Showing papers on "NS5B published in 2023"

Description of an Equine Hepacivirus Cluster in a Horse Stable in Italy

Abstract: Equine hepacivirus (EqHV), also known as Hepacivirus A, represents the most closely related genetic homologue of human hepatitis C virus (HCV). Although detected worldwide, limited information on the clinical features of this infection is available and on the mechanisms by which EqHV is transmitted. In this study, we describe a spread of infection of EqHV that occurred in a small stable of horses in southern Italy. The RNA of EqHV was detected in 6/13 (46.2%) sera of the horses introduced into the herd, at different times, over a period of approximately one year. Based on the sequencing analyses of genomic portions located in the NS5B, 5′UTR, and NS3 genes, the viruses detected in the animals were genetically highly related (100% nt identity) to each other. The nearly full-length genome of the virus identified from two horses was generated. For one animal with a profile of chronic infection, the genome sequence was determined with a 7-month interval, revealing 26nt changes resulting in 11 nonsynonymous intrahost nucleotide variations. Overall, based on the epidemiological information, we support the hypothesis that horizontal transmission occurred in the herd.

Pharmacoinformatics-based strategy in designing and profiling of some Pyrazole analogues as novel hepatitis C virus inhibitors with pharmacokinetic analysis

Abstract: Hepatitis C virus (HCV) infection promotes death rates all over the world. Sofosbuvir is a standard drug for the cure of HCV but unfortunately, it receives a lot of attention for its pricing problems. As a result, it is crucial to consider alternative HCV treatments that are both cost-effective and free of side effects. We report how a pharmacoinformatics-based technique was used to generate and profile certain Pyrazole analogues as novel hepatitis C virus inhibitors by exploring the PubChem drug repository for the lead molecule with further optimization. The proposed molecules all interact by filling the protein target’s binding domain to inhibit the receptor. With binding energy of −35.72 kcal/mol, compound 17e was found as a highly potent NS5B inhibitor, exceeding Sofosbuvir, the FDA-approved NS5B inhibitor with a binding energy of −30.34 kcal/mol. Additionally, the ADMET assessment of the selected molecules (17e) shows outstanding quality with a drug score of 0.74 when especially in comparison to Sofosbuvir, which has a drug score of 0.31. Future studies should therefore focus on the molecular dynamics, synthesis, in vivo testing, and in vitro evaluation of these substances to validate our hypothesis.

Hepatitis C virus genotype 5 variability in treatment naïve patients in South Africa.

Abstract: INTRODUCTION Hepatitis C virus (HCV) genotype 5 was originally identified in South Africa, where it represents 35-60% of all HCV infections. There are limited data on resistance associated variants (RAVs) in South Africa. Thus, we investigated variability within the NS3/NS4A, NS5A, and NS5B genes of treatment-naïve patients individuals with HCV genotype 5 infection at the Dr George Mukhari Academic Hospital (DGMAH) in Pretoria, South Africa. METHODS Nested PCR was performed to amplify the NS3/4A, NS5A and NS5B genes. RAVs were evaluated using the Geno2pheno tool. RESULTS In the NS3/4A gene, F56S and T122A were detected in one sample each. The D168E mutation was detected in 7 samples. Within the NS5A gene, the T62M mutation was detected in 2 individuals. In the NS5B gene, 8 of 12 individuals (67%) had the A421V mutation, while all 12 individuals (100%) had the S486A mutation. DISCUSSION RAVs were detected frequently among treatment-naïve individuals with HCV genotype 5 infection in South Africa. Thus, resistance testing may be prudent when initiating treatment of patients with genotype 5 infection. Additional population-based studies are needed to understand the prevalence of these RAVs during HCV genotype 5 infection.

[Analysis of resistance-associated substitutions in hepatitis C virus sequences from Kyrgyzstan].

Abstract: INTRODUCTION The countries of Central Asia, including Kyrgyzstan, are characterized by high prevalence and morbidity of HCV infection. Identification of HCV genotype and mutations associated with resistance to direct-acting antiviral (DAA) plays an important role either in conducting molecular epidemiological studies or choosing the treatment tactics. The aim of the work was to research of the genotype diversity of HCV variants circulating in Kyrgyzstan and the identification among them the mutations associated with the development of resistance to DAA. MATERIALS AND METHODS 38 serum samples from HCV-infected residents of Kyrgyzstan were analyzed in this study. The nucleotide sequences of viral gene fragments (NS3, NS5A, NS5B) were determined by Sangers sequencing and deposited in the international GenBank database under the numbers ON841497ON841534 (NS5B), ON841535ON841566 (NS5A), and ON841567ON841584 (NS3). RESULTS The HCV subtypes 1b (52.6%; 95% CI 37.367.5%), 3a (44.8%; 95% CI 30.260.2%) and 1a (2.6%; 95% CI 0.513.4%) are circulating in Kyrgyzstan. 37% (95% CI 1959%) of subtype 1b isolates had C316N mutation in the NS5A gene; 46% (95% CI 2370%) had F37L mutation in the NS5A gene; 45% (95% CI 2272%) had Y56F mutation in the NS3 gene. Among subtype 3a isolates, resistance-associated mutations in NS5B fragment were not found. 22% (95% CI 945%) of subtype 3a sequences had a Y93H mutation in the NS5A gene. A combination of Y56F + Q168 + I170 mutations was identified among all sequences of NS3 gene. DAA resistance mutations were not found in NS3, NS5A, NS5B genes of subtype 1a sequence. CONCLUSION A rather high prevalence of mutations associated with resistance or significant decrease in sensitivity to DAA among HCV sequences from Kyrgyzstan was shown. Updating of data on HCV genetic diversity is necessary for timely planning of measures to combat epidemic.

C316N Polymorphism associated with resistance to HCV polymerase NS5B in treatment-naïve patient with chronic hepatitis C

Abstract: High genetic variability of the hepatitis C virus (HCV) due to copying errors during the viral cycle leads to the development of mutations, and resistance-associated variants (RAVs), even with the advent of direct-acting antivirals (DAAs). Assessment of the presence of these mutations is essential for targeted treatment regimens and proper infection management, as treatment is related to genotypes and developing mutations. The study investigates the presence of resistance mutations in the nonstructural protein 5B (NS5B) region in treatment naïve patients. 100 positive plasma samples from patients presented for a follow-up service of chronic HCV infection (CHC) at the National Institute of Hygiene (NIH) of Rabat-Morocco. NS5B sequencing revealed the presence of C316N in one treatment naïve patient of subtype 1b. Additionally, six treatment-naïve patients with subtypes 2a and 2i exhibited the presence of the M289L mutation.

Molecular Docking: Bioactive Compounds in Indramayu Mango (Mangifera indica L.) Peel Waste as NS5B Hepatitis C Virus (HCV) Inhibitor

Abstract: Background: Hepatitis C is caused by hepatitis C virus (HCV) infection. HCV infection is one of the biggest causes of chronic liver disease. About 60-80% of patients with acute hepatitis C will develop chronic hepatitis C. Objective: This study aimed to analyze the potential of mango peel compounds as HCV NS5B inhibitors. Methods: The methods in this study are ligand preparation, physicochemical and pharmacokinetic predictions, protein structure preparation, molecular docking, data analysis, and visualization. Results: The results showed that the test ligands had binding free energies close to the reference ligands, namely Mangiferin -7.862 kcal/mol and respectively D-(+)-Maltose -6.453 kcal/mol, Dibutyl – phthalate -6.326 kcal/mol, bis-β-D-fructofuranose 1,2':2,3'-dianhydride -6.249 kcal/mol, 16-Heptadecyne-1,2,4-triol -5.476 kcal/mol, 3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid -5,360 kcal/mol, Trigonelline -4.905 kcal/mol, Hexitol -4.552 kcal/mol, α-Glucoheptitol -4.403 kcal/mol. All the test ligands bind the NS5B active site with hydrogen bonds. Furthermore, the ligand-receptor complex has a dissociation constant value and hydrogen bond length. Conclusion: The results showed that Mangiferin was the most potential ligand in inhibiting NS5B HCV of all the test ligands used.

Genotype frequency and pattern of transmission and of Hepatitis C virus (HCV) from the Capital city and proximate areas of the Pakistan

Abstract: Abstract Background Hepatitis C infection is pandemic public health problem in Pakistan and 71 million people carry the virus around the world. Pakistan is facing a gigantic challenge of hepatitis C infection. Pakistan was ranked 2nd in the world for the chronic hepatitis C infection. In Pakistan, around 10 million people were affected with HCV infection. Understanding of the transmission of the disease and its genotypes distribution were vital for prevention, treatment and eradication. This study aimed to determine the transmission risk factors, distribution and prevalence of HCV genotypes by sequence analysis of conserved regions and genotypic specific RT-PCR kit. Methods The analysis was carried out among 400 chronic HCV patients attending a tertiary care hospital from the Capital city and adjacent areas during period 2019–2022. The study subjects were carried out on those patients who were referred to the virology research laboratory from liver clinic in Islamabad. Baseline characteristics of the patients were collected including the possible transmission risk factor and different questionnaire options. Viral load was determined using Qiagen Quantitative PCR kit ((Lot No. 163042348) on Rotor Gene, ABI Quantstudion 3/5 and SLAN PCR systems. Genotyping of four hundred (n = 400) samples were performed by Sansure genotypic specific RT-PCR kit (Lot No. S3034E) and sequencing 5′ untranslated (5′ UTR) region. Analyzed sequences were manually read and compared with published database sequences to determine the genotypes using different bioinformatic tools. Thirty samples were also sequenced for Core/E1 and NS5B regions. The genotypes of other (n = 200) subjects were determined by Sansure HCV Real Time PCR genotyping kit. Results Four hundred samples were tested for all genotypes. Genotype 3 was found to be most foremost (93.75%). Other genotypes were detected in ratio of genotype 1 (3.25%), genotype 2 (1.25%), genotype 4 (1.25%). Genotype 5 and 6 were not detected in any samples. Two recombinant strains for Hepatitis C were observed (0.5%). One untyped sample was reported but it was a variant of genotype 3. Baseline parameters showed that the male gender (51.%%), mean age (43 years), mean ALTs (105 U/L) levels and viral load (2x103-1x107 U/mL) were observed during this analysis. Most of the Hepatitis C patients were used bad risky practices such injectable medical procedures and unsafe items of barber (major risk factors). Conclusion Sequence analysis and real time PCR methods indicated that a high percentage of HCV infected patients in North Pakistan and they were infected with 3a genotype. The patterns of HCV genotypes frequency distributions were almost similar to those of India but different from Iran and China. Healthcare related practices and barbers were the main drivers of HCV transmission. So, healthcare monitoring and sterilization of barber’s tools will be highly desired to control HCV and blood borne infections in Pakistan.