Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5' non-coding region

Serological determination of hepatitis C virus genotype: comparison with a standardized genotyping assay

In patients with chronic hepatitis C, determination of hepatitis C virus (HCV) genotype could be routinely run in the future to tailor treatment schedules. The suitabilities of two versions of a serological, so-called serotyping assay (Murex HCV Serotyping Assay version 1-3 [SA1-3] and Murex HCV Serotyping Assay version 1-6 [SA1-6]; Murex Diagnostics Ltd.), based on the detection of genotype-specific antibodies directed to epitopes encoded by the NS4 region of the genome, for the routine determination of HCV genotypes were studied. The results were compared with those of a molecular biology-based genotyping method (HCV Line Probe Assay [INNO-LiPA HCV]; Innogenetics S.A.), based on hybridization of PCR products onto genotype-specific probes designed in the 5' noncoding region of the genome, obtained with pretreatment serum samples from 88 patients with chronic hepatitis C eligible for interferon therapy. Definitive genotyping was performed by sequence analysis of three regions of the viral genome in all samples with discrepant typing results found among at least two of the three assays studied. In all instances, sequence analysis confirmed the result of the INNO-LiPA HCV test. The sensitivity of SA1-3 was 75% relative to the results obtained by the genotyping assay. The results were concordant with those of genotyping for 92% of the samples typeable by SA1-3. The sensitivity of SA1-6 was 89% relative to the results obtained by the genotyping assay. The results were concordant with those of genotyping for 94% of the samples typeable by SA1-6. Overall, SA1-6 had increased sensitivity relative to SA1-3 but remained less sensitive than the genotyping assay on the basis of PCR amplification of HCV RNA. Cross-reactivities between different HCV genotypes could be responsible for the mistyping of 8 (SA1-3) and 6% (SA1-6) of the samples. Subtyping of 1a and 1b is still not possible with the existing peptides, but discriminating between subtypes may not be necessary for routine use.

Review: molecular epidemiology of hepatitis C virus

Molecular techniques have been used to investigate the epidemiology of hepatitis C virus (HCV) at several different levels. At a global level, the time of divergence of the diverse HCV genotypes isolated from different geographical regions has been estimated from the rate of divergence observed among a cohort of individuals infected from a common source. Estimates of more than 300 years for virus subtypes and more than 500-2000 years for virus types are consistent with their current geographical distributions. Analysis of virus sequences has also provided evidence for a common source of infection in several large-scale outbreaks of HCV infection, although where there is evidence that the implicated source contains more than one variant it may be difficult to distinguish individuals infected by different sources. Finally, sequence analysis has been used to investigate the vertical or horizontal transmission of HCV between pairs of individuals. The hypervariable region of the E2 gene is the most informative region to study if samples are available soon after the transmission event, but evidence for more distant events can still be obtained from analysis of genes such as NS5b and E1. Interpretation of some studies is complicated by the conservation of the gene region studied, or by the failure to make comparisons with sequences from epidemiologically unrelated viruses.

Comparative evaluation of five rapid methods for identifying subtype 1b and 2c hepatitis C virus isolates

A panel of 61 HCV isolates belonging to five different subtypes were used to evaluate five methods for rapid typing of HCV RNA: an in-house type-specific polymerase chain reaction based on the core region (type-specific PCR), a commercial amplification of the core region followed by hybridisation to probe coated wells (DEIA), a commercial amplification of the 5'-UTR region followed by hybridisation to probes immobilised on strips (LiPA), an in-house restriction fragment polymorphism analysis of the 5'UTR (RFLP), and a commercial serological method using synthetic peptides from the NS4 region (serotyping). The correct viral type was identified in 90% of cases by DEIA, in 82% of cases by type-specific PCR, in 80% of cases by LiPA and RFLP, and in 67% of cases by serotyping. Correct identification of the virus subtype was much less frequent and was beyond the performance characteristics of some assays. Major problems were found in the identification of isolates belonging to type 2. This was probably at least partly due to the fact that all type 2 isolates in the viral panel were of subtype 2c, which has been considered rare until recently.

Acute hepatitis C viral infection during pregnancy: failure of mother to infant transmission

A pregnant woman developed an acute hepatitis C virus (HCV) type 3a infection during the second trimester of pregnancy. The clinical virological features are presented, including HCV RNA quantification of maternal serum samples collected during pregnancy. These findings are discussed in light of the child's remaining uninfected after 5 years of follow-up.

Renal disease in hepatitis C-positive liver transplant recipients

Glomerular abnormalities are frequent in patients undergoing liver transplantation; however, renal dysfunction following transplantation is mainly attributed to cyclosporine toxicity. Membranoproliferative glomerulonephritis (MPGN) is seen in patients infected with hepatitis C virus (HCV), the virus responsible for 30% of the end-stage liver disease leading to liver transplantation. To determine the incidence of renal abnormalities in liver transplant recipients and the association with HCV, we undertook a longitudinal study in HCV-positive (n=91) and HCV-negative (n=106) liver transplant recipients. Mean creatinine clearance before transplantation was 94 ml/min/1.73 m2 in HCV+ patients and 88 ml/min/1.73 m2 in HCV- patients. By 3 months after transplantation, the mean creatinine clearance decreased by approximately one third in both groups. A greater proportion of HCV+ patients excreted >2 g protein/day after transplantation (P=0.05) and had renal biopsies showing MPGN than did HCV- recipients (4/10 HCV+ patients vs. 0/7 HCV- patients; P=0.1). In the HCV+ group, proteinuria was not associated with recurrent HCV hepatitis, DQ matching, posttransplant diabetes, or hypertension. Treatment of HCV-related MPGN with interferon-alpha2b appeared to stabilize proteinuria and renal function but did not reverse renal dysfunction nor cause liver allograft rejection. After transplantation, HCV+ patients had similar renal function over 3 years after transplantation, compared with HCV- patients, but they had an increased risk of proteinuria and occurrence of MPGN that was only partially responsive to interferon.

Evaluation of two simplified methods for genotyping hepatitis C virus

A number of different approaches have been used for genotyping hepatitis C virus (HCV). Two simplified methods were evaluated, both of which used polymerase chain reaction (PCR) to amplify products from the 5' non-coding region of HCV: non-isotopic restriction fragment length polymorphism (RFLP) analysis and type-specific PCR. Sixty-four viraemic patients suffering from chronic HCV infection were studied using these two techniques; 25/64 samples were further tested with a commercial serotyping ELISA based on synthetic NS4 antigen (Murex, U.K.). The results of the three typing methods were generally in agreement with each other. When only the predominant genotype identified by each method was analysed, the 3 methods had 100% agreement. RFLP did not detect any mixed infections and it was unsuccessful in 16/64 (25%) samples. Both type-specific PCR and serotyping ELISA detected mixed infections. However, serotyping ELISA did not give typeable results in 7/25 (28%) samples, whereas type-specific PCR gave typeable results in all 64 samples. Type-specific PCR detected more mixed infections than serotyping ELISA. Direct sequencing of four PCR products with indeterminate RFLP confirmed changes in restriction enzyme recognition sites. The sequences also confirmed the validity of the predominant genotype in cases of apparent mixed infections. It is possible that some of these cases were artefacts as a result of quasispecies.

Evidence that hepatitis C virus resistance to interferon is mediated through repression of the PKR protein kinase by the nonstructural 5A protein

Hepatitis C virus (HCV) is the major cause of non-A non-B hepatitis and a leading cause of liver dysfunction worldwide. While the current therapy for chronic HCV infection is parenteral administration of type 1 interferon (IFN), only a fraction of HCV-infected individuals completely respond to treatment. Previous studies have correlated the IFN sensitivity of strain HCV-1b with mutations within a discrete region of the viral nonstructural 5A protein (NS5A), termed the interferon sensitivity determining region (ISDR), suggesting that NS5A may contribute to the IFN-resistant phenotype of HCV. To determine the importance of HCV NS5A and the NS5A ISDR in mediating HCV IFN resistance, we tested whether the NS5A protein could regulate the IFN-induced protein kinase, PKR, a mediator of IFN-induced antiviral resistance and a target of viral and cellular inhibitors. Using multiple approaches, including biochemical, transfection, and yeast genetics analyses, we can now report that NS5A represses PKR through a direct interaction with the protein kinase catalytic domain and that both PKR repression and interaction requires the ISDR. Thus, inactivation of PKR may be one mechanism by which HCV avoids the antiviral effects of IFN. Finally the inhibition of the PKR protein kinase, by NS5A is the first described function for this HCV protein.

Development of a simple restriction fragment length polymorphism (RFLP) based assay for HCV genotyping and comparative analysis with genotyping and serotyping tests

The distribution between the different hepatitis C virus genotypes and subtypes has potentially important clinical and epidemiological implications. With this view a simple restriction fragment length polymorphism (RFLP) based assay was developed to identify the three major genotypes, 1, 2 and 3 and distinguish subtype 1a from 1b. This RFLP test uses a combination of three restriction endonuclease digestions, BstN1, BstU1 and Sau3a, respectively. Comparison with a 5'UTR based assay (LiPA), showed a 98% concordance with the RFLP based assay. In addition, good concordance is shown between these data and those obtained with a serological assay based on NS4 peptides.

Relation of hepatitis C virus genotypes to risk factors and hepatic disease in Spanish patients

OBJECTIVE: To ascertain the prevalence of hepatitis C virus (HCV) genotypes in Spain and their distribution by risk factors. METHODS: The study covered 216 patients with hepatitis C. Of these, 63 were intravenous drug users (IVDU), 44 had received transfusions, and 30 were hemodialyzed, and in 79 the risk factors were unknown. Antibodies against HCV were detected by second-generation enzyme immunoassay (EIA) and confirmed by immunoblot. HCV RNA presence was investigated by reverse transcription---polymerase chain reaction (RT-PCR), and a reverse hybridization test of the amplifications was used for the genotyping. RESULTS: The most frequently encountered genotypes were 1b (48.1%), 1a (21.3%) and 3a (11.1%). HCV genotypes 1a (42.8%) and 3a (20.6%) were the most prevalent genotypes in IVDU patients, while 1b was the most frequent in patients with unknown risk factors (62.0%), transfused patients (68.1%) and hemodialyzed patients (50.0%). Mixed infections were detected in nine cases (4.1%); three appeared in IVDU patients (4.7% of the total IVDUs), two in transfused patients (4.5%) and four (50%) in patients with unknown risk factors. No statistically significant differences were found in average ages of the IVDU patients with different genotypes. Non-IVDU patients having genotype 3a presented the lowest average age of all. No significant statistical differences were observed in alanine aminotransferase levels among patient groups with different genotypes (p>0.05 in all cases). Subtype 1b was present in six of the seven cases of cirrhosis (85.7%) and in nine of the 18 cases of active chronic hepatitis (50.0%).

Subtype 2c of hepatitis C virus is highly prevalent in Italy and is heterogeneous in the NS5A region

Hepatitis C virus (HCV) isolates, obtained from 50 Italian patients with community-acquired infection, that had previously been classified as subtype 2a or 2b by current rapid genotyping methods were further characterized by partial sequence analysis. All the isolates were reclassified: 45 within subtype 2c and the other 5 as subtype 1b, 3a, or 4d. Thus, subtype 2c is much more prevalent than previously recognized, with about 30% of all HCV strains detected in Italy being subtype 2c. In contrast, isolates of subtypes 2a and 2b appear to be infrequent, if not absent. Further studies showed that subtype 2c isolates are heterogeneous in the NS5A region, in that they may or may not contain a 57-nucleotide (nt) segment spanning from nt 7533 to nt 7589 of the viral genome. Partial nucleotide sequencing of the NS5B region of four 2c subtypes excluded the possibility that the isolates possessing or not possessing the 57-nt segment in the NS5A region may have resulted from recombination phenomena.

Comparison of plasma virus loads among individuals infected with hepatitis C virus (HCV) genotypes 1, 2, and 3 by quantiplex HCV RNA assay versions 1 and 2, Roche Monitor assay, and an in-house limiting dilution method

The accuracy of different methods for the quantitation of hepatitis C virus in plasma was measured with samples from individuals infected with different genotypes and by using RNA transcripts of predetermined concentrations. Highly reproducible results were observed upon repeat testing of samples by both the original version of the Chiron branched-DNA (bDNA) assay (Quantiplex RNA assay; bDNA-1) and the currently available version (Quantiplex HCV RNA 2.0 assay; bDNA-2). A greater variability was observed in the Roche Monitor assay (correlation coefficient of 0.537, compared with 0.942 and 0.964 for the bDNA-1 and bDNA-2 assays, respectively). Significant differences in the efficiency of detection of genotypes 1, 2, and 3 were observed for the bDNA-1 and Roche Monitor assays, whereas the bDNA-2 assay and nested PCR at limiting dilution were able to quantify genotypes with equal sensitivity. By quantifying RNA transcripts of different genotypes, the sensitivities of the Roche Monitor assay for sequences of the type 2 and type 3 transcripts were estimated to be 11 and 8% of those achieved for genotype 1. When correction factors based upon these results and those from quantitation of circulating viral RNA sequences in samples from blood donors were used, the genotype-specific differences in virus load in samples from blood donors were no longer observed, consistent with previous studies with corrected values from the bDNA-1 assay. These results suggest that many of the previous studies evaluating the effect of genotype and virus load on the response to interferon using methods such as the Roche Monitor assay and other competitive PCR methods require reinterpretation. Differences in efficiency of quantitation should be taken into account in future investigations of the relationship between genotype and virus load.

Assessment of commercial enzyme immunoassay for hepatitis C virus serotyping

AIMS

To assess a commercial enzyme immunoassay (EIA) for the serotyping of hepatitis C virus (HCV) for routine use in a diagnostic laboratory setting, as well as for noting the serotype prevalence of selected specimens.

METHODS

Seventy six serum specimens, submitted to the laboratory for routine hepatitis studies between May 1992 and February 1996 and stored at -20 degrees C, were evaluated. These specimens were categorised into specific hepatic, renal, and paediatric clinical conditions. The specimens all tested positive for HCV antibodies on a screening EIA, with confirmation on a recombinant immunoblot assay (RIBA). Certain specimens were also HCV RNA positive by the reverse transcription polymerase chain reaction (RT-PCR). All the specimens were serotyped using the newly developed serotyping EIA.

RESULTS

Twenty seven (35.5%) specimens were typable. Type 5 predominated (56%), followed by type 1 (33%), types 1 and 6 (7%) and type 3 (4%). The serotype 5 specimens showed 85% and 90% reactivity with recombinant antigens c100-3 and c22-3c, respectively; serotype 1 specimens showed 75% and 100% reactivity with these antigens. All serotype 5 specimens reacted with the c33-c antigen, but only 60% of serotype 1 specimens reacted with this antigen. The differences in the reactivity of the serotype 5 and serotype 1 specimens for c33-c antigen in the RIBA were significant, but no significant differences in reactivity for antigens c-1-1, c100-3, and c22-3 were noted. Serotype 3 specimens showed equal reactivity with all four antigens used in the RIBA.

CONCLUSION

The serotyping EIA was easy to use, rapid, and cost effective compared with molecular assays. This assay seems to be ideal for the routine diagnostic laboratory setting, but could not be used for certain clinical specimens. The demonstration of serotypes 5, 1, and 3 was not unexpected in this cohort. The occurrence of serotype 6, although concurrent and more likely to be a false cross reaction with serotype 1 peptides, requires confirmation by molecular genotyping before it can be claimed that this type is present in South Africa.

Hepatitis C virus: molecular biology and genetic variability

The pathogenetic mechanisms of hepatitis C virus (HCV) infection are poorly known. An understanding of HCV biology and the potential clinical impact of HCV genetic variability is essential to managing, treating, and preventing HCV infections. HCV is a member of the Flaviviridae viral family. Its genome is a positive, single-strand RNA molecule. The structure of the HCV particles is poorly known due to the lack of an efficient cell culture system as well as a striking heterogeneity in density. The core protein may have a regulatory role on both viral and cellular gene expression. The mechanisms of HCV-RNA replication may include synthesis of negative strand intermediates, which drive synthesis of new positive RNA genomes. New procedures have been developed to better identify and characterize the HCV-RNA genome. The mechanisms of HCV persistence are currently unknown, although it is known that HCV chronicity develops despite humoral and cellular responses to HCV proteins. HCV-RNA shows significant genetic variability with an estimated rate of nucleotide change of approximately 10(-3) substitutions/site/year. Currently, three major HCV genotypes and three to seven minor subtypes can be distinguished. The geographical distribution of these genotypes and subtypes varies significantly. It appears that poor clinical response to interferon (IFN) is more common with HCV genotype 1. In addition, some studies have shown an association between chronic infection, severe chronic hepatitis, and cirrhosis with subtype 1b. Further, there is evidence for a potential direct effect of HCV in liver carcinogenesis, with subtype 1b possibly being an independent risk factor for hepatic carcinoma development. HCV-RNA circulates as a population of RNA molecules, which creates a heterogeneity referred to as "quasispecies." It is possible that some HCV strains might have direct clinical implications. It may be that highly heterogeneous populations observed prior to treatment might correlate with a lower rate of response to IFN therapy.

Genotyping of hepatitis C virus isolates from Basque Country, Spain

The genotype of HCV was determined in 161 chronic HCV-infected patients. The patients were classified into three groups on the basis of the origin of the HCV infection: 50 patients had a history of intravenous drug use (IVDU) but no HIV infection; 41 patients had received blood transfusions, and 70 patients had no known exposure. The distribution of HCV genotypes was associated with the origin of infection and age of patients: genotype 1b was predominant among patients who had received blood transfusions and those without evidence of parenteral exposure (84.6% and 67.7%, respectively), whereas genotype 3a was present in 65.3% of IVDUs. Patients with genotype 1b were older than those with genotypes 1a or 3a: 50.3 +/- 12 vs. 34.1 +/- 9.9 and 31 +/- 5.4 years, respectively. These findings suggest that the pattern of HCV genotypes in our region is changing and that genotype 1b may be substituted by 3a as the dominant genotype in the future.

Infection with hepatitis G virus among recipients of plasma products

BACKGROUND

Hepatitis G virus (HGV or GBV-C) is a newly discovered human flavivirus distantly related to hepatitis C virus (HCV). Little information is available on its natural history or routes of transmission, although it can be transmitted parenterally. We investigated the prevalence of persistent infection of HGV and HCV in patients exposed to non-virus-inactivated pooled blood products associated with transmission of HCV.

METHODS

RNA was extracted from the plasma of 112 patients with haemophilia and 57 with hypogammaglobulinaemia, as well as from 64 different batches of archived coagulation-factor concentrates and immunoglobulins. RNA was reverse transcribed and amplified with primers from the 5' non-coding region of HCV and HGV by a nested polymerase chain reaction (PCR). Viral RNA was quantified by titration of complementary DNA before amplification.

FINDINGS

Among non-renumerated UK blood donors HGV infection (detected by PCR) was more common than HCV infection (four [3.2%] of 125 compared with 137 [0.076%] of 180658 in southeast Scotland). Testing of batches of factor VIII and factor IX concentrates prepared without viral inactivation procedures showed high frequencies of contamination with HGV (16 of 17 factor VIII batches positive; six of six factor IX batches positive), with no difference between renumerated and non-renumerated donors. However, among 95 haemophiliacs who had received non-virus-inactivated concentrates, 13 (14%) were positive for HGV compared with 79 (83%) who were positive for HCV. Two of 37 recipients of long-term immunoglobulin replacement therapy were positive for HGV. Virus inactivation of blood products substantially reduced or eliminated contamination by HGV RNA sequences.

INTERPRETATION

Despite the extremely high level of HGV contamination of non-virus-inactivated blood products, their use was not associated with high rates of persistent infection in recipients. The infectivity of HGV in blood products may be lower than that of HCV, or the virus may be less able to establish persistent infection in humans. Whatever the case, the high prevalence of active HGV infection in the general population remains difficult to explain.

Identification of numerous hepatitis C virus genotypes in Montreal, Canada

Hepatitis C virus genotypes were determined for 358 viremic individuals in Montreal, Canada, by restriction endonuclease analysis of PCR products and phylogenetic analysis of core gene sequences. Types 1, 2, and 3 occurred in 62.8, 14.2, and 13.7%, respectively; types 4 and 5 were found in 3.9 and 4.5%, respectively; and genotypes 6a and 7c and a novel genotype each occurred in 0.3%. Types 4, 6, and 7 and the novel genotype were mostly from persons who had immigrated to Canada.

A sensitive PCR assay system for the quantitation of viral genome equivalents: hepatitis C virus (HCV)

A sensitive and reliable quantitative method has been developed for the detection and quantitation of hepatitis C virus (HCV) target sequences. In this procedure, termed "laser induced fluorescence PCR' (LIF-PCR), reverse transcriptase PCR (RT-PCR) is performed and the PCR products are detected and quantified by laser-induced fluorescence. Precise quantitation of the viral target sequences is accomplished by the use of two calibrators that are amplified by the same set of primers as the target template. A high degree of reliability is achieved by co-processing, co-amplification and co-detection of the calibrators, together with the nucleic acid to be determined. Genome equivalents of HCV containing biological samples, including samples from international test panels, were accurately quantitated with this procedure.

Hepatitis C virus detection by single-round PCR specific for the terminal 3' noncoding region

A single-round PCR method with primers specific for the 3' noncoding region (NCR) of hepatitis C virus (HCV) has been developed. Using a double RNAzol-B extraction, a high-temperature reverse-transcription step with SuperScript II reverse transcriptase, and a 40-cycle two-temperature PCR with a TaqStart antibody hot-start procedure, we were able to detect a 92-nucleotide fragment of the recently discovered 98-nucleotide highly conserved sequence at the 3' terminus of the HCV genome. Direct sequencing of the PCR products confirmed the specificity of the PCR and demonstrated conservation in this region. Only one nucleotide change in 14 specimens was found. End point dilution titration of sera with known viral RNA titers showed the sensitivity of the single-round 3' NCR PCR to be comparable to those of the established nested 5' NCR assays (fewer than 25 HCV genome equivalents). To evaluate specificity and sensitivity, a panel of 116 serum samples characterized by nested 5'-end PCR, genotyping, and quantitative assays was tested. A high degree of concordance (96%) between the 3' NCR and 5' NCR PCR results was found. The sequence conservation at the 3' end of the HCV genome among common genotypes and the savings in time, labor, and reagents from a single-round PCR make this assay a useful addition to the detection systems available to identify and monitor HCV infection.

Hepatitis C genotypes in Finland determined by RFLP

Genotyping of hepatitis C virus (HCV) is important because of its clinical and epidemiological implications. We report here the distribution of HCV genotypes in various patient groups in Finland using a rapid and reliable HCV typing method based on restriction fragment length polymorphism (RFLP) of the amplified DNA from the 5' non-coding region of the genome. The reaction product from the primary, diagnostic PCR (nested, one tube system) was used in genotyping. From 264 Finnish sera we identified HCV genotypes 1a (14%), 1b (24%), 2b (20%). 3a (41%) and 1a + 1b (1%). Only one patient with genotype 2a was identified. From four Egyptian blood donors, types 1b and 4 were found. Genotype 3a was more often associated with i.v. drug abuse and younger age profile (less than 30 years).

Comparative study of three methods for genotyping hepatitis C virus strains in samples from Spanish patients

Hepatitis C virus (HCV) genotypes may be investigated by a variety of laboratory methods that target different parts of the HCV genome and have various degrees of technical difficulty. Since the choice of a particular method is difficult, we compared the performance of (i) a type-specific PCR with type-specific primers from the core region, (ii) molecular hybridization of the PCR-amplified 5' noncoding region to type-specific probes, and (iii) identification of type-specific antibodies against epitopes of nonstructural region 4 by enzyme-linked immunosorbent assay (ELISA). One hundred fifty-one patients with biopsy-proved chronic hepatitis and HCV RNA in serum were investigated. The HCV genotype was identified in 99%, 100%, and 85% of the cases by type-specific PCR, probe hybridization, and ELISA, respectively. The type-specific PCR disclosed infection with type 1a in 3%, type 1b in 74%, and type 3a in 4% of the cases and suggested infection with two or more HCV types, including 2a/2c and 2b, in the remaining 18%. Apparently mixed infections were more prevalent in patients with past intravenous drug use (P < 0.001), but cloning and sequencing of PCR products did not confirm a mixed infection in any of the four cases investigated. Concordant results were obtained by the three procedures with virtually all of the samples in which the type-specific PCR revealed a single HCV genotype. Type-specific hybridization and ELISA usually recognized the genotype producing the strongest DNA band in samples in which type-specific PCR suggested a mixed infection. In conclusion, the three procedures evaluated in this study are reliable for investigation of HCV genotype. Type-specific PCR provides information about HCV subtypes, but a mixed infection detected with this method should be interpreted with caution.

Detection and clinical features of hepatitis C virus type 6 infections in blood donors from Hong Kong

The genotype distribution of hepatitis C virus (HCV) was investigated in 212 viraemic blood donors from Hong Kong. A subset of the samples was investigated using three different genotyping assays to establish the accuracy of each in this population. These assays were restriction fragment length polymorphism (RFLP) of amplified 5' noncoding region (5'NCR) sequences, RFLP of the core region, and a serotyping assay using peptides from two antigenic regions of NS4. Genotypes detected in Hong Kong blood donors were 1a (6.2%), 1b (58.8%), 2a (1.4%), 2b (1.4%), 3a (1.9%), and 6a (27.0%). All genotyping assays produced concordant results. No evidence was obtained for the presence of type 6 group variants recently identified in Southeast Asia, other than type 6a. A serotyping assay based upon the detection of type-specific antibody to epitopes in NS4 produced similar results to the genotyping assays (98% concordance), but a reduced sensitivity (75%) compared with genotyping methods. Sequence variation in NS4 was not the cause of the reduced rate of detection of type 6 antibody in this population. Eighty-four percent donors infected with type 6a were male, compared to 75% donors infected with type 1b. The median alanine transaminase (ALT) level in type 6 infected donors was lower than in type 1b, (43.8 and 51.1 U/l, respectively) although these values were not statistically significant (P = 0.094). There was no significant difference between the ages of donors infected with types 1b and 6a. Risk factors for HCV infection in the blood donors included blood transfusion, intravenous drug abuse, and tattooing. A significantly greater number of donors infected with HCV-6a reported a history of drug abuse (66%) than donors infected with HCV-1b (7%).

alpha-Glutathione S-transferase levels in chronic hepatitis C infection and the effect of alpha-interferon therapy

Serum alpha-glutathione S-transferase (alpha-GST) has been shown to be a sensitive marker of liver injury. We compared the relationship of both serum alpha-GST and alanine transaminase (ALT) with liver biopsy inflammatory activity in patients who had chronic hepatitis C infection (HCV), and examined the effects of alpha-interferon therapy on serum alpha-GST and ALT concentrations. Of 32 patients with chronic HCV infection studied, 17 received alpha-interferon 4.5 MU three times per week for 3 months and 15 acted as controls. Liver biopsy just prior to treatment was scored for the grade of inflammation (Scheuer histological activity index). Serum alpha-GST and ALT were assayed just prior to biopsy and 3 months later. Neither serum alpha-GST nor ALT levels showed any correlation with baseline inflammation on liver biopsy. alpha-Interferon significantly reduced serum alpha-GST concentration at 3 months (P = 0.01). ALT fell with treatment but not significantly (P = 0.05). Small falls in alpha-GST and ALT were noted in the control group, and when these were considered the significance of the changes in alpha-GST and ALT with treatment was lost (P = 0.35 and P = 0.09, respectively). This study shows that serum alpha-GST is not a useful marker of the degree of liver inflammation in chronic HCV infection, though it may be of more value than ALT in monitoring response to treatment with alpha-interferon.

Response to interferon-alpha of Egyptian patients infected with hepatitis C virus genotype 4

Hepatitis C virus (HCV) genotype 4 is the principal HCV genotype found in Egypt and the Middle East. Little is known concerning its propensity to cause disease and the frequency with which infected individuals respond to interferon-alpha (IFN-alpha). We have investigated the response to treatment in a cohort of 100 chronic hepatitis C patients infected with genotype 4. All patients had biopsy-proven chronic active liver disease. Each was treated with 3 million units (MU) IFN-alpha, thrice weekly. Response was monitored, in 92 patients who completed treatment, by alanine aminotransferase (ALT) measurements and by polymerase chain reaction (PCR) for HCV. ALT levels remained abnormal in 64 patients during treatment (69.6%). Of the 28 patients who showed a biochemical response during treatment (30.4%), 18 maintained this over the 6-month posttreatment period. Amongst the sustained biochemical responders, HCV RNA was cleared from serum in only four of the 18 (22.2%) in this period. Histological improvement was observed in 26/51 (50.9%) of the patients who had a second biopsy. Hence, patients infected with HCV genotype 4 show a poor response to IFN-alpha therapy compared with genotypes 2 and 3, but a similar response to IFN-alpha compared with those infected with type 1b HCV. These findings have major implications for treatment strategies in the Middle East, including Egypt, where HCV genotype 4 is widely distributed.

Identification of GBV-C hepatitis G RNA in chronic hepatitis C patients

Sera from patients with chronic hepatitis C were examined for the presence of GBV-C/HGV RNA by RT-PCR. The amplified products, derived from the 5' non-coding, NS3, and NS5a regions, were detected in 19 (19%) of the 100 HCV RNA-positive samples. Analysis of GBV-C/HGV prevalence rates revealed that dual infections are related to shared parenteral risk factors. Intravenous drug abuse and multiple transfusions were the factors clearly associated with a simultaneous HCV and GBV-C/HGV infection. Apart from this, patients with dual infections had a statistically significant lower mean age compared to those patients infected solely by HCV. Determination of HCV genotypes involved in GBV-C/HGV coinfection by RFLP analysis showed no correlation between the presence of GBV-C/HGV and a distinct HCV genotype. The study demonstrates that, based on the assessment of risk criteria, GBV-C/HGV is transmitted efficiently parenterally and is frequently linked to hepatitis C coinfection, regardless of HCV genotype.

Heterogeneity of hepatitis C virus

A great deal of information on the molecular heterogeneity of hepatitis C virus (HCV) has been achieved since its discovery in 1989. However, little is known about the clinical significance of these variations. Based on the degree of sequence variation, HCV has been classified into six major groups or types, differing by 31-34% at the nucleotide level over the entire virus genome. Each type is divided into several subtypes that differ by 20-23% in nucleotide sequence. Viruses within the same subtype are up to 10% divergent and, within infected individuals, vary by up to 1.5%. Genotype distributions are not homogeneous around the world and may reflect both historical and recent parenteral routes of transmission. The clinical implication of these genomic variations are not yet fully elucidated: genotype 1b has been associated with end-stage liver disease, including liver cirrhosis and hepatocellular carcinoma, but this finding might rather reflect its earlier introduction to the populations studied. Consistent evidence exists that types 2 and 3 have a higher response rate to interferon treatment than type 1, although the interplay between genotype and viral load in determining the response is still unclear. Immunohistochemical studies indicate a stronger activation of the endogenous interferon system in the liver of patients infected with type 1 compared to those infected with types 2 and 3, explaining, at least in part, its low responsiveness to exogenous interferon treatment. Biological, sequence-dependent variations of genotypes have been poorly investigated to date, but differential efficiency of translation activity of the 5' non-coding region has been reported. The availability of "in vitro" systems for evaluating pathogenetic aspects and neutralization mechanisms will improve the present knowledge on this world-wide infectious disease and on the clinical usefulness of distinguishing between genotypes.

Genotype analysis of hepatitis C virus among blood donors and inmates in Metro Manila, The Philippines

Antibodies against hepatitis C virus (HCV) were detected in 18 (2.3%) of 800 sera from commercial blood donors and 23 (4.6%) of 502 sera from inmates in Metro Manila, the Philippines. The difference in the antibody prevalence between the two groups was statistically significant (P < 0.05). HCV RNA was detected in 14 (78%) of the 18 antibody-positive sera from blood donors and 19 (83%) of the 23 antibody-positive sera from inmates. Genotype analysis revealed that HCV-2a (7%). Among inmates, on the other hand, HCV-1a (68%) was most common, followed by HCV-1b (11%), HCV-2a (5%) and HCV-2b (5%). Overall, HCV-1a and HCV-1b appeared to be predominant among them. Thus, the genotype prevalence in the Philippines was distinct from those in other Southeast Asian countries such as Thailand, Vietnam and Indonesia, and also distinct from those in the Far East including Taiwan, Mainland China and Japan.

Relevance of RIBA-3 supplementary test to HCV PCR positivity and genotypes for HCV confirmation of blood donors

HCV antibody screening of 624,910 blood donations resulted in 3,832 samples being referred for confirmation. All were tested by RIBA-3 with 2,710 negative, 945 indeterminate and 177 positive results. HCV RNA was detected by PCR in an average of 69.5% of RIBA-3 positives (4 bands 84.1%; 3 bands 74.1%; 2 bands 34.1%) and only 0.53% of RIBA-3 indeterminates. Eighty-four percent of samples with a total RIBA-3 band intensity score (maximum 16) of > or = 8 were PCR positive compared with only 22% of those with a score of < 8. Total mean band intensities for HCV genotype 1 samples (n = 65) were 13.2, genotype 2 (n = 17) 11.4 and genotype 3 (n = 65) 11.2 with type 1 samples showing greater reactivity with c100 and c33 antibodies. No PCR positive type 1 samples were found with RIBA-3 total band scores less than 8, no PCR positive type 2 samples less than 6, whilst PCR positive type 3 samples were found with scores as low as 2. NS5 indeterminates were the most common (40.2%) single band pattern but yielded no PCR positive samples, followed by c33 (23.3%) with one PCR positive and c100 (20.2%) with one PCR positive whilst c22 indeterminates were least common (16.3%) but included three PCR positive donors. All five RIBA-3 indeterminate PCR positive donors were type 3.

Sequence analysis of the 5' non coding region of Turkish HCV isolates: implications for PCR diagnosis

Hepatitis C virus (HCV) is a positive-strand RNA virus related to pestiviruses and flaviviruses. The 5' noncoding region (NCR) of the virus genome consists of 324-341 nucleotides and is generally highly conserved among different HCV isolates which has made this region the choice for primer selection in amplification of HCV sequences by polymerase chain reaction (PCR). In this study, we report the partial nucleotide sequences of the 5'-NCR from type 1a (n = 4), type 1b (n = 6) and type 4 (n = 1) Turkish HCV isolates. Sequence information was obtained by direct sequencing of RT-PCR product using biotinylated primers and single strands were sequenced using T7 DNA polymerase after binding to streptavidin coated magnetic beads. In comparison to prototype type 1a consensus sequence, all type 1b sequences had A-G substitution at position - 99. Nucleotid changes from the prototype 1a sequence were found in 12 of the 174 nucleotide positions. The most variable domain spans 51 nucleotides (positions - 167 to - 117) where nine polymorphic sites were identified. Although the nucleotide sequence of the 5'-noncoding region is highly conserved there are type-specific polymorphic sites within this region that has to be taken into consideration in the design of oligonucleotide primers for reliable amplification of sequences from different HCV genotypes.

A second-generation method of genotyping hepatitis C virus by the polymerase chain reaction with sense and antisense primers deduced from the core gene

A second-generation method of genotyping hepatitis C virus (HCV) was developed by the polymerase chain reaction (PCR) with sense as well as antisense primers deduced from the core gene. HCV RNA specimens extracted from sera were reverse-transcribed and amplified with universal primers in the first round of PCR to obtain fragments of 433 base pairs representing nucleotides 319-751. In the second round of PCR, portions of PCR products were amplified separately with sense and antisense primers specific for each of the five common genotypes prevailing across the world, i.e., I/1a, II/1b, III/2a, IV/2b and V/3a. The specificity of the method was verified by a panel of 177 HCV isolates of various genotypes in the genetic groups 1-9. It allowed clear differentiation of genotype I/1a from II/1b which was not always accomplished by the previous method. When 501 sera from blood donors and hepatitis patients with HCV viremia from various countries were genotyped by the second-generation method, 478 (95.4%) were classified into the five genotypes. HCV RNA samples from 23 (4.6%) sera were not classifiable into any of the five common genotypes and, by sequence analysis, 22 were found to be of four genotypes in group 4 and one of genotype 1c in Simmond's classification.

Hepatitis C virus (HCV) subtype prevalence in Chiang Mai, Thailand, and identification of novel subtypes of HCV major type 6

Subtype analysis of hepatitis C viruses (HCVs) obtained from patients with chronic liver disease in Chiang Mai, Thailand, was performed. Of 46 HCV isolates, 13 (28%) were shown to belong to HCV subtype 3a (HCV-3a), 10 (22%) to belong to HCV-1a, 7 (15%) to belong to HCV-1b, 1 (2%) to belong to HCV-3b, and 1 (2%) to belong to a variant group, as determined from partial nucleotide sequences of the NS5B region of the viral genome. Analysis of 5' untranslated region sequences identified five other isolates (11%) of HCV type 1 and two other isolates (4%) of type 3. Detailed phylogenetic positions for the variant described above and those previously obtained from blood donors and drug addicts in Chiang Mai were determined by a six-parameter neighbor-joining method on the basis of core, E1, and NS5B region sequences. The results revealed that those sequence variants represent novel subtypes of HCV type 6. The HCV type 6 isolates appear to be antigenically different from isolates of HCV types 1 and 2, as determined by a serotyping method that utilizes recombinant peptides corresponding to a portion of the NS4 protein. The significance of subtype analysis around this area is discussed.

Survey of type 6 group variants of hepatitis C virus in Southeast Asia by using a core-based genotyping assay

Previous surveys of the prevalences of genotypes of hepatitis C virus (HCV) in different populations have often used genotyping assays based upon analysis of amplified sequences from the 5' noncoding region (5'NCR), such as restriction fragment length polymorphism (RFLP) or hybridization with type-specific probes (e.g., InnoLipa). Although highly conserved, this region contains several type-specific nucleotide polymorphisms that allow major genotypes 1 to 6 to be reliably identified. Recently, however, novel HCV variants found in Vietnam and Thailand that are distantly related to the type 6a genotype (type 6 group) by phylogenetic analysis of coding regions of the genome often have sequences in the 5'NCR that are similar or identical to those of type 1 and could therefore not be identified by an assay of sequences in this region. We developed a new genotyping assay based upon RFLP of sequences amplified from the more variable core region to investigate their distribution elsewhere in southeast (SE) Asia. Among 108 samples from blood donors in seven areas that were identified as type 1 by RFLP in the 5'NCR, type 6 group variants were found in Thailand (7 from 28 samples originally identified as type 1) and Burma (Myanmar) (1 of 3) but were not found in Hong Kong (n = 43), Macau (n = 8), Taiwan (n = 6), Singapore (n = 2), or Malaysia (n = 18). Although this small survey suggests a relatively limited distribution for type 6 group variants in SE Asia, larger studies will be required to explore their distribution in other geographical regions and the extent to which their presence would limit the practical usefulness of 5'NCR-based genotyping assays for clinical or epidemiological purposes.

Virology of hepatitis C virus

Hepatitis C virus (HCV) has been identified as the main causative agent of posttransfusion non-A, non-B hepatitis. Through recently developed diagnostic assays, routine serologic screening of blood donors has prevented most cases of posttransfusion hepatitis. The purpose of this paper is to comprehensively review current information regarding the virology of HCV. Recent findings on the genome organization, its relationship to other viruses, the replication of HCV ribonucleic acid, HCV translation, and HCV polyprotein expression and processing are discussed. Also reviewed are virus assembly and release, the variability of HCV and its classification into genotypes, the geographic distribution of HCV genotypes, and the biologic differences between HCV genotypes. The assays used in HCV genotyping are discussed in terms of reliability and consistency of results, and the molecular epidemiology of HCV infection is reviewed. These approaches to HCV epidemiology will prove valuable in documenting the spread of HCV in different risk groups, evaluating alternative (nonparenteral) routes of transmission, and in understanding more about the origins and evolution of HCV.

Prevalence of hepatitis C genotypes among patients with chronic hepatitis C in Norway. Construct Group

Among 116 patients with biopsy-confirmed chronic hepatitis C (Riba 2 or Riba 3 positive) in a multicenter study in southern Norway on interferon, we determined hepatitis C virus genotype by restriction fragment length polymorphism (RFLP) of the 5' NCR. The RFLP method was supplemented by and compared with a serological typing method based on the detection of type-specific antibody to peptide from the NS-4 region. A total of 102/106 (96%) patient sera showed detectable type-specific antibody to NS-4 peptides and corresponded in all cases, except two, to the genotype detected by polymerase chain reaction. Combining the results from RFLP genotyping and serotyping, genotype 1 was found in 40 (35%) (27 with 1a and 10 with 1b, 3 subtypes not determined), genotype 2 in 15 (13%) (subtype 2b in 14 and 1 subtype not determined), and genotype 3 in 58 (50%) of patients. The low mean age of the patients (34 years), the low prevalence of cirrhosis (3.5%), the short duration of the disease, and a high prevalence of intravenous-drug abusers may account for the low prevalence of infection with genotype 1b (9%). The epidemiological features of hepatitis C patients are markedly different from patient groups described in southern Europe in terms of risk factors, age, and genotype distribution.

Genotypes of hepatitis C virus isolates from different parts of the world

Hepatitis C virus (HCV) causes most cases of posttransfusion non-A, non-B hepatitis. HCV isolates were classified by their genetic relatedness into at least six genotypes and a series of subtypes. Methods for typing included amplification of certain genomic regions using universal or type/subtype specific primers, restriction fragment length polymorphism analysis, differential hybridization, nucleotide sequencing, and serologic genotyping. HCV genotypes and their subtypes coexist in various geographic locations but show different prevalences. The identification of genotypes/subtypes is useful for studies on the molecular epidemiology and pathogenesis of HCV infection.

Biological and clinicopathological features associated with hepatitis C virus type 5 infections

BACKGROUND/AIMS

The biological and clinicopathological features of hepatitis C virus infections of type 1 and type 2 have been well documented. However, little is known about the nature of HCV type 5 infections, which have been found to occur in South Africa but rarely elsewhere.

METHODS

We investigated the HCV genotypes in 125 viremic blood donors and 125 viremic patients by restriction endonuclease analysis of amplified 5' non-coding region sequences. Donors and patients infected with type 5 were further studied. Serum HCV RNA levels were assessed by a differential-size PCR-aided transcript titration assay.

RESULTS

HCV type 5 infections were identified in seven (5.6%) of the blood donors and in five (4.0%) of the patients. Sera from these 12 persons reacted with the core and NS3 antigens in both RIBA-2 and RIBA-3 tests. Six (50%) and 10 (83%) sera reacted with the NS4 antigens in RIBA-2 and RIBA-3 tests, respectively. HCV type 5 was found to replicate to high titers that ranged from 10(6.0) to 10(8.0) molecules/ml. Transfusion was the most frequently observed risk factor (5 of 12) and persons infected with type 5 were generally older than those infected with other types (< 40 years vs. > or = 40 years, p = 0.01). Cirrhosis was found in two of six (33%) donors and three of four (75%) patients. The duration of infection appeared to be an important determinant for the presence of cirrhosis.

CONCLUSIONS

In this small group of Canadians infected with HCV type 5, a high proportion developed severe liver disease.

Progress towards the comprehensive control of hepatitis B in Africa: a view from South Africa

The carrier rate of hepatitis B virus (HBV) in black Africans averages 10.4% throughout the continent. Even within each country, however, there may be wide variations. HBV carriage in black Africans is largely established in early childhood, mostly through horizontal transmission. Perinatal transmission also occurs but to a much lesser extent than in the Far East. For unknown reasons, HBeAg positivity rates are much lower in black Africans of childbearing age than in women in the Far East. Universal HBV vaccination of infants in South Africa started in April 1995. Effective integration into the Expanded Programme on Vaccination will probably be necessary if administration of second and third doses is to be ensured. Fortunately, a natural process of urbanisation is also having a beneficial effect on the black carrier rate in South Africa, as urban carrier rates tend to be much lower than those in rural area. Within the next 20 years, therefore, there should be a great reduction in the numbers of acute HBV infections and new carriers. However, it will take much longer before there is any substantial impact on the burden of the longterm sequelae of HBV infection--that is, cirrhosis and hepatocellular carcinoma.

Greater diversity of hepatitis C virus genotypes found in Hong Kong than in mainland China

A hepatitis C virus (HCV) genotyping PCR assay based on type-specific primers was expanded to include genotype 6a as well as genotypes 1a, 1b, 2a, and 3a. The nucleotide sequences of a 194-bp fragment in the center of the HCV core gene showed that the homologies between genotype 6a and genotypes 1a, 1b, 2a, 2b, 3a, and 5 were 81.2, 82.1, 73.8, 77.3, 81.4, and 78.9%, respectively. A high degree of homology (99.6%) was seen in the amplified core region among eight clinically unrelated genotype 6a isolates. Although the Hong Kong Chinese patients had predominantly genotype 1b (70%), it was noteworthy that genotype 6a was the second most common genotype (14%). Four other HCV genotypes--1a, 1b, 2a, and 2b--were also present. In contrast, HCV infection by mainland China was confined to genotypes 1b and 2a. Thus, we found a greater diversity of HCV genotypes in Hong Kong than in mainland China.