Untranslated Region Of Hepatitis C Virus Research Articles

Phylogenetic analysis of the 5\u02b9 untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan

Hepatitis C virus (HCV), a small, single-stranded RNA virus with a 9.6 kb genome, is one of the most common causes of liver diseases. Sequencing of the 5ʹ untranslated region (UTR) is usually used for HCV genotyping, but it is less important in numerous subtypes due to its scarce sequence variations. This study aimed to identify genotypes using the 5ʹ UTR of HCV from cirrhotic patients of Khyber Pakhtunkhwa (KP). Serum RNA samples (44) were screened by real time PCR to determine the HCV viral load. Nested PCR was performed to identify cDNA and the 5ʹ UTR. The HCV 5′ UTR was sequenced using the Sanger method. MEGA-7 software was used to analyze evolutionary relatedness. After 5ʹ UTR sequencing, 26 samples (59%) were identified as genotype 3, and 2 samples (6%) were identified as genotypes 1, 2 and 4. The most predominant genotype was 3a, and genotype 4 was rarely reported in the phylogenetic tree. Analysis of the HCV 5ʹ UTR is an efficient alternative method for confirmation of various genotypes. Phylogenetic analysis showed that genotype 3 was dominant in the area of KP, Pakistan.

Sporadic Reappearance of Minute Amounts of Hepatitis C Virus RNA After Successful Therapy Stimulates Cellular Immune Responses

Several studies have reported hepatitis C virus (HCV) RNA sequences in the circulation after treatment-induced or spontaneous recovery. We investigated whether the HCV RNA represents persistence of HCV infection or reinfection. We studied 117 patients who recovered from HCV infection (98 following therapy and 19 spontaneously). A reverse-transcription polymerase chain reaction assay was used to detect the 5'-untranslated region of HCV. T-cell responses were studied by enzyme-linked immunospot for interferon-γ. Plasma samples from 15% of treatment-recovered patients and no spontaneously recovered patient tested positive for HCV RNA. Lymphocytes from 3 patients who responded to therapy and 1 who recovered spontaneously tested positive. The frequency of HCV RNA detection in plasma correlated inversely with the time after the end of treatment. Post-treatment HCV 5'-untranslated region sequences matched pretreatment sequences in 85% of cases. T-cell responses were significantly greater at time points with detectable trace amounts of HCV RNA than at time points without detectable HCV RNA (P = .035) and were primarily against nonstructural HCV antigens. The immune hierarchy was preserved over 5 years in patients whose post-treatment HCV RNA sequences matched pretreatment sequences, indicating HCV RNA persistence. An altered immune hierarchy with dominant immune responses, shifting from nonstructural to structural antigens, was observed in a single patient whose post-treatment HCV genotype differed from that of the pretreatment genotype, indicating HCV reinfection. Trace amounts of HCV RNA of pretreatment sequence persisted and reappeared sporadically in the circulation within 8 years after recovery from hepatitis C but not thereafter, indicating that patients are cured of HCV infection. Reappearance of HCV RNA induced HCV-specific T-cell responses.

The seroprevalence of hepatitis C virus (HCV) among 559,890 first-time volunteer blood donors in China reflects regional heterogeneity in HCV prevalence and changes in blood donor recruitment models.

A decrease in the prevalence of hepatitis C virus antibody (anti-HCV) has been reported among voluntary blood donors in some regions of China. However, the prevalence of HCV among volunteer blood donors in other regions of China has not been reported. The aim of this study was to investigate the seroprevalence of HCV among 559,890 first-time volunteer blood donors recruited during 2004 through 2007 at the Guangzhou Blood Center, China. Anti-HCV was detected using two different third-generation enzyme immunoassay kits. HCV RNA was detected using reverse transcription-polymerase chain reaction (RT-PCR) targeting the 5'-untranslated region of HCV. Among 559,890 donors, 1877 (0.335%) were positive for anti-HCV. The anti-HCV+ rate was significantly higher in males than females (0.37% vs. 0.28%; p < 0.001) and significantly lower among donors living in Guangdong Province than donors who had migrated from other locations (0.30% vs. 0.40%; p < 0.001). Among the 1877 anti-HCV+ donors, 450 were randomly selected for HCV nucleic acid amplification by RT-PCR. Of these, 270 (60%) were HCV RNA+ and 180 (40%) were HCV RNA-. Many donors from outside Guangdong Province were migrant laborers from other areas in China, suggesting that there is regional heterogenicity in HCV prevalence within China. The overall anti-HCV+ rate reported here is among the lowest reported among blood donors in China reflecting the effect of the current recruitment of exclusively volunteer donors.

Rapid Genotyping of Hepatitis C Virus by Primer-Specific Extension Analysis

Quick and accurate genotyping of hepatitis C virus (HCV) is becoming increasingly important for clinical management of chronic infection and as an epidemiological marker. Furthermore, the incidence of HCV infection with mixed genotypes has clinical significance that is not addressed by most genotyping methods. We have developed a fluorescence-based genotyping assay called primer-specific extension analysis (PSEA) for the most prevalent HCV genotypes and have demonstrated the capacity of PSEA-HCV for detecting mixed-genotype HCV infections. PSEA-HCV detects genotype-specific sequence differences in the 5' untranslated region of HCV in products amplified by the COBAS AMPLICOR HCV Test, v2.0. Simulated mixed HCV infection of plasma with RNase-resistant RNA controls demonstrates that PSEA-HCV can detect as many as five genotypes in one specimen. Furthermore, in dual-genotype simulations, PSEA-HCV can unequivocally detect both genotypes, with one genotype representing only 3.1% of the mixture (313/10,000 IU in starting plasma). Compared to INNO-LiPA HCV II, both assays determined the same genotype for 191/199 (96%) patient specimens (175 subtype and 16 genotype-only identifications). Following the initial evaluation, PSEA-HCV was used routinely to genotype HCV from patient specimens submitted to our laboratory (n=312). Seventeen (5.4%) mixed infections were identified. The distribution of single-infection HCV genotypes in our population was 60.9% type 1 (n=190), 12.8% type 2 (n=40), 20.2% type 3 (n=63), 0.3% type 4 (n=1), and 0.3% other (n=1). In conclusion, PSEA-HCV provides an inexpensive, high-throughput screening tool for rapid genotyping of HCV while reliably identifying mixed HCV infections.

Hepatitis C Genotype Determination by Melting Curve Analysis with a Single Set of Fluorescence Resonance Energy Transfer Probes

The genotype of hepatitis C virus (HCV) is a predictor of antiviral therapeutic response. We describe an approach for HCV genotype determination by real-time PCR and melting curve analysis. After automated nucleic acid extraction, we used reverse transcription-PCR in a block cycler to amplify nucleotides 6-329 of the 5'-untranslated region of HCV. The product was further amplified by single-tube real-time seminested PCR in a LightCycler instrument (Roche). The final product was analyzed by melting curves with the use of fluorescence resonance energy transfer (FRET) probes. The FRET sensor probe was directed at nucleotides 151-170 of type 1 HCV and was designed to distinguish types 1a/b, 2a/c, 2b, 3a, and 4, with melting temperatures (T(m)s) predicted to differ by 1 degrees C. Genotypes were compared in a blinded fashion with those of the INNO-LiPA(TM) test (Bayer Diagnostics) on 111 serum samples. In preliminary experiments, the Mg(2+) concentration was found to be critical in allowing clear separation of melting points, with the best separation at a Mg(2+) concentration of 2 mmol/L. The results for 111 samples clustered at expected T(m)s for genotypes 1a/b (n = 78), 2a/c (n = 2), 2b (n = 11), 3a (n = 14), and 4 (n = 2). Of the 111 samples, results for 110 were concordant with the comparison method at the level of type 1, 2, 3, or 4. Subtyping results were discordant for two samples, both of type 2. For 108 samples concordant with INNO-LiPA at the genotype and subtype levels, the mean T(m)s were 64.1, 59.5, 54.2, 52.6, and 50.1 degrees C for types 1a/b, 2a/c, 4, 2b, and 3a, respectively, with SDs of 0.2, 0.3, 0.3, 0.2, and 0.3 degrees C. All 78 samples identified as type 1 were concordant with results of the comparison method. Melting analysis with a single pair of FRET probes can rapidly provide information about HCV genotypes and identifies type 1 samples with high specificity.

Single nucleotide insertion in the 5′-untranslated region of hepatitis C virus with clearance of the viral RNA in a liver transplant recipient during acute hepatitis B virus superinfection

Hepatitis C virus (HCV) infection is an important etiology in patients undergoing orthotopic liver transplantation (OLT) world-wide. Antiviral therapy-related clearance of HCV RNA may occur both in patients with chronic HCV infection and in transplanted patients for HCV-related liver cirrhosis, but the role of the 5'-untranslated region (UTR) of HCV containing the internal ribosome entry site (IRES), which directs the translation of the viral open reading frame has not hitherto been evaluated. We studied the 5'-UTR in an HCV-infected recipient of a liver graft that showed spontaneous clearance of HCV RNA during an acute hepatitis B virus (HBV) superinfection. Sequencing of the 5'-UTR of HCV showed a nucleotide A insertion at position 193 of the IRES.

Specific interaction of hepatitis C virus protease/helicase NS3 with the 3'-terminal sequences of viral positive- and negative-strand RNA.

The hepatitis C virus (HCV)-encoded protease/helicase NS3 is likely to be involved in viral RNA replication. We have expressed and purified recombinant NS3 (protease and helicase domains) and Delta pNS3 (helicase domain only) and examined their abilities to interact with the 3'-terminal sequence of both positive and negative strands of HCV RNA. These regions of RNA were chosen because initiation of RNA synthesis is likely to occur at or near the 3' untranslated region (UTR). The results presented here demonstrate that NS3 (and Delta pNS3) interacts efficiently and specifically with the 3'-terminal sequences of both positive- and negative-strand RNA but not with the corresponding complementary 5'-terminal RNA sequences. The interaction of NS3 with the 3'-terminal negative strand [called 3'(-) UTR(127)] was specific in that only homologous (and not heterologous) RNA competed efficiently in the binding reaction. A predicted stem-loop structure present at the 3' terminus (nucleotides 5 to 20 from the 3' end) of the negative-strand RNA appears to be important for NS3 binding to the negative-strand UTR. Deletion of the stem-loop structure almost totally impaired NS3 (and Delta pNS3) binding. Additional mutagenesis showed that three G-C pairs within the stem were critical for helicase-RNA interaction. The data presented here also suggested that both a double-stranded structure and the 3'-proximal guanosine residues in the stem were important determinants of protein binding. In contrast to the relatively stringent requirement for 3'(-) UTR binding, specific interaction of NS3 (or Delta pNS3) with the 3'-terminal sequences of the positive-strand RNA [3'(+) UTR] appears to require the entire 3'(+) UTR of HCV. Deletion of either the 98-nucleotide 3'-terminal conserved region or the 5' half sequence containing the variable region and the poly(U) and/or poly(UC) stretch significantly impaired RNA-protein interaction. The implication of NS3 binding to the 3'-terminal sequences of viral positive- and negative-strand RNA in viral replication is discussed.

A Human Liver Cell Line Exhibits Efficient Translation of HCV RNAs Produced by a Recombinant Adenovirus Expressing T7 RNA Polymerase

Anin vitrosystem that supports the efficient growth of hepatitis C virus (HCV) and reflects its completein vitroreplication cycle has not yet been established. The establishment of a minigene RNA of HCV in mammalian cells could facilitate the study of virus–cell interactions and the molecular pathogenesis of this virus. We constructed a replication-deficient recombinant adenovirus expressing bacteriophage T7 RNA polymerase under the control of CAG promoter (AdexCAT7). A high level of T7 RNA polymerase was detectable for at least 11 days after inoculation. Cells infected with AdexCAT7 were then transfected with plasmids carrying the authentic T7 promoter, the 5′ untranslated region (UTR) of encephalomyocarditis virus, a luciferase gene, and a T7 terminator (pT7EMCVLuc) or carrying the modified T7 promoter, the 5′UTR of HCV, a luciferase gene, the coding region of C-terminal of NS5B and the 3′UTR of HCV, a ribozyme of hepatitis D virus and a T7 terminator (pT7HCVLuc). Most of the cell lines examined supported a higher expression of luciferase by transfection with pT7EMCVLuc than with pT7HCVLuc. However, one cell line, FLC4, derived from a human hepatocellular carcinoma, exhibited very high reporter gene expression with pT7HCVLuc. In this cell line, transfection with RNA synthesizedin vitrofrom pT7HCVLuc induced a higher level of reporter gene expression than RNA from pT7EMCVLuc. The T7-adenovirus system for the synthesis of HCV minigenesin vivoprovides useful information on the molecular mechanisms of HCV translation in human liver cells.

Hepatitis C virus genotypes in Australia.

The relative distribution of Australian hepatitis C virus (HCV) genotypes was determined for 500 isolates. Genotyping was performed using a commercial reverse phase hybridization assay after amplification of the 5' untranslated region of HCV by the polymerase chain reaction. Australian isolates comprised, predominantly, genotype 1 (55%) and genotype 3 (38%) with genotype 2 accounting for only 7%. Genotype 3a was the most common subtype. When the major risk groups of injecting drug users or transfusion-acquired hepatitis C were compared, there was a significantly higher incidence of genotype 1b in the transfusion-acquired group (P < 0.03). When the age of the patients was analysed, genotype 3a was more prevalent in the 21-40-year age group than the 41-60-year age group (P < 0.05). There was no significant difference in genotype distribution between males and females. HCV genotypes 1, 2 and 3 are most often found in developed countries but the relatively high prevalence of genotype 3a in Australia is unusual.

Regression of monoclonal B-cell expansion in patients affected by mixed cryoglobulinemia responsive to alpha-interferon therapy.

Several authors have reported on the effectiveness of alpha-interferon (IFN-alpha) in the treatment of patients with mixed cryoglobulinemia. This prompted the authors to investigate the long term effects of this drug on clinical, hematologic, and virologic parameters in a group of 20 patients (13 women and 7 men) affected by mixed cryoglobulinemia. In all patients, bone marrow biopsy, phenotyping of marrow cells, and polymerase chain reaction (PCR) immunoglobulin gene rearrangement in peripheral blood lymphocytes were performed before therapy and at the end of the follow-up. A liver biopsy was obtained in patients with biochemical signs of chronic liver disease. The presence of hepatitis C virus (HCV) RNA in serum was assessed by detection of anti-HCV antibodies, and by PCR amplification of the 5' untranslated region of HCV. The HCV genotype was also determined by PCR amplification of the core region of the virus with type-specific primers. The treatment schedule followed by all patients was 3 million units of recombinant IFN-alpha 2b 3 times weekly for 1 year. In 6 patients, the marrow histology before therapy showed a massive (more than 50%) monomorphous infiltration by plasmacytoid lymphocytes, indicating the presence of low grade non-Hodgkin's lymphoma. Anti-HCV antibodies were present in 19 (95%) subjects, and HCV-RNA was detectable in all patients. In addition, all patients affected by Type II mixed cryoglobulinemia showed a monoclonal B-cell expansion in peripheral blood mononuclear cells (PBMC). With therapy, 5 patients (25%) achieved a complete response and 11 patients (55%) a partial response, whereas minor responses were observed in the remaining 4 patients (20%). One of the complete responders and all patients showing partial responses relapsed a few months after therapy withdrawal. At the end of the follow-up, four patients had obtained a complete remission. Bone marrow examination showed that B-lymphocytic monoclonal infiltrate disappeared in three patients. Moreover, these three patients had become negative for B-cell expansion in PBMC. Lack of response, or relapse, was associated with the presence of Type II HCV. HCV may be the cause of mixed cryoglobulinemia. The disease is associated with a high prevalence of bone marrow B-cell lymphomas. IFN-alpha appears to be an effective agent for the treatment of mixed cryoglobulinemia. It also seems able to determine regression of the lymphoproliferative disorder. The HCV genotype appears to be the most important predictive factor for the response to antiviral therapy.

Detection of hepatitis B and hepatitis C viral sequences in fulminant hepatic failure of unknown etiology.

In a significant number of patients, the etiology of fulminant hepatic failure (FHF) is unknown. To determine whether hepatitis B virus (HBV) and hepatitis C virus (HCV) play a role in patients without serologic markers of HBV and HCV infection, the authors examined tissue samples from 15 liver explants with massive hepatic necrosis for the presence of viral sequences by the polymerase chain reaction (PCR). The specimens were derived from nine patients with FHF of unknown etiology; two with serum hepatitis B surface antigen (HBsAg); two with antibodies to HCV; one with antibodies to hepatitis A virus (HAV) and anti-HBc of the IgM class; and one with isoniazid toxicity. Nucleic acids were extracted from frozen liver samples. RNA was used as a template for reverse transcription, followed by double PCR with nested primers for the 5'-untranslated region of HCV. DNA was tested by single PCR for S gene sequences of HBV. Hepatitis B virus sequences were detected in the specimens of the two HBsAg positive patients, the anti-HAV/anti-HBc positive patient, and three of nine patients with FHF of unknown etiology. Hepatitis C virus sequences were present in the explant of one patient with FHF of unknown etiology, but not in the two patients with antibodies to HCV. In two specimens with molecular findings of HBV infection (1 from a patient with serum HBsAg and 1 without), there was immunohistochemical evidence of coinfection or superinfection with hepatitis delta virus (HDV). In conclusion, in this patient population, HBV, alone or with HDV or HAV, causes fulminant hepatic failure more often than HCV infection. However, in the majority of patients, the etiology of fulminant hepatic failure remains unknown.

Hepatitis C virus serological and polymerase chain reactions in human immunodeficiency virus-positive and -negative patients

Background: Polytransfused patients may be dually infected with hepatitis C virus (HCV) and human immunodeficiency virus (HIV). Objectives: To assess the correlation of antibodies to HCV with viral RNA in serum as determined by polymerase chain reaction (PCR) in anti HIV-positive and -negative haemophiliacs. Study design: Serum from 150 Patients with or without HIV infection were examined for anti-HCV by second generation enzyme-linked immunosorbent assay (ELISA) and recombinant immunoblotting assay (RIBA). A sample was also tested in a nested-reverse transcription PCR for a conserved sequence of the 5′ untranslated region of HCV. PCR-positive specimens were titrated and a type-specific PCR using viral core gene sequences was used to determine distribution of HCV viral types. Results: Eighty-seven percent of the patients were positive in ELISA. All the positives but 2 were either positive of indeterminate in RIBA. The frequency of indeterminate RIBA results was 33% among HIV-positive subjects and less than 1% among HIV-negative ones. PCR was positive in 68% of 73 RIBA-positive or -indeterminate individuals and negative in all HCV-seronegative individuals examined. No significant differences were observed in HCV viral type, prevalence or titers of viraemia between HIV-positive or -negative patients. Conclusions: The majority (68%) of anti-HCV-positive haemophiliacs examined in this study had HCV RNA in their sera and anti-HCV profile determined by RIBA had no apparent influence on viraemia. The presence of HIV infection in these patients had no significant impact on HCV RNA prevalence, titer or HCV type distribution.