Hepatitis C virus (HCV) genotyping by annealing reverse transcription-PCR products with genotype-specific capture probes

Liver Stiffness Is Markedly Decreased After Chronic Hepatitis C Treatment

AIM

The aim of the study was to demonstrate the liver stiffness (LS) change in chronic hepatitis C (CHC) patients obtained by elastography point quantification technique in before and after antiviral treatment (AVT).

MATERIAL AND METHODS

This prospective study included 84 patients diagnosed with CHC who had not previously received treatment for CHC and who had an indication for using direct-acting AVT. Necessary measurements were recorded with noninvasive liver fibrosis (LF) examinations. Posttreatment control of patients was carried out (ombitasvir + paritaprevir + ritonavir) + 3 months after the start of treatment for those treated with dasabuvir and 6 months after the start of treatment for patients treated with sofosbuvir + ribavirin. Liver stiffness changed after AVT is accepted as (Δ-LS), LS before AVT-LS after AVT.

RESULTS

Basal LS was found to decrease significantly after AVT (8.00 ± 2.56 kPa vs 6.95 ± 2.86 kPa, P < 0.05). Similar aspartate aminotransferase-to-platelet ratio index and platelet number fibrosis 4 indices were observed before and after AVT (P > 0.05). It was observed that Δ-LS value after AVT was lower in patients with Child-Pugh class A cirrhosis than patients without cirrhosis (P < 0.05). In the comparison between Δ-LS value after AVT and LF score determined by liver biopsy, it was seen that the greatest Δ-LS value was in patients with fibrosis score of 3. An independent relationship was found between Δ-LS after AVT and LF score determined by biopsy (P < 0.05).

CONCLUSIONS

The LS value determined by the elastography point quantification technique is more effective than other noninvasive laboratory methods in demonstrating the CHC treatment response in clinical practice.

Frequency of Hepatitis C Virus Genotypes in Patients Who Had Hepatocellular Carcinoma in Gastroenterological Hospitals of Tabriz

BACKGROUND

Generally, hepatitis C has been identified as one of the major health issues that about 3% of the world's population have been threatened and affected by it (about 170 million people), and also, it can be considered a factor in acute and chronic hepatitis.

METHODS

The aim of this study is to determine the prevalence of HCV genotypes in Azerbaijan patients. In this study, sampling was done on the referred patients to the hospitals (Mahallati and Behbud Hospital). RNA was extracted after isolation of plasma, and then, after the synthesizing of cDNA, the sample was carried out to the laboratory for performing the real-time PCR in order to determine the genotypes.

RESULTS

The evaluation of HCV genotypes in positive plasma samples showed that dominant subsets were remarkable and the mean age of the patients was 37/3 ± 11/8 (in the age range of 2-63). Among the 235 patients,139 of them (59%) were male. Statistically, the average number of women was more than men (T test, P < 0/05). 1b genotype was reported 70% in the patients above 40 years old, and also, it was reported as 71/6% in the patients under 40 years old that was not statistically significant. The incidence of serotype 3a was higher among the patients younger than 40 years old (3a was 18.1% vs. 15%), and this serotype was prevalent among men (3a was 18.7% vs. 14.6%), which was statistically significant.

CONCLUSION

The findings indicate that among Azerbaijan's patients with chronic hepatitis C, genotypes 1b (71.1%) and 3a (17%) were dominant.

Prevalence of HCV and/or HBV coinfection in Iranian HIV-infected patients

Aim: HIV-infected patients risk coinfection with HBV and HCV. This study aimed to investigate molecular epidemiology of HBV and HCV coinfection in Iranian HIV-infected individuals. Materials & methods: In this cross-sectional study, serological markers of HBV and HCV infection (hepatitis B surface antigen [HBsAg], hepatitis B e-antigen [HBeAg], hepatitis B e-antibody [HBeAb] and hepatitis B core antibody [HBcAb]) and anti-HCV antibodies [anti-HCV Abs] were tested in 198 Iranian HIV-infected patients. From plasma, HBV viral load was determined using COBAS TaqMan 48, and HCV-RNA was detected by reverse transcriptase-nested PCR. Results: 85 out of 198 (42.9%) patients were anti-HCV Ab positive and 42/198 (21.2%) had detectable HCV-RNA. Eight (4.0%) had traceable HBV-DNA. All these patients were infected by HBV genotype D. 55 (27.8%) were HBcAb positive. Nine (4.4%) were HBsAg and anti-HCV Ab positive. Conclusion: None were HIV-RNA/HCV-RNA/HBV-DNA positive, 21.2% were HIV-RNA/HCV-RNA positive and 4.0% were HIV-RNA/HBV-DNA positive. Therefore, studies on diagnosing these infections in HIV-infected individuals may be valuable.

Rapid detection of the New Delhi metallo-b-lactamase 1 (NDM-1) gene by loop-mediated isothermal amplification (LAMP)

BACKGROUND

New Delhi Metallo-b-lactamase (NDM-1) is an enzyme emerging around the world conferring resistance to a wide range of β-lactams agents and whose early detection is extremely important. We proposed to standardize the detection of the bla_NDM-1 gene using the LOOP-mediated isothermal amplification technique (LAMP).

METHODS

In all, 14 Gram-negative bacterial strains isolated from patients presenting pneumonia associated with mechanical ventilation were used for the bla_NDM-1 standardization by LAMP. Klebsiella pneumoniae ATCC BAA-2473 and two clinical strains were used as a positive control. All results were compared to the reaction in polymerase chain reaction (PCR), considered gold standard for this detection.

RESULTS

There was an excellent correlation between the two techniques employed, since all measured clinical strains were negative in both employed tests and two clinical, and a reference strains were positive.

CONCLUSIONS

The lamp technique seems to be an excellent option for the rapid detection of bla_NDM-1. The amplification time is much shorter than other molecular techniques, the PCR machine is not necessary, it is easy of implementation and costs is low.

Hepatitis C Virus RNA Strands Detection in Peripheral Blood Mononuclear Cells Legitimizes Virus Eradication in Negative Serum PCR Naïve and Post-treatment Patients

Background and Aims: Hepatitis C virus (HCV) hepatotropism is associated with intra-peripheral blood mononuclear cell (PBMC) infection that causes post-treatment relapse in RNA seronegative patients. Our understanding of the association of non-viremic hepatic fibrosis with positive anti-HCV IgG antibodies and active hepatocellular damage might be increased by PBMCs screening for intracellular infection. Thus, the goals of this study included evaluation of PBMCs PCR for diagnosing HCV infection, addressing PBMCs plus serum real-time (SRT) PCR benefits over SRT-PCR alone, studying intra-PBMCs distribution of RNA sense and antisense strands, and identifying treatment feasibility in solitary intracellular infection. Methods: Enzyme-linked immunosorbent assay, SRT-PCR and PBMCs PCR were used to evaluate HCV infection in 401 subjects. The patients were classified into groups of negative controls (n = 30), positive controls (n = 63), non-viremia post-treatment (experienced; n = 166) and naïve (n = 49) cases, and non-viremia positive PBMCs PCR naïve (n = 35) and experienced (n = 58) patients. Results: The diagnosis of true positive and negative by PBMCs PCR and SRT-PCR had 100% and 96.7% compatibility respectively. PBMCs PCR detected intracellular HCV infection in 49 out of 215 non-viremia patients; among them, naïve cirrhotics had significantly higher number of intracellular infection than the naïve non-cirrhotic (p < 0.001) and experienced patients (p < 0.0001). Antisense and sense strands were respectively recognized in naïve and experienced cases (p = 0.01218). Intracellular HCV strands were detected in 18.02% of experienced patients. Recognition of intracellular RNA strands showed significant decline in experienced compared to naïve patients (p < 0.05). Conclusion: PBMCs PCR is a valid diagnostic test that can diagnose intracellular HCV when SRT-PCR is negative. Antisense and sense strands are respectively recognized more often in naïve and experienced patients. The expected overall relapsing rate in our cohort was 18.02%. Intra-PBMC infections are associated with liver cirrhosis in naïve non-viremia patients. Eradication of intracellular strands is recommended to avoid RNA seroconversion. Ethical approval certificate: Registration number 10231.

A method for rapid detection and genotype identification of hepatitis C virus 1-6 by one-step reverse transcription loop-mediated isothermal amplification

OBJECTIVE

Hepatitis C virus (HCV) is probably the leading cause of liver cirrhosis and hepatocellular carcinoma globally. Diagnostic tools conventionally used for the detection and identification of HCV infection are technically demanding, time-consuming, and costly for resource-limited environments. This study reports the development of the first rapid loop-mediated reverse transcription isothermal amplification assay that rapidly detects and identifies HCV genotypes in blood components.

METHODS

RNA extracted from donor plasma and serum specimens was applied to a one-step reverse transcription loop-mediated isothermal amplification reaction performed with HCV-specific oligonucleotides. Reactions were conducted at 63.5 °C for 30-60 min. The diagnostic characteristics of the assay were investigated and validated with clinical specimens.

RESULTS

Electrophoretic analysis of amplification revealed detection and identification of HCV genotypes 1-6. Positive amplification revealed unique ladder-like banding patterns that identified each HCV genotype. The assay demonstrated a sensitivity of 91.5% and specificity of 100%. Rapid naked-eye detection of HCV infection was facilitated by observation of an intense fluorescent glow of amplified targets under UV illumination.

CONCLUSION

These diagnostic characteristics highlight the potential utility of this assay for the rapid detection and genotype identification of HCV infection in field and point-of-care settings in endemic regions and resource-limited environments.

Effects of ribavirin monotherapy on the viral population in patients with chronic hepatitis C genotype 1: direct sequencing and pyrosequencing of the HCV regions

Ribavirin remains essential to chronic hepatitis C treatment. This paper investigates the influence of ribavirin priming to steady state before combined pegylated-interferon/ribavirin treatment on viral kinetics, ribavirin trough concentrations, genetic variability within HCV-core, -NS5B and -NS5A, and response to antiviral therapy. A prospective cohort study was made of 27 chronic hepatitis C genotype 1 naïve patients who received four weeks of ribavirin followed by pegIFN-α-2a/ribavirin for 48 weeks (Group A). The results obtained were compared with those for a control/historical group (Group B). In addition, direct sequencing and pyrosequencing were applied to determine ribavirin monotherapy-induced sequence changes. The rapid, early, and sustained virological response values obtained were 48%, 89%, and 52%, respectively, in Group A, and 52%, 90%, and 52% in Group B (P > 0.05). In the four-week combined treatment, the Group A patients showed a greater decrease in HCV-RNA (2.3 log10  IU/ml vs. 1.2 log10  IU/ml; P = 0.04), lower alanine aminotransferase levels (23.5 ± 1.33 U/L vs. 60.11 ± 18 U/L; P < 0.001) and higher mean ribavirin trough concentrations (3.28 ± 1.26 mg/L vs. 1.74 ± 0.7 mg/L; P = 0.001). No general increase in rates of nucleotide substitutions in the ribavirin monotherapy-treated patients was observed in NS5B, ISDR, or PKRbd, but there was a decrease in silent mutations in the HCV core (P = 0.04). This result was confirmed by pyrosequencing in the NS5A region. It is concluded that the ribavirin priming combined treatment with pegIFN-α-2a does not improve sustained virological response rates in HCV genotype 1 naïve infected patients. However, the greater reductions in viral load and alanine aminotransferase levels, together with the higher ribavirin trough concentration values obtained, could reflect the greater effectiveness of the treatment. Ribavirin does not have a mutagenic effect on the virus in patients with chronic hepatitis C.

Distribution of hepatitis C virus genotypes among azerbaijani patients in capital city of iran-tehran

BACKGROUND

Determination of the Hepatitis C virus (HCV) genotype distributed in a particular area has an important role on public health throughout the world.

OBJECTIVES

The aim of this study was to determine the frequency of HCV genotypes in Azerbaijani patients.

PATIENTS AND METHODS

From March 2010 until March 2012, 235 Azerbaijani patients with established chronic hepatitis C, referred to Hospitals related to Iran University of Medical Sciences and Tehran Hepatitis Center, Clinical department of Baqiyatallah Research Center for Gastroeneterology and Liver Disease, were enrolled in this cross sectional study. About 5 mL of peripheral blood was collected from patients and after separation of plasma, viral RNA extracted. HCV-RNA were amplified by RT-nested PCR using primers from the 5´-UTR and genotyped by RFLP assay, and then HCV genotypes were confirmed using sequencing of cloned PCR products into pJET1.2/blunt cloning vector.

RESULTS

HCV genotyping of positive plasma samples demonstrated that predominant HCV subtype was noted for 1b (71.1%) followed by subtype 3a (17.0%), genotype 2 (6.8%), 1a (1.7%), and mixed infection (3.4%). The mean ± SD age of patients was 37.3 ± 11.8 (range: 2-63) years. Out of 235 patients, 139 (59.1%) were male. The frequency of HCV subtype 3a was higher in patients under 40 years old (3a: 18.1% vs. 15.0%), and subtype 3a was higher in male patients (3a: 18.7% vs. 14.6%).

CONCLUSIONS

The current study shows that the predominant HCV genotype among Azerbaijani patients with established chronic hepatitis C is subtype 1b (71.1%) followed by subtype 3a (17.0%).

Introduction of an automated system for the diagnosis and quantification of hepatitis B and hepatitis C viruses

Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infections pose major public health problems because of their prevalence worldwide. Consequently, screening for these infections is an important part of routine laboratory activity. Serological and molecular markers are key elements in diagnosis, prognosis and treatment monitoring for HBV and HCV infections. Today, automated chemiluminescence immunoassay (CLIA) analyzers are widely used for virological diagnosis, particularly in high-volume clinical laboratories. Molecular biology techniques are routinely used to detect and quantify viral genomes as well as to analyze their sequence; in order to determine their genotype and detect resistance to antiviral drugs. Real-time PCR, which provides high sensitivity and a broad dynamic range, has gradually replaced other signal and target amplification technologies for the quantification and detection of nucleic acid. The next-generation DNA sequencing techniques are still restricted to research laboratories.The serological and molecular marker methods available for HBV and HCV are discussed in this article, along with their utility and limitations for use in Chronic Hepatitis B (CHB) diagnosis and monitoring.

Expression of core antigen of HCV genotype 3a and its evaluation as screening agent for HCV infection in Pakistan

Background

Pakistan is facing a threat from hepatitis C infection which is increasing at an alarming rate throughout the country. More specific and sensitive screening assays are needed to timely and correctly diagnose this infection.

Methods

After RNA extraction from specimen (HCV-3a), cDNA was synthesized that was used to amplify full length core gene of HCV 3a. After verification through PCR, DNA sequencing and BLAST, a properly oriented positive recombinant plasmid for core gene was digested with proper restriction enzymes to release the target gene which was then inserted downstream of GST encoding DNA in the same open reading frame at proper restriction sites in multiple cloning site of pGEX4t2 expression vector. Recombinant expression vector for each gene was transformed in E. coli BL21 (DE3) and induced with IPTG for recombinant fusion protein production that was then purified through affinity chromatography. Western blot and Enzyme Linked Immunosorbant Assay (ELISA) were used to detect immuno-reactivity of the recombinant protein.

Results

The HCV core antigen produced in prokaryotic expression system was reactive and used to develop a screening assay. After validating the positivity (100%) and negativity (100%) of in-house anti-HCV screening assay through a standardized panel of 200 HCV positive and 200 HCV negative sera, a group of 120 serum specimens of suspected HCV infection were subjected to comparative analysis of our method with commercially available assay. The comparison confirmed that our method is more specific than the commercially available assays for HCV strains circulating in this specific geographical region of the world and could thus be used for HCV screening in Pakistan.

Conclusion

In this study, we devised a screening assay after successful PCR amplification, isolation, sequencing, expression and purification of core antigen of HCV genotype 3a. Our developed screening assay is more sensitive, specific and reproducible than the commercially available screening assays in Pakistan.

Hepatitis C virus RNA assays: current and emerging technologies and their clinical applications

Molecular diagnostic assays represent a cornerstone in the management of hepatitis C virus (HCV) patients. Qualitative and quantitative HCV molecular assays are used for the diagnosis of acute and chronic HCV infections, viral genotyping, viral-load determination, treatment monitoring and prognosis. Reverse-transcription PCR, transcription-mediated amplification and branched DNA amplification are commonly employed for detection of HCV RNA. Recently, new HCV molecular assays that employ nanostructures have emerged and have been proposed as suitable for both low- and high-resource settings, without sacrificing sensitivity and specificity. This article will present current and future HCV molecular diagnostic assays with a focus on their clinical applications.

Hepatitis C virus genotypes circulating in district Swat of Khyber Pakhtoonkhaw, Pakistan

Hepatitis C virus (HCV) is the leading cause of chronic hepatitis worldwide and its subtypes/genotypes are clinically important for clinical management and vaccine development. The present study describes frequency distribution of different HCV genotypes and their treatment status in HCV RNA positive patients from district Swat. A total of 185 HCV infected sera were analyzed by molecular genotyping assay. The most prevalent genotype was 3a (34.1%), followed by 2a (8.1%), 3b (7%) and 1a (5.4%). The samples found untypable by the present method of genotypes was 37.8% while, patients with mixed genotype infections were 7.6%. More than 80% of untypable cases were from those HCV patients who had received interferon plus ribavirin standard therapy in the past and either were non-responders and were relapsed thereafter or were under treatment. In conclusion, genotype 3a is the most prevalent HCV genotype in the region. A high prevalence rate of untypable genotypes is present in treated patients that need further investigation for the successful genotyping by developing new assays or using viral sequencing method.

Hepatitis C virus: How genetic variability affects pathobiology of disease

As an RNA virus, hepatitis C virus (HCV) shows a characteristically high level of nucleotide diversity. Accumulation of nucleotide substitutions in the virus has resulted in diversification into quasispecies, subtypes and distinct genotypes. Pathobiological studies linking nucleotide and amino acid sequences with clinical findings have identified relationships between certain genotypes and characteristic biological properties. Genotype 3 HCV infection was found to be associated with a high level of liver steatosis. Genotypes 1 and 4 were found to be more resistant to interferon (IFN) based therapies than genotypes 2 and 3. Studies of genotype 1 sequences obtained from patients treated with IFN have identified a relationship between favorable response to interferon therapy and amino acid substitutions in the NS5A region (interferon response determining region; ISDR). Further studies have identified a relationship between the effect of IFN therapy and other regions of the NS5A protein. More recently, a relationship has been found between poor response to peg-IFN plus ribavirin combination therapy and substitutions at amino acid 70 and 91 in the core protein. Furthermore, a correlation between human genetic variation in the IL28B (IFN-lamda 3) locus and core amino acid substitutions has been characterized. In this review we briefly summarize the discovery, classification and nomenclature of HCV genotypes and subtypes. We also discuss amino acid substitutions within specific regions that have been reported to be associated with outcome of IFN and peg-IFN plus ribavirin combination therapy.

Distribution of different hepatitis C virus genotypes in patients with hepatitis C virus infection

AIM: To investigate the presence of mixed infection and discrepancy between hepatitis C virus (HCV) genotypes in plasma, peripheral blood mononuclear cells (PBMCs), and liver biopsy specimens.

METHODS: From September 2008 up to April 2009, 133 patients with chronic hepatitis C referred to Firouzgar Hospital for initiation of an antiviral therapy were recruited in the study. Five milliliters of peripheral blood was collected from each patient and liver biopsy was performed in those who gave consent or had indications. HCV genotyping was done using INNO-LiPA™ HCV II in serum, PBMCs, and liver biopsy specimens and then confirmed by sequencing of 5’-UTR fragments.

RESULTS: The mean age of patients was 30.3 ± 17.1 years. Multiple transfusion was seen in 124 (93.2%) of patients. Multiple HCV genotypes were found in 3 (2.3%) of 133 plasma samples, 9 (6.8%) of 133 PBMC samples, and 8 (18.2%) of 44 liver biopsy specimens. It is notable that the different genotypes found in PBMCs were not the same as those found in plasma and liver biopsy specimens.

CONCLUSION: Our study shows that a significant proportion of patients with chronic hepatitis C are affected by multiple HCV genotypes which may not be detectable only in serum of patients.