatment for most non-responder patients is present in before-treatment samples, suggesting it is adapted to evade treatment. In contrast, the population found in before treatment samples from most end-of-treatment responder patients either are selected out or appears in low frequency after relapse, therefore changing the population structure. The exceptions illustrate the uniqueness of the evolutionary process, and therefore the treatment resistance process, in each patient.Conclusion:Although evolutionary behavior throughout treatment showed that each patient presented different population dynamics unrelated to therapy outcome, it seems that the viral population from non-responders that resists the treatment already had strains that could evade therapy before it started. © 2013 Bittar et al.

Influência da salinidade do fluido na avaliação da compactação e da resistividade elétrica de dois solos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Fabricação e caracterização metalográfica e mecânica de tiras de ligas metálicas fundidas e tixolaminadas no estado semi-sólido de diferentes intervalos de solidificação

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise por ferramentas de bioinformática da proteína não-estrutural 5A do vírus da hepatite C genótipo 1 e 3 em amostras pré-tratamento

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Lesões traumáticas de pele causadas pelos espinhos de Mimosa pudica e Mimosa debilis em equídeos

Foram realizadas pesquisas sobre a natureza e causa de lesões de pele em equídeos em uma propriedade no município de Castanhal, região Nordeste do Estado do Pará. Foram realizadas visitas técnicas, estudos epidemiológicos, coletas de sangue, biópsias de pele afetada e a inspeção da pastagem. O estudo incluiu 25 equídeos, dos quais 14 machos e 11 fêmeas, de seis meses e oito anos de idade. Os animais apresentaram lesões ulcerativas, de bordos irregulares, na cabeça (narinas, focinho, lábios superiores e inferiores e chanfro), na cavidade oral (vestíbulo bucal e gengiva) e nos membros (boletos, metacarpos e metatarsos e articulação escápulo-umeral). No exame histopatológico foram observados focos de erosões cutâneas, caracterizados por perda e necrose da epiderme, com espongiose, degeneração vesicular da epiderme remanescente e leve infiltrado inflamatório na derme subjacente, constituído predominantemente por macrófagos e, em menor grau, eosinófilos. Na inspeção da pastagem, constituída de Brachiaria humidicola, foi constatada grande invasão de duas plantas providas de espinhos, Mimosa pudica e Mimosa debilis, ambas da família Leg. Mimosoideae. Concluiu-se, que as lesões de pele foram causadas pela ação traumática dos espinhos de Mimosa pudica e Mimosa debilis.

Intoxicação por Cestrum laevigatum (Solanaceae) em bubalinos

Com base no histórico e em dados clínico-patológicos, bem como a inspeção das pastagens, foi estabelecido o diagnóstico de intoxicação por Cestrum laevigatum Schlecht. em uma mortandade de búfalos no município de Itaguaí, RJ. A intoxicação foi reproduzida em dois búfalos. Amostras de folhas dessecadas de C. laevigatum foram administradas manualmente por via oral a quatro bubalinos da raça Murrah, em doses únicas correspondentes a 20g/kg e 40g/kg da planta fresca. A dose correspondente a 40g/kg provocou o aparecimento dos sinais clínicos que consistiram principalmente em apatia, anorexia, ausência dos movimentos ruminais, dismetria, excitação e agressividade, e levaram à morte os dois animais em até 65 horas após a administração da planta. Dos outros dois bufalos que receberam a dose correspondente a de 20g/kg da planta fresca, um apresentou sinais clínicos, caracterizados principalmente por diminuição dos movimentos ruminais, e recuperou-se em 97h22min após a administração da planta; o outro não apresentou sinais clínicos. Os exames laboratoriais para avaliação bioquímica indicaram lesão hepática. Em um búfalo que morreu, as principais alterações macroscópicas foram fígado de cor alaranjada, com superfície externa e de corte com nítido aspecto de noz moscada; no outro, o fígado tinha a superfície externa e de corte de cor alaranjada, sem aspecto de noz moscada. Outras alterações encontradas nos dois búfalos foram leve edema da parede da vesícula biliar, endocárdio do ventrículo esquerdo com equimoses extensas e endocárdio do ventrículo direito com algumas petéquias; mucosa do abomaso levemente avermelhada e conteúdo levemente ressecado; intestino grosso com pouco conteúdo, levemente ressecado e envolto por muco. Os exames histopatológicos revelaram no fígado, acentuada necrose de coagulação dos hepatócitos nas zonas centrais e intermediárias dos lóbulos. Na periferia dessas regiões necrosadas observou-se um halo de hepatócitos com vacuolização.

Intoxicação natural e experimental por Metternichia princeps (Solanaceae) em caprinos

Entre os anos de 2007 e 2009 ocorreu uma doença nefrotóxica de evolução subaguda com alta mortandade em caprinos em uma propriedade no município de Itaguaí, estado do Rio de Janeiro. Levantou-se a suspeita de que Metternichia princeps, planta pertencente à família Solanaceae, seria a causa. Através de experimentação em caprinos o quadro clínico-patológico de intoxicação por esta planta e a dose letal foram estabelecidos. Na experimentação foram utilizados 12 caprinos de diferentes raças, de ambos os sexos, jovens a adultos, com pesos acima de 15 kg. Os animais que receberam as doses de 30g/kg em 5 dias, 15g/kg em 3 dias, doses únicas de 10g/kg e de 5g/kg, morreram. Dos três animais que receberam as doses únicas de 2,5g/kg, dois morreram e um não apresentou sinais clínicos e o animal que recebeu a dose única de 1,25g/kg, também não apresentou sinais clínicos. O início dos sinais clínicos após a administração da planta variou entre 7h e 46h45min. A evolução variou entre 3h6min e 126h40min. Os primeiros sinais clínicos apresentados foram inapetência, adipsia, apatia e relutância ao movimento. Em seguida os animais entravam em decúbito esternal e ao serem colocados em estação, mantinham os membros anteriores flexionados, apoiavam apenas os posteriores no chão até evoluírem para flexão dos quatro membros e seguia-se o decúbito lateral. À necropsia destacaram-se o edema de tecido adiposo perirrenal, rins pálidos e, ao corte, com estriação esbranquiçada desde o córtex até a região medular. À histopatologia foi verificada acentuada necrose coagulativa das células epiteliais dos túbulos uriníferos. Comparativamente aos casos naturais, os caprinos intoxicados experimentalmente por M. princeps apresentaram quadro clínico-patológico semelhante. Desta maneira foi comprovado que Metternichia princeps é responsável pela doença nefrotóxica em caprinos no Rio de Janeiro; a menor dose que causou a morte dos caprinos nos experimentos foi 2,5g/kg.

Surto de encefalomielite equina Leste na Ilha de Marajó, Pará

Nove casos de encefalomielite equina foram estudados na Ilha de Marajó, estado do Pará, Brasil. Os equinos apresentavam dificuldade em se manter em estação, andavam em círculo, tinham acentuada depressão, pálpebras cerradas, paralisia da língua, tremores musculares, bruxismo, anorexia e desidratação. Alguns apresentavam diminuição dos reflexos auricular, palpebral, de ameaça, diminuição do tônus da língua e taquicardia. Posição de auto-auscultação foi observada com frequência. Os animais muitas vezes eram encontrados apoiados em troncos e cercas para se manterem em estação. À necropsia verificou-se hemorragia das leptomeninges e da medula, alguns apresentaram ainda aderência das leptomeninges. À histopatologia verificou-se encefalite difusa que afetava principalmente a substância cinzenta, com meningite e coroidite. Foi observada perivasculite mononuclear. Em dois equinos identificou-se o vírus da encefalomielite equina Leste pela reação de Semi-Nested transcrição reversa de polimerase em cadeia (Semi-Nested RT-PCR).

Synthesis and evaluation of novel dapsone-thalidomide hybrids for the treatment of type 2 leprosy reactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Vertical transmission of hepatitis C virus: A tale of multiple outcomes

Globally, hepatitis C virus (HCV) infection affects approximately 130 million people and 3 million new infections occur annually. HCV is also recognized as an important cause of chronic liver disease in children. The absence of proofreading properties of the HCV RNA polymerase leads to a highly error prone replication process, allowing HCV to escape host immune response. The adaptive nature of HCV evolution dictates the outcome of the disease in many ways. Here, we investigated the molecular evolution of HCV in three unrelated children who acquired chronic HCV infection as a result of mother-to-child transmission, two of whom were also coinfected with HIV-1. The persistence of discrete HCV variants and their population structure were assessed using median joining network and Bayesian approaches. While patterns of viral evolution clearly differed between subjects, immune system dysfunction related to HIV coinfection or persistent HCV seronegativity stand as potential mechanisms to explain the lack of molecular evolution observed in these three cases. In contrast, treatment of HCV infection with PegIFN, which did not lead to sustained virologic responses in all 3 cases, was not associated with commensurate variations in the complexity of the variant spectrum. Finally, the differences in the degree of divergence suggest that the mode of transmission of the virus was not the main factor driving viral evolution. (C) 2013 Elsevier B. V. All rights reserved.

Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Hepatitis C virus molecular evolution: Transmission, disease progression and antiviral therapy

Hepatitis C virus (HCV) infection represents an important public health problem worldwide. Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors. Virus molecular evolution plays an important role in HCV transmission, disease progression and therapy outcome. The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures (e.g., host immune responses and antiviral therapy). HCV molecular evolution is shaped by different mechanisms including a high mutation rate, genetic bottlenecks, genetic drift, recombination, temporal variations and compartmentalization. These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner. Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV. As a result, superior sustained viral responses have been attained. The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer, more potent antivirals, bringing us one step closer to the interferon-free era. (C) 2014 Baishideng Publishing Group Inc. All rights reserved.

Pirossequenciamento de alta cobertura da região hipervariável 1 do Vírus da Hepatite C

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)