Variability and resistance mutations in the hepatitis C virus NS3 protease in patients not treated with protease inhibitors

The goal of treatment of chronic hepatitis C is to achieve a sustained virological response, which is defined as exhibiting undetectable hepatitis C virus (HCV) RNA levels in serum following therapy for at least six months. However, the current treatment is only effective in 50% of patients infected with HCV genotype 1, the most prevalent genotype in Brazil. Inhibitors of the serine protease non-structural protein 3 (NS3) have therefore been developed to improve the responses of HCV-infected patients. However, the emergence of drug-resistant variants has been the major obstacle to therapeutic success. The goal of this study was to evaluate the presence of resistance mutations and genetic polymorphisms in the NS3 genomic region of HCV from 37 patients infected with HCV genotype 1 had not been treated with protease inhibitors. Plasma viral RNA was used to amplify and sequence the HCV NS3 gene. The results indicate that the catalytic triad is conserved. A large number of substitutions were observed in codons 153, 40 and 91; the resistant variants T54A, T54S, V55A, R155K and A156T were also detected. This study shows that resistance mutations and genetic polymorphisms are present in the NS3 region of HCV in patients who have not been treated with protease inhibitors, data that are important in determining the efficiency of this new class of drugs in Brazil.

Vírus da hepatite B: avaliação da resposta sorológica à vacina em funcionários de limpeza de hospital-escola

A hepatite viral B constitui um dos mais importantes problemas de saúde pública em todos os continentes. O vírus da hepatite B se transmite por via parenteral e, sobretudo, por via sexual. O objetivo foi avaliar a população ativa dos funcionários de limpeza do hospital da Faculdade de Medicina de Botucatu-UNESP, que receberam esquema completo de vacinação contra a hepatite B, medir os níveis de anticorpo contra o AgHBs (anti-HBs) e avaliar a sua relação com as condições epidemiológicas gerais, de vida pessoal e profissional e de risco de infecção pelo vírus da hepatite B.

Molecular models of NS3 protease variants of the Hepatitis C virus

Background: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed.Results: the atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures.Conclusions: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.

Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response

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

Optimization of an amperometric biosensor for the detection of hepatitis C virus using fractional factorial designs

Fractional factorial design and factorial with center point design were applied to the development of an amperometric biosensor for the detection of the hepatitis C virus. Biomolecules were immobilized by adsorption on graphite electrodes modified with siloxane-poly(propyleneoxide) hybrid matrix prepared using the sol-gel method. Several parameters were optimized, such as the streptavidin concentration at 0.01 mg mL(-1) and 1.0% bovine serum albumin, the incubation time of the electrodes in the complementary DNA solution for 30 minutes and a 1: 1500 dilution of the avidin-peroxidase conjugate, among others. The application of chemometric studies has been efficient, since the best conditions have been established with a restricted number of experiments, indicating the influence of different factors on the system.

Label-free DNA detection of hepatitis C virus based on modified conducting polypyrrole films at microelectrodes and atomic force microscopy tip-integrated electrodes

We present a new strategy for the label-free electrochemical detection of DNA hybridization for detecting hepatitis C virus based on electrostatic modulation of the ion-exchange kinetics of a polypyrrole film deposited at microelectrodes. Synthetic single-stranded 18-mer HCV genotype-1-specific probe DNA has been immobilized at a 2,5-bis(2-thienyl)-N-(3-phosphoryl-n-alkyl)pyrrole film established by electropolymerization at the previously formed polypyrrole layer. HCV DNA sequences (244-mer) resulting from the reverse transcriptase-linked polymerase chain reaction amplification of the original viral RNA were monitored by affecting the ion-exchange properties of the polypyrrole film. The performance of this miniaturized DNA sensor system was studied in respect to selectivity, sensitivity, and reproducibility. The limit of detection was determined at 1.82 x 10(-21) mol L-1. Control experiments were performed with cDNA from HCV genotypes 2a/c, 2b, and 3 and did not show any unspecific binding. Additionally, the influence of the spacer length of 2,5-bis(2-thienyl)-N-(3-phosphoryl-n-alkyl)pyrrole on the behavior of the DNA sensor was investigated. This biosensing scheme was finally extended to the electrochemical detection of DNA at submicrometer-sized DNA biosensors integrated into bifunctional atomic force scanning electrochemical microscopy probes. The 18-mer DNA target was again monitored by following the ion-exchange properties of the polypyrrole film. Control experiments were performed with 12-base pair mismatched sequences.

In vitro detection of hepatitis C virus in platelets from uninfected individuals exposed to the virus

Introduction ,,,,,Despite hepatocytes being the target cells of hepatitis C virus (HCV), viral ribonucleic acid RNA has been detected in other cells, including platelets, which have been described as carriers of the virus in the circulation of infected patients. Platelets do not express cluster differentiation 81 CD81, the main receptor for the virus in hepatocytes, although this receptor protein has been found in megakaryocytes. Still, it is not clear if HCV interacts with platelets directly or if this interaction is a consequence of its association with megakaryocytes. The aim of this study was to evaluate the interaction of HCV with platelets from non-infected individuals, after in vitro exposure to the virus. ,,,, ,,,, ,,,,,Methods ,,,,,Platelets obtained from 50 blood donors not infected by HCV were incubated in vitro at 37°C for 48h with serum containing 100,000IU∕mL of genotype 1 HCV. After incubation, RNA extracted from the platelets was assayed for the presence of HCV by reverse transcription – polymerase chain reaction RT-PCR. ,,,, ,,,, ,,,,,Results ,,,,,After incubation in the presence of virus, all samples of platelets showed HCV RNA. ,,,, ,,,, ,,,,,Conclusions ,,,,,The results demonstrate that, in vitro, the virus interacts with platelets despite the absence of the receptor CD81, suggesting that other molecules could be involved in this association.

Using pegylated interferon alfa-2b and ribavirin to treat chronic hepatitis patients infected with hepatitis C virus genotype 1: Are nonresponders and relapsers different populations?

The combination of pegylated interferon (PEG-INF) and ribavirin is currently the best treatment for chronic hepatitis C, providing a sustained virological response (SVR) in 54%-63% of patients. In patients infected with hepatitis C virus (HCV) genotype 1, the SVR rate is 42%-52%. To evaluate the treatment efficacy of this drug combination, we conducted an open, prospective study of 58 consecutive treatment-naive patients infected with HCV genotype 1 and treated at a university hospital, comparing those presenting an SVR (SVRs), nonresponders (NRs), and relapsers (RELs). Among the intent-to-treat patients, an end-of-treatment virological response was achieved in 69 % of the sample as a whole and in 52 % of the SVRs. We found that being an SVR was significantly associated with mild fibrosis (p = 0.04) and with undetectable HCV RNA at weeks 12 and 24 of treatment (p < 0.0001). Comparing the SVR and REL groups, we observed that being older than 40 was significantly associated with being a REL (p = 0.04). Being an NR was found to be associated with severe fibrosis and moderate inflammatory infiltrates (portal or periportal). In the polytomous logistic regression, no independent factors were associated with the REL group when compared with the SVR group. We conclude that RELs and NRs differ in comparison with SVRs. The RELs accounted for 17% of the sample. The HCV RNA test results at weeks 12 and 24 of treatment, although independent predictors of non-response (OR: 4.8 and 8.2, respectively), did not differ between SVRs and RELs.

Progression of liver fibrosis in blood donors infected with hepatitis C virus

Background/Aims. Chronic hepatitis by HCV is progressive towards cirrhosis, with variable rate. We evaluated the rate of fibrosis progression (RFP), risk factors associated with advanced fibrosis (F3 and F4), and estimated the evolution time to cirrhosis. Methods. We transversely selected 142 blood donors infected only with HCV, with a known route of infection, submitted to liver biopsy at admission. RFP= ratio between stage of fibrosis (METAVIR)/estimated duration of infection in years. Non-parametric tests and logistic regression analysis, with significance level of 5% were used. Results. Median RFP was 0.086 U/year (0.05 - 0.142). Ten patients had F4 and 25 had F3. Median RFP values were significantly different (p=0.001) from one age group at contamination to the others and ALT and AST levels. There were no differences in the expected evolution to cirrhosis between intermediate fibrosers (F2) and the rapid fibrosers (F3 and F4). The independent variables associated with advanced fibrosis were ALT (OR 7.2) and GGT (OR 6.4) and age at inclusion (OR 1.12). Conclusion. This study suggests that RFP is extremely variable, it is exponential with age, and mainly influenced by host characteristics, especially age at contamination and possibly ethnical group. These asymptomatic patients had high percentage of fibrosis F2, F3 and F4.

Structural studies of Helicase NS3 variants from Hepatitis C virus genotype 3 in virological sustained responder and non-responder patients

Background. About 130 million people are infected with the hepatitis C virus (HCV) worldwide, but effective treatment options are not yet available. One of the most promising targets for antiviral therapy is nonstructural protein 3 (NS3). To identify possible changes in the structure of NS3 associated with virological sustained response or non-response of patients, a model was constructed for each helicase NS3 protein coding sequence. From this, the goal was to verify the interaction between helicases variants and their ligands. Findings. Evidence was found that the NS3 helicase portion of non-responder patients contained substitutions in its ATP and RNA binding sites. K210E substitution can cause an imbalance in the distribution of loads, leading to a decrease in the number of ligations between the essential amino acids required for the hydrolysis of ATP. W501R substitution causes an imbalance in the distribution of loads, leading and forcing the RNA to interact with the amino acid Thr269, but not preventing binding of ribavirin inhibitor. Conclusions. Useful information is provided on the genetic profiling of the HCV genotype 3, specifically the coding region of the NS3 protein, improving our understanding of the viral genome and the regions of its protein catalytic site. © 2010 Rahal 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 do vírus da hepatite B na infecção crônica pelo vírus da hepatite C: perfil das séricas e histopatologia hepática

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Vírus da hepatite B: avaliação do risco de infecção e da resposta sorológica à vacina em funcionários de limpeza do Hospital das Clínicas da Faculdade de Medicina de Botucatu - UNESP

Pós-graduação em Doenças Tropicais - FMB

Carcinoma hepatocelular e as infecções pelos vírus das hepatites B e C na Amazônia Oriental: estudo clínico-sorológico e de biologia molecular

Com o objetivo de contribuir para um melhor conhecimento do eventual envolvimento das infecções pelos vírus das hepatites B e C, na etiopatogenia do carcinoma hapatocelular (CHC) na Amazônia Oriental, estudaram-se 36 pacientes internados em três hospitais públicos em Belém (PA), de janeiro de 1992 a março de 1999. Os critérios de inclusão adotados foram: o clínico, associado à imagenologia compatível, níveis séricos de alfafetoproteína (AFP) acima de 400ng/ml e/ou histopatologia compatível. Foram avaliados os aspectos clínicos, exames bioquímicos e hematológicos, imagenologia, histopatologia, níveis séricos de AFP e exames sorológicos das hepatites B e C. A presença dos ácidos nucléicos virais, o HBV-DNA e o HCV-RNA, foi avaliada a partir da detecção no soro pela reação em cadeia da polimerase. Observou-se um predomínio do sexo masculino (p<0.01), com reação M/F de 6,2: 1. Média e medianas gerais de idade foram, respectivamente, 50,8 e 53,0 anos, com amplitude de 6-81 anos. A maioria dos pacientes (52,7%) era procedente da zona rural, sendo a profissão de lavrador a mais freqüente (p<0,01). Etilismo foi encontrado em 33,3% dos casos. Dor abdominal e hepatomegalia, presentes em 94,4% dos casos, foram os sintomas e sinais mais freqüentes. Observou-se a presença de cirrose em 83,3% dos casos, sendo 80% enquadrados nas classes B e C (child-pugh). Cinqüenta por cento apresentaram complicações durante o diagnóstico, sendo as mais freqüentes a encefalopatia hepática e a hemorragia digestiva alta, relacionadas à doença hepática crônica de base. Marcadores sorológicos de infecção pelo HBV e pelo HCV foram encontrados em, respectivamente, 88,9% e 8,3% da casuística. Em 11,1% não se encontrou marcador sorológico. O HbsAg foi encontrado em 58, 3%. Anti-HBc foi encontrado em 86%, estando associado ao anti- HBs em 25%. Entre os HbsAg positivos: o anti- Hbe foi encontrado em 85%; o antiHBc IgM em 57,1%; e o anti-HD não foi detectado. O HBV- DNA foi encontrado em 37,7% do total de casos e em 65% dos HbsAG positivos. O HCV-RNA foi encontrado em 8,5% da amostra estudada e em 100% dos casos anti-HCV positivos. Não foi observada positividade para o HBV-DNA e para o HCV-RNA em soros de pacientes HbsAG ou anti- HCV negativos. A AFP esteve acima da normalidade em 88,9% dos casos, estando acima de 400 ng/ml em 75% e em 27,8% a titulações foi superior a 70.000 ng/ml. A ultrassonografia abdominal mostrou tumores com múltiplos nódulos em 63,9% e, nódulo único em 36,1% dos casos. O tipo histológico predominante foi carcinoma bem diferenciado do tipo trabecular (p<0,05). Os casos HbsAg positivos apresentaram menor média de idade e níveis de AFP mais elevados (p<0,01). A maioria dos pacientes se encontravam em fase avançada de doenças com uma taxa de óbito durante o diagnóstico de 38,9%. Conclui-se que, na Amazônia Oriental, a infecção pelo HBV parece exercer importância na etiologia do CHC, ressaltando-se a necessidade de incrementação de medidas preventivas, como vacinação e programa de detecção precoce do tumor em populações de risco. São necessários estudos adicionais controlados ou direcionados, para os possíveis co-fatores de importância na região, o que pode contribuir para um melhor entendimento dos mecanismos envolvidos na hepatocarcinogênese.