Simultaneous determination of HCV genotype and NS5B resistance associated substitutions using dried serum spots from São Paulo state, Brazil

Hepatitis C virus (HCV) is responsible for more than 180 million infections worldwide, and about 80 % of infections are reported in Low and Middle-income countries (LMICs). Therapy is based on the administration of interferon (INF), ribavirin (RBV) or more recently Direct-Acting Antivirals (DAAs). However, amino acid substitutions associated with resistance (RAS) have been extensively described and can contribute to treatment failure, and diagnosis of RAS requires considerable infrastructure, not always locally available. Dried serum spots (DSS) sampling is an alternative specimen collection method, which embeds drops of serum onto filter paper to be transported by posting to a centralized laboratory. Here, we assessed feasibility of genotypic analysis of HCV from DSS in a cohort of 80 patients from São Paulo state Brazil. HCV RNA was detected on DSS specimens in 83 % of samples of HCV infected patients. HCV genotypes 1a, 1b, 2a, 2c and 3a were determined using the sequence of the palm domain of NS5B region, and RAS C316N/Y, Q309R and V321I were identified in HCV 1b samples. Concerning therapy outcome, 75 % of the patients who used INF +RBV as a previous protocol of treatment did not respond to DAAs, and 25 % were end-of-treatment responders. It suggests that therapy with INF plus RBV may contribute for non-response to a second therapeutic protocol with DAAs. One patient that presented RAS (V321I) was classified as non-responder, and combination of RAS C316N and Q309R does not necessarily imply in resistance to treatment in this cohort of patients. Data presented herein highlights the relevance of studying circulating variants for a better understanding of HCV variability and resistance to the therapy. Furthermore, the feasibility of carrying out genotyping and RAS phenotyping analysis by using DSS card for the potential of informing future treatment interventions could be relevant to overcome the limitations of processing samples in several location worldwide, especially in LMICs

Nanopore sequencing from extraction-free direct PCR of dried serum spots for portable hepatitis B virus drug-resistance typing

© 2020 Background: Effective drug regimens for the treatment of hepatitis B virus (HBV) infections are essential to achieve the World Health Organisation commitment to eliminate viral hepatitis by 2030. Lamivudine (3TC) is widely used in countries with high levels of chronic HBV, however resistance has been shown to occur in up to 50 % of individuals receiving continuous monotherapy for 4 years. Telbivudine (LdT) is now more commonly used in place of lamivudine but is ineffective against 3TC-resistant HBV. Genotyping and identification of resistanceassociated substitutions (RAS) is not practical in many locations. Objectives: A novel assay was designed to enable HBV genotyping and characterisation of resistance mutations directly from serum samples stored on filter paper, using Sanger and MinION sequencing. Study design: The assay was applied to a cohort of 30 samples stored on filter paper for several years with HBV viral loads ranging from 8.2 × 108 to 635 IU/mL. A set of 6 high-titre samples were used in a proof-of-principle study using the MinION sequencer. Results: The assay allowed determination of HBV genotype and elucidation of RAS down to 600 IU/mL using a 550bp amplicon. Sequencing of a 1.2 kb amplicon using a MinION sequencer gave results consistent with Sanger sequencing and allowed the identification of minor populations of variants. Conclusions: We present two approaches for reliable HBV sequencing and RAS identification using methods suitable for resource-limited environments. This is the first demonstration of extraction-free DNA sequencing direct from DSS using MinION and these workflows are adaptable to the investigation of other DNA viruses

Multiple effects of toxins isolated from Crotalus durissus terrificus on the hepatitis C virus life cycle

Hepatitis C virus (HCV) is one of the main causes of liver disease and transplantation worldwide. Current therapy is expensive, presents additional side effects and viral resistance has been described. Therefore, studies for developing more efficient antivirals against HCV are needed. Compounds isolated from animal venoms have shown antiviral activity against some viruses such as Dengue virus, Yellow fever virus and Measles virus. In this study, we evaluated the effect of the complex crotoxin (CX) and its subunits crotapotin (CP) and phospholipase A2 (PLA2-CB) isolated from the venom of Crotalus durissus terrificus on HCV life cycle. Huh 7.5 cells were infected with HCVcc JFH-1 strain in the presence or absence of these toxins and virus was titrated by focus formation units assay or by qPCR. Toxins were added to the cells at different time points depending on the stage of virus life cycle to be evaluated. The results showed that treatment with PLA2-CB inhibited HCV entry and replication but no effect on HCV release was observed. CX reduced virus entry and release but not replication. By treating cells with CP, an antiviral effect was observed on HCV release, the only stage inhibited by this compound. Our data demonstrated the multiple antiviral effects of toxins from animal venoms on HCV life cycle

Atividade antiviral de compostos naturais no ciclo replicativo do HCV

A Hepatite C é uma doença causada pelo vírus da Hepatite C (HCV), que afeta milhares de pessoas em todo o mundo. Representa um problema de saúde pública, sendo uma das principais causas de doenças e transplantes relacionados ao fígado. Não há uma vacina contra o HCV e os tratamentos atuais não são eficazes para todos os pacientes tratados, apresentando muitos efeitos colaterais e alto custo de desenvolvimento. Desta forma, fica evidente a necessidade do desenvolvimento de novas abordagens terapêuticas que produzam uma melhor resposta virológica sustentada, efeitos colaterais mais brandos e menor custo de produção. Neste contexto, compostos naturais podem fornecer uma fonte alternativa para a identificação de produtos com potencial terapêutico. O presente trabalho teve como objetivo avaliar os efeitos de compostos naturais, isolados do veneno da serpente Crotalus durissus terrificus (complexo heterodimérico crotoxina e suas subunidades crotapotina e Fosfolipase A2), e do extrato das folhas de Pterogyne nitens (sorbifolina e pedalitina), no ciclo replicativo do HCV in vitro. Estes compostos foram testados quanto às suas atividades antivirais por meio de infecção e tratamento de células Huh-7.5, e realização de ensaios de luciferase, western-blotting e imunofluorescência. Os dados obtidos demonstraram que tanto os compostos isolados de C. durissus terrificus quanto de P. nitens possuem efeito anti-HCV, sendo que alguns compostos inibiram mais de uma etapa do ciclo replicativo viral. Portanto, os múltiplos efeitos anti-HCV apresentados pelo tratamento com esses compostos demonstraram o potencial terapêutico de fontes naturais no tratamento da Hepatite C.Hepatitis C is a disease caused by Hepatitis C virus (HCV) that affects thousands of people worldwide. Represents a public health problem, being one of the main causes of liver disease and transplantation. There is no vaccine for HCV and the current therapy is not effective for all treated patients, presents many side effects and high cost of development. Thus, there is an evident need to develop new therapeutic approaches which result in a better sustained virologic response, milder side effects and lower production cost. In this context, natural compounds can provide an alternative source for the identification of products with therapeutic potential. This study aimed to evaluate the effects of natural compounds, isolated from Crotalus durissus terrificus venom (heterodimeric complex crotoxin and its subunits crotapotin and phospholipase A2), and from leaves extract of Pterogyne nitens (sorbifolin e pedalitin), on HCV life cycle in vitro. These compounds were screened for their antiviral activities by infecting and treating Huh-7.5 cells, and performing luciferase, western blotting and immunofluorescence assays. The data obtained demonstrated that both compounds isolated from Crotalus durissus terrificus and from P. nitens possess anti-, and some compounds inhibited more than one step of the virus life cycle. Therefore, the multiple anti-HCV effects presented by the treatment with these compounds demonstrated the therapeutic potential of natural sources in the treatment of Hepatitis C.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Natural compounds isolated from Brazilian plants are potent inhibitors of hepatitis C virus replication in vitro

Compounds extracted from plants can provide an alternative approach to new therapies. They present characteristics such as high chemical diversity, lower cost of production and milder or inexistent side effects compared with conventional treatment. The Brazilian flora represents a vast, largely untapped, resource of potential antiviral compounds. In this study, we investigate the antiviral effects of a panel of natural compounds isolated from Brazilian plants species on hepatitis C virus (HCV) genome replication. To do this we used firefly luciferase-based HCV sub-genomic replicons of genotypes 2a (JFH-1), 1b and 3a and the compounds were assessed for their effects on both HCV replication and cellular toxicity. Initial screening of compounds was performed using the maximum non-toxic concentration and 4 compounds that exhibited a useful therapeutic index (favourable ratio of cytotoxicity to antiviral potency) were selected for extra analysis. The compounds APS (EC50 = 2.3 lM), a natural alkaloid isolated from Maytrenus ilicifolia, and the lignans 3⁄ 43 (EC50 = 4.0 lM), 3⁄ 20 (EC50 = 8.2 lM) and 5⁄ 362 (EC50 = 38.9 lM) from Peperomia blanda dramatically inhibited HCV replication as judged by reductions in luciferase activity and HCV protein expression in both the subgenomic and infectious systems. We further show that these compounds are active against a daclatasvir resistance mutant subgenomic replicon. Consistent with inhibition of genome replication, production of infectious JFH-1 virus was significantly reduced by all 4 compounds. These data are the first description of Brazilian natural compounds possessing anti-HCV activity and further analyses are being performed in order to investigate the mode of action of those compounds.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Salivary Detection of Zika Virus Infection Using ATR-FTIR Spectroscopy Coupled with Machine Learning Algorithms and Univariate Analysis: A Proof-of-Concept Animal Study

Zika virus (ZIKV) diagnosis is currently performed through an invasive, painful, and costly procedure using molecular biology. Consequently, the search for a non-invasive, more cost-effective, reagent-free, and sustainable method for ZIKV diagnosis is of great relevance. It is critical to prepare a global strategy for the next ZIKV outbreak given its devastating consequences, particularly in pregnant women. Attenuated total reflection–Fourier transform infrared (ATR-FTIR) spectroscopy has been used to discriminate systemic diseases using saliva; however, the salivary diagnostic application in viral diseases is unknown. To test this hypothesis, we intradermally challenged interferon-gamma gene knockout C57/BL6 mice with ZIKV (50 µL,105 FFU, n = 7) or vehicle (50 µL, n = 8). Saliva samples were collected on day three (due to the peak of viremia) and the spleen was also harvested. Changes in the salivary spectral profile were analyzed by Student’s t test (p −1 as a potential candidate to discriminate ZIKV and control salivary samples. Three PCs explained 93.2% of the cumulative variance in PCA analysis and the spectrochemical analysis with LDA achieved an accuracy of 93.3%, with a specificity of 87.5% and sensitivity of 100%. The LDA-SVM analysis showed 100% discrimination between both classes. Our results suggest that ATR-FTIR applied to saliva might have high accuracy in ZIKV diagnosis with potential as a non-invasive and cost-effective diagnostic tool

Multiple effects of toxins isolated from Crotalus durissus terrificus on the hepatitis C virus life cycle.

Hepatitis C virus (HCV) is one of the main causes of liver disease and transplantation worldwide. Current therapy is expensive, presents additional side effects and viral resistance has been described. Therefore, studies for developing more efficient antivirals against HCV are needed. Compounds isolated from animal venoms have shown antiviral activity against some viruses such as Dengue virus, Yellow fever virus and Measles virus. In this study, we evaluated the effect of the complex crotoxin (CX) and its subunits crotapotin (CP) and phospholipase A2 (PLA2-CB) isolated from the venom of Crotalus durissus terrificus on HCV life cycle. Huh 7.5 cells were infected with HCVcc JFH-1 strain in the presence or absence of these toxins and virus was titrated by focus formation units assay or by qPCR. Toxins were added to the cells at different time points depending on the stage of virus life cycle to be evaluated. The results showed that treatment with PLA2-CB inhibited HCV entry and replication but no effect on HCV release was observed. CX reduced virus entry and release but not replication. By treating cells with CP, an antiviral effect was observed on HCV release, the only stage inhibited by this compound. Our data demonstrated the multiple antiviral effects of toxins from animal venoms on HCV life cycle

Antiviral Activity of Quercetin Hydrate against Zika Virus

Zika virus (ZIKV) has re-emerged in recent decades, leading to outbreaks of Zika fever in Africa, Asia, and Central and South America. Despite its drastic re-emergence and clinical impact, no vaccines or antiviral compounds are available to prevent or control ZIKV infection. This study evaluated the potential antiviral activity of quercetin hydrate against ZIKV infection and demonstrated that this substance inhibits virus particle production in A549 and Vero cells under different treatment conditions. In vitro antiviral activity was long-lasting (still observed 72 h post-infection), suggesting that quercetin hydrate affects multiple rounds of ZIKV replication. Molecular docking indicates that quercetin hydrate can efficiently interact with the specific allosteric binding site cavity of the NS2B-NS3 proteases and NS1-dimer. These results identify quercetin as a potential compound to combat ZIKV infection in vitro

Crystal structure of the complex crotoxin from <i>Crotalus durissus terrificus</i> venom.

<p>The basic subunit (PLA₂-CB) is displayed in blue (A). The overall structure of crotoxin complex (B). The three chains of acid subunit (crotapotin) is shown in red [α], light pink [β] and pink [γ] and (C) (PDB ID: 3R0L).</p

Effect of toxins on CD81 cell receptors.

<p>Huh-7.5 cells were incubated with CD81/TAPA1 antibody and 10 μg/ml of CX, PLA₂-CB or PBS. Then cells were washed and incubated with secondary antibody Alexa Fluor 594. Cells were fixed with 4% paraformaldehyde and labelled for nuclei with DAPI and analyzed on Fluorescence microscopy ZEN lite 2012.</p