Hepatitis C virus (HCV) core serotypes in chronic HCV infection

Comparative Immunogenicity in Rabbits of the Polypeptides Encoded by the 5' Terminus of Hepatitis C Virus RNA

Recent studies on the primate protection from HCV infection stressed the importance of immune response against structural viral proteins. Strong immune response against nucleocapsid (core) protein was difficult to achieve, requesting further experimentation in large animals. Here, we analyzed the immunogenicity of core aa 1–173, 1–152, and 147–191 and of its main alternative reading frame product F-protein in rabbits. Core aa 147–191 was synthesized; other polypeptides were obtained by expression in E. coli. Rabbits were immunized by polypeptide primes followed by multiple boosts and screened for specific anti-protein and anti-peptide antibodies. Antibody titers to core aa 147–191 reached 10⁵; core aa 1–152, 5 × 10⁵; core aa 1–173 and F-protein, 10⁶. Strong immunogenicity of the last two proteins indicated that they may compete for the induction of immune response. The C-terminally truncated core was also weakly immunogenic on the T-cell level. To enhance core-specific cellular response, we immunized rabbits with the core aa 1–152 gene forbidding F-protein formation. Repeated DNA immunization induced a weak antibody and sustained proliferative response of broad specificity confirming a gain of cellular immunogenicity. Epitopes recognized in rabbits overlapped those in HCV infection. Our data promotes the use of rabbits for the immunogenicity tests of prototype HCV vaccines.

Serotyping of hepatitis C virus in hemodialysis patients: comparison with a standardized genotyping assay

The aims of this study were to investigate the prevalence of hepatitis C virus (HCV) genotypes and serotypes in anti-HCV-positive hemodialysis patients and determine the concordance between genotyping and serotyping methods. Sixty-two hemodialysis patients were included in this study. HCV RNA was determined using polymerase chain reaction assay and genotypes using a line probe assay. HCV serotyping was performed with competitive enzyme-linked immunosorbent assay. Genotype 4 (52 patients) was the most predominant genotype, followed by type 1 (10 patients). The most prevalent HCV serotype was type 4 (41 patients), followed by serotype 1 (6 patients). We detected multiple serotypes in 4 patients and untypeable strains in 11. The overall sensitivity of serotyping assay was 82% for the study patients. According to the genotyping results, the sensitivity of serotyping was 60% and 86.5% for HCV types 1 and 4, respectively. There was a 100% concordance between results of serotyping and genotyping in the identification of HCV type 1 and 91% concordance in HCV type 4. Serological typing method may be of great value in microbiology laboratories that require a simple assay for identification of HCV genotypes, although the sensitivity of this assay may be limited by the immunocompetence of infected hemodialysis patients.

Advances in the molecular diagnosis of hepatitis C and their clinical implications

Serologic assays for diagnosis of hepatitis C infection may yield indeterminate results despite improvements in sensitivity and specificity through second- and third-generation assays. Direct detection of hepatitis C virus (HCV) RNA based on qualitative reverse transcription-polymerase chain reaction or transcription-mediated amplification allows diagnosis in the early stages of acute infection and in patients unable to mount an antibody response. Quantitative HCV RNA assays are useful for selecting appropriate antiviral therapies, but until recently they have lacked comparability between tests. More sensitive qualitative assays should be used for determining duration of treatment or recognizing a sustained virologic response to therapy. Hepatitis C virus genotyping can be performed from a limited sequence analysis of the viral genome by using various techniques. Although newer genotyping methods are relatively practicable and are satisfactory for the discrimination of the majority of genotypes, discrimination between subtypes can be challenging. Serologic typing of HCV lacks sensitivity and specificity compared with molecular-based techniques. Recent advances in serologic assays and nucleic acid detection techniques allow physicians to make accurate diagnoses, and these assays serve as important tools in treatment planning.

Advances in the molecular diagnosis of hepatitis C and their clinical implications

Serologic assays for diagnosis of hepatitis C infection may yield indeterminate results despite improvements in sensitivity and specificity through second- and third-generation assays. Direct detection of hepatitis C virus (HCV) RNA based on qualitative reverse transcription-polymerase chain reaction or transcription-mediated amplification allows diagnosis in the early stages of acute infection and in patients unable to mount an antibody response. Quantitative HCV RNA assays are useful for selecting appropriate antiviral therapies, but until recently they have lacked comparability between tests. More sensitive qualitative assays should be used for determining duration of treatment or recognizing a sustained virologic response to therapy. Hepatitis C virus genotyping can be performed from a limited sequence analysis of the viral genome by using various techniques. Although newer genotyping methods are relatively practicable and are satisfactory for the discrimination of the majority of genotypes, discrimination between subtypes can be challenging. Serologic typing of HCV lacks sensitivity and specificity compared with molecular-based techniques. Recent advances in serologic assays and nucleic acid detection techniques allow physicians to make accurate diagnoses, and these assays serve as important tools in treatment planning.

Genomic and phylogenetic analysis of hepatitis C virus isolates from argentine patients: a six-year retrospective study

Typing of hepatitis C virus (HCV) isolates from Argentine patients was performed by using different methodologies in a population of 243 patients. HCV subtype was assigned based upon restriction fragment length polymorphism (RFLP). HCV RNA genomes obtained from serum samples were classified as belonging to clade 1 (53.5%), 2 (23. 0%), or 3 (8.6%); 14.8% of samples showed HCV mixed infections, more frequently implying different subtypes within the same clade. In addition to RFLP typing, phylogenetic relatedness among sequences from both 5' untranslated region (n = 50) and nonstructural 5B coding region (n = 15) was established.

Serotyping and genotyping of hepatitis C virus in Taiwanese patients with type C chronic liver disease and uraemic patients on maintenance haemodialysis

BACKGROUND

To evaluate a recombinant immunoblot hepatitis C virus (HCV) serotyping assay, which determines HCV serotypes 1, 2, and 3 by detecting type-specific antibodies to core-and NS-4-derived peptides.

METHODS

Immunoreactivity of type-specific antibodies among 173 chronic hepatitis C patients and 43 haemodialysis patients in Taiwan was examined and the serotyping results were compared with genotyping by Okamoto's method. Serial specimens from 29 patients undergoing interferon-alpha therapy were also evaluated.

RESULTS

Of the 205 specimens for which genotyping data were available, 51.2% were of serotype 1, 31.7% of serotype 2, 1.0% of serotype 3, 2.4% of either serotype 1 or 3, and the remaining 13.7% were untypable. The serotypable rate was significantly lower in haemodialysis patients than in chronic hepatitis C patients (70.0% vs 94.9%; P < 0.001). Serotyping of genotype 2b specimens was significantly more dependent on core peptide bands than other genotypes. Using genotyping as the reference, the overall sensitivity, specificity and concordance of the recombinant immunoblot HCV serotyping assay were 86.3%, 97.2% and 83.9%, respectively. However, the serotyping assay had significantly lower sensitivity (69.2%), specificity (77.8%) and concordance (53.8%) for genotype 2b specimens. Of nine HCV complete responders, one lost type-specific antibodies 6 months after the cessation of interferon-alpha treatment.

CONCLUSIONS

These results suggest that, except for less than optimal performance with immunocompromised or genotype 2b patients, the HCV serotyping assay is a practical and useful method for HCV typing in the clinical setting in Taiwan.

Clinical significance of hepatitis C virus genotypes

On the basis of phylogenetic analysis of nucleotide sequences, multiple genotypes and subtypes of hepatitis C virus (HCV) have been identified. Characterization of these genetic groups is likely to facilitate and contribute to the development of an effective vaccine against infection with HCV. Differences among HCV genotypes in geographic distributions have provided investigators with an epidemiologic marker that can be used to trace the source of HCV infection in a given population. HCV genotype 1 may represent a more aggressive strain and one that is less likely to respond to interferon treatment than HCV genotype 2 or 3. However, these observations require confirmation before HCV genotyping can be used in clinical settings.

Clinical significance of hepatitis C virus genotypes

On the basis of phylogenetic analysis of nucleotide sequences, multiple genotypes and subtypes of hepatitis C virus (HCV) have been identified. Characterization of these genetic groups is likely to facilitate and contribute to the development of an effective vaccine against infection with HCV. Differences among HCV genotypes in geographic distributions have provided investigators with an epidemiologic marker that can be used to trace the source of HCV infection in a given population. HCV genotype 1 may represent a more aggressive strain and one that is less likely to respond to interferon treatment than HCV genotype 2 or 3. However, these observations require confirmation before HCV genotyping can be used in clinical settings.

HCV genotypes--role in pathogenesis of disease and response to therapy

Hepatitis C virus (HCV) shows considerable variation in its genomic structure, allowing classification into six main genotypes. Epidemiological studies have shown marked differences in genotype distribution by geographical region, and between patient groups. Improved understanding of the rate of nucleotide sequence mutation in HCV has allowed the approximate time of divergence of major genotypes to be estimated, and the origin and spread of the present epidemic of hepatitis C to be better defined. Improved methods of genotype definition over the last few years have enabled the importance of genotype in the progression of HCV-related disease and response to anti-viral therapy to be studied. Present data strongly indicates that HCV genotype is an important determinant of response to treatment, but the effect of genotype on disease progression has been harder to clarify. This is largely due to the absence of model systems of HCV infection, the epidemiological differences in patient groups infected with the different genotypes, and the lack of good prospective longitudinal clinical data. As a result of advances in methodology, and recent results of large clinical trials of combination therapy, a knowledge of HCV genotype is now central to the clinician in the management of patients with chronic hepatitis C.

Clinical significance of hepatitis C virus genotypes

The advent of genotyping assays has stimulated investigators around the world to study the molecular epidemiology of hepatitis C virus (HCV) infection in specific patient categories, as well as possible correlations with the clinical and histological features of chronic liver disease and response to antiviral treatment. While a general consensus has been reached on the worldwide epidemiology and distribution of HCV types in certain risk categories (i.e. intravenous drug users), the association between genotype 1b and severe liver disease is still controversial. Although generalized use of genotyping is not presently recommended for clinical or epidemiological monitoring, several studies emphasize to the importance of HCV genotyping as part of a therapeutic algorithm. This recommendation is based on overwhelming evidence in support of a correlation between genotype 1 and a poor response to interferon-a alone or in combination with ribavirin.

Long-term treatment of chronic hepatitis C with ursodeoxycholic acid: influence of HCV genotypes and severity of liver disease

AIMS/BACKGROUND

Current therapy for chronic hepatitis C virus (HCV) infection is based on the administration of interferon alpha (IFN) alone or in combination with other anti-viral agents. However, such therapy is effective in only a minority of selected patients. Long-term ursodeoxycholic acid (UDCA) treatment has been reported to improve liver function and structure especially in cholestatic disorders. We investigated the effect of long-term UDCA treatment on liver function in respect to the severity of chronic liver disease and HCV genotypes.

METHODS

Forty-five patients with non-cholestatic laparoscopy-biopsy proven HCV-associated chronic hepatitis (n=16) or cirrhosis (n=29) who had not responded to, or were unsuitable for IFN, were randomly assigned to receive UDCA (600 mg/day; n=23) or no therapy (n=22) for 12 months. At entry, all patients were evaluated by means of conventional and quantitative liver function tests (LFTs), including galactose elimination capacity and antipyrine clearance, HCV antibodies, HCV-RNA and HCV genotypes. LFTs were measured at 6 and at 12 months, whereas HCV-RNA was determined again after treatment.

RESULTS

Baseline characteristics were comparable in the two study groups. Long-term UDCA therapy was well tolerated. Based on the analysis of variance, there was a significant decrease in serum transaminase, LDH and GGT levels in UDCA treated patients. By contrast, the activities of these enzymes increased in untreated patients, with AST levels reaching statistical significance only. Statistical analysis also showed that the improvement in biochemical markers was more pronounced in UDCA treated patients with liver cirrhosis than in those with chronic hepatitis but was similar in patients with HCV genotype 1b and non-1b. However, HCV-RNA was positive in all patients after treatment. Quantitative LFTs remained, on average, stable over the 12 months of the trial in all groups.

CONCLUSIONS

Long-term UDCA treatment is well tolerated in patients with HCV-associated chronic liver disease. The effect appears to be greater in cirrhotics than in patients with chronic hepatitis but is independent of HCV genotypes. Thus, long-term UDCA treatment, despite the absence of an anti-viral effect, seems beneficial in reducing disease activity in patients with chronic hepatitis or cirrhosis who are unsuitable for IFN therapy.

Quantitative antibody responses to structural (Core) and nonstructural (NS3, NS4, and NS5) hepatitis C virus proteins among seroconverting injecting drug users: impact of epitope variation and relationship to detection of HCV RNA in blood

To gain insight into the natural history of hepatitis C virus (HCV), 13 human immunodeficiency virus (HIV)-seronegative injecting drug users were studied who seroconverted for HCV as determined by third-generation enzyme-linked immunosorbent assay, showed an ensuing antibody response to HCV, and were not treated with any antiviral drugs during follow-up. Subjects included 13 untreated HIV-negative individuals, of whom 5 (38.5%) apparently cleared HCV and were polymerase chain reaction (PCR)-negative in at least 3 consecutive samples, 3 (23.1%) showed transient viremia and were PCR-negative in 1 sample during the study period, and the other 5 (38.5%) showed persistent viremia. Viremia was determined longitudinally by reverse-transcription PCR (RT-PCR) and quantified by branched DNA (bDNA). HCV genotypes were determined on serial samples during follow-up. Quantitative antibody levels to core, NS3, NS4, and NS5 were determined using the Chiron RIBA HCV-titering Strip Immunoblot Assay, which is based on HCV genotype 1. The antibody responses to core, NS3, NS4, and NS5 were erratic. In individuals infected with HCV genotype 1, significantly higher median antibody responses to core (P =.02) and to NS4 (P =.04) were found as compared with those infected with other genotypes, showing a significant impact of HCV genotype specificity of the assay. In groups infected with HCV genotype 1, significantly higher median NS3 antibody titers (2.61 relative intensity [RI] vs. 0.38 RI; P =.003) were found in the individuals with persistent viremia than in those with apparent resolution of HCV RNA in blood. In groups infected with genotypes other than genotype 1, significantly higher median NS3 antibody titers (0.89 RI vs. 0.03 RI; P =.0004) and NS5 antibody titers (1.86 RI vs. 0.01 RI; P =.006) were found in the individuals with persistent viremia than in those with apparent resolution of HCV RNA in blood. Individuals with viral persistence had higher HCV-RNA loads with higher antibody responses as compared with individuals with apparent viral clearance from blood. Apparent viral clearance from blood was observed in an unexpectedly high percentage (38.5%), associated with a significant decrease of antibodies to NS3, independent of HCV genotype, as compared with individuals with persistent viremia (P <.005). Apparent viral clearance from blood with gradual loss of antibodies to various HCV proteins, independent of HCV genotype, was observed in 4 of the 5 individuals within approximately 1 year after HCV seroconversion, whereas 1 of these individuals apparently cleared the virus from blood, with complete seroreversion.

Characterization of anti-hepatitis C virus-positive sera not genotyped by restriction fragment length polymorphism or serology

BACKGROUND

The hepatitis C virus genome is extremely heterogeneous and has been classified into six major genotypes. Genotyping of hepatitis C has been achieved through both direct molecular approach and indirect detection of host genotype-specific antibodies by serological methods. The purpose of this study was to characterize anti-hepatitis C positive sera samples that were not genotyped either by restriction fragment length polymorphism or by serology.

METHODS

Two hundred and two patients from northern California with established chronic hepatitis C virus infection were studied by restriction fragment length polymorphism analysis of the 5'-untranslated region amplicon. A serological genotyping assay, based on synthetic peptides derived from non-structural region 4 of the hepatitis C virus genome, was used to determine serological genotype.

RESULTS

Of the 202 patients studied, 187 (93%) were polymerase chain reaction-positive. One hundred and eighty-six patients were able to be genotyped by restriction fragment length polymorphism, compared with 144/202 (71%) of patients genotyped by serology (P < 0.0001). Only two of 202 samples showed discordant genotyping results. The distribution of hepatitis C virus genotypes in northern California was found to be type 1a, 41%; 1b, 35%; 2a, 3%; 2b, 10%; 3a, 11%; and 4, < 1%. There was no association between hepatitis C genotypes and age, gender distribution, ethnic origin, presumptive mode of transmission, serum alanine aminotransferase levels and the proportion of patients with cirrhosis. Of the 15 patients who were not genotypable by the molecular assay, four patients were genotyped by serology, with hepatitis C virus genotypes 1, 2 and 3 represented. Of the 58 samples that were not genotyped by serology, 47 were genotyped based on the molecular assay, and the distribution of hepatitis C virus genotypes was similar to that of the overall study population.

CONCLUSIONS

These data showed that: (i) molecular genotyping assay based on 5'-untranslated region is more sensitive than serologic genotyping based on the non-structural-4 region but the results were highly concordant; (ii) hepatitis C virus genotypes 1-4 are present in northern California, with genotype 1 being the most prevalent; and (iii) the failure to determine hepatitis C virus genotype based on molecular or serological genotyping assay does not appear to be related to specific hepatitis C genotypes.

Genotyping HCV isolates from Italy by type-specific PCR assay in the core region

A revision of the polymerase chain reaction (PCR) core procedure was performed for genotyping hepatitis C virus (HCV) in 139 patients from Italy. This procedure, developed prior to the identification of new genotypes, may be inadequate in several geographical areas. We proposed a new typing mixture in which primers for types 2c and 4, that are reported to be circulating in Italy, were added and a primer for type 2b was substituted. Using the modified procedure, 139 HCV-positive patients were analysed. The HCV genotype was identified in 96.4% of the cases. We observed double infections and unclassified genotypes in 5 (3.6%) and 5 (3.6%) patients, respectively. The classification of isolates into genotypes and subtypes 2b, 2c and 4 was confirmed by sequence analysis. Furthermore, the efficiency and accuracy of the modified core procedure were evaluated by parallel testing of 107 out of 139 samples using the line probe assay, and demonstrated a 98.9% degree of concordance. The results demonstrated the specificity of the selected primers for type 2c, 2b and 4 and confirmed the circulation of types 2c and 4 in Italy. In conclusion, the proposed modified PCR procedure is the only primer-specific PCR genotyping method available for identification of the 2c and 4 genotypes reported to be circulated in Italy and other European countries.

[Update on hepatitis C virus: its variability and the implications]

Hepatitis C virus (HCV) is the main etiologic factor of post-transfusional and sporadic hepatitis, called non-A non-B in the past. These infections are characterized by a very high number of chronic carriers always with a persistent viral increase, but often at a slow pace. The seriousness of liver disease differs from one individual to another, varying from an asymptomatic form with minor or no liver injuries, to cirrhosis and hepatocellular carcinoma. Physiopathological mechanisms involved in liver injuries are still poorly understood. The direct role of immune response and of possible genetic factors is still under study. This review aims at summing up the discovery of HCV, its structure, and its variability in the various genome regions in the same individual and from one individual to another. The different methods and techniques to analyze this variability are also reviewed, as well as the various suggested ways of classifying the different types. The geographical distribution and both clinical and biological consequences of this variability are also discussed.

Hepatitis C

Hepatitis C virus (HCV) infection afflicts millions of people in the United States and worldwide. We examine the epidemiology of HCV infection, the molecular biology of the virus, the pathophysiology of infection, the clinical diagnosis and manifestations of infection, and the treatment of HCV infection.

Characteristics of patients with dual infection by hepatitis B and C viruses

BACKGROUND/AIMS

The purpose of this study was to compare the epidemiological, biochemical, virological and histological characteristics of patients with chronic hepatitis B and C with those of patients suffering from chronic hepatitis C alone.

METHODS

Twenty-three patients with chronic hepatitis C, who were anti-HCV positive and HBs antigen positive, were studied and subdivided into two groups according to the presence or absence of HBV DNA replication. They were compared to 69 age- and sex-matched patients with chronic hepatitis who were anti-HCV positive and HBs antigen negative. All patients were HCV RNA positive by PCR, anti-HIV negative and anti-HDV negative. HBV DNA and HCV RNA were detected in serum by means of a branched DNA assay and PCR. The HCV serotypes were determined by the Chiron Riba HCV serotyping SIA technique. The histological characteristics included the Knodell score.

RESULTS

Epidemiological, biochemical and virological parameters were not different between the two groups. Only the prevalence of cirrhosis was greater in chronic hepatitis B and C patients than in patients with chronic hepatitis C alone (p = 0.01). Among chronic hepatitis B and C patients, HCV RNA level was significantly lower in HBV DNA positive than in HBV DNA negative patients (p = 0.01). Indeed, histological lesions were more severe in HBV DNA positive than in HBV DNA negative patients, including prevalence of cirrhosis (p = 0.01), Knodell score (p = 0.05) and, among the latter, piecemeal necrosis (p = 0.01) and fibrosis (p = 0.05). The characteristics of patients with dual infection did not differ according to the mode of contamination and duration of HBV disease, except for a shorter duration in patients contaminated by drug abuse than in other patients.

CONCLUSIONS

These results suggest that HBV DNA replication inhibits HCV RNA replication in patients with chronic active hepatitis B and C but increases the severity of histological lesions.

Antigenic variation of core, NS3, and NS5 proteins among genotypes of hepatitis C virus

Assays that detect antibody to hepatitis C virus (HCV) are used to screen blood donors and patients with hepatitis. Current enzyme-linked immunosorbent assay (ELISA)-based methods are invariably based upon antigens from expressed recombinant proteins or oligopeptides from HCV type 1. Some HCV antigens used in screening assays are coded by regions of the HCV genome that show extensive variability; therefore, HCV type 1-based assays may be less effective for the detection of antibody elicited by infection with other genotypes. In this study, we have measured antibody reactivity of sera from 110 hepatitis C patients infected with type 1b, 3a, or 4a to genotype-specific and cross-reactive epitopes present in recombinant proteins from HCV genotypes 1b (core, NS3, and NS5), 3a (NS3, NS5), and 4a (core, NS3), corresponding to those used in current third-generation screening ELISAs. By comparing the serological reactivities of sera to type-homologous and type-heterologous antigens, we detected a significant type-specific component to the reactivity to NS3 (61 to 77% of the total reactivity) and NS5 (60% of the total reactivity). Furthermore, despite the similarities in the amino acid sequences of the core antigens of type 1b and type 4a, we also found significantly greater reactivity to type-homologous antigens, with approximately 25% of reactivity being type specific. These findings are consistent with previous findings of fivefold weaker reactivity of sera from HCV type 2- and HCV type 3-infected blood donors in the currently used third-generation ELISAs and suggest that these assays are suboptimal for screening populations in which the predominant genotype is not type 1.

Serotyping and genotyping of hepatitis C virus (HCV) strains in chronic HCV infection. Commission Hepatologie du CREGG. Club de Reflexion des Cabinets de Groupes en GastroEnterologie

Hepatitis C virus (HCV) genotypes can be established by methods based on PCR typing and serological typing. The accuracy of these methods depends on their sensitivity and specificity. These should be compared with the reference method, direct sequencing, and analysis of viral genomes. Among the serologic methods recently developed, the performance of a new serotyping assay (RIBA HCV 3.0 SIA, Chiron corporation, Emeryville) was assessed using a panel of 147 well-characterized French isolates from chronic hepatitis C patients. Definitive genotypes of the isolates were established by direct sequencing in 5' NC and in some cases in NS-5B. HCV serotypes 1, 2, and 3 were determined by measuring type specific antibodies to core and NS-4 derived peptide antigens. Of the 147 sera, serotypic-specific antibodies were detected in 136 (sensitivity, 92.5%). The specificity of the RIBA SIA HCV serotyping assay was 92.6% (including samples with mixed results); without these, the specificity was 80.1%. Analysis of the 28 discrepant samples showed that (1) a different serotype was found in 18 samples including five for genotype 1, three for genotype 2, two for genotype 3, five for genotype 4, and three for genotype 5, and that (2) ten patients showed a reactivity with mixed serotypes, one had circulating antibodies to type 1 or 2, and nine had circulating antibodies to type 1 or 3. In summary, except for genotypes 4 and 5, the results of the test were well correlated (85.7%) with those of direct sequence genotyping. The former test is rapid and does not require the strict HCV RNA storage and preservation conditions of the latter. This new method may thus be considered as an alternative for HCV typing. However, although it is convenient, its lower sensitivity compared to the molecular typing method and the discrepant results limit its routine use in a clinical context.

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.

Evaluation and comparison of different hepatitis C virus genotyping and serotyping assays

BACKGROUND/AIMS

Evidence that the geno/subtype of hepatitis C virus (HCV) is predictive of the response to interferon-alpha therapy suggests that typing methods are clinically useful. In the present study, HCV isolates obtained from 74 patients with chronic hepatitis C were used to evaluate three genotyping and two serotyping assays.

METHODS

The reverse hybridization assay and the DNA immunoassay are based on immobilized type-specific probes for the 5'-noncoding and the core region, respectively. A third genotyping assay utilized type-specific primers for amplification of the core region. Serotyping assays detect type-specific antibodies of the nonstructural-4 region (enzyme immunoassay) or of the core and nonstructural-4 region (recombinant immunoblot assay). Gold standard geno/subtyping of HCV isolates was performed by sequence and phylogenetic analysis of the nonstructural-5B region.

RESULTS

All genotyping systems amplified the respective target region of the HCV genome with high sensitivity. The reverse hybridization assay and the DNA immunoassay correctly identified HCV-1, -2, and -3. The DNA immunoassay misinterpreted all HCV-4 isolates as HCV-4 and -5 coinfection. In the type-specific amplification assay, coinfections of subtypes HCV-1a and HCV-3a with HCV-1b could not be excluded. The reverse hybridization assay misinterpreted 1/14 HCV-1a isolates as HCV-1h, and vice versa 3/36 HCV-1b isolates as HCV-1a. Furthermore, differentiation between HCV-2a and -2c was not possible using this assay. The DNA immunoassay correctly identified all HCV subtypes. The serotyping assays, recombinant immunoblot assay and enzyme immunoassay identified HCV-1, -2, and -3 in 93% and 89% of cases, respectively. HCV-4, however, could only be recognized by the enzyme immunoassay.

CONCLUSIONS

The reverse hybridization assay and the DNA immunoassay specifically identified HCV genotypes 1, 2, and 3, while crossreactivity occurred in the primer-specific amplification assay. The DNA immunoassay achieved the best performance in HCV subtyping. Both serotyping systems correctly identified HCV-1, -2, and -3 in about 90% of cases, but lack the possibility of subtyping.

Hepatitis C virus replicative levels and efficiency of genotyping by specific PCR and antibody assay

We studied factors which influence the detection of hepatitis C virus genotypes by the group-specific PCR of the sequence within the core region gene and by the newly developed genotype-specific NS4 antibody assay. Genotyping was performed on 75 hepatitis C virus carriers in Japan, where patients with hepatitis C viremia are exclusively infected with genotype 1b, 2a, and 2b. PCR failed to identify genotypes in 8 (11%) patients, whereas 12 (16%) patients, including the 8 patients mentioned above, could not be genotyped by the serological assay. Serological genotypes showed almost complete agreement with those found by the PCR except that double infection was revealed in only two of the eight patients serologically judged to be coinfected with genotypes 1 and 2. In each assay, disease activity and levels of viremia assessed by a competitive reverse transcription PCR assay were significantly lower in patients infected with untypeable isolates than in those infected with typeable ones (P < 0.01). The PCR could identify the genotypes of isolates from all 64 patients with levels of viremia of > or = 10(6) copies/ml, and the genotype-specific antibody responses were found in 60 (94%) patients. In contrast, isolates from only 3 (27%) of 11 patients with low levels of viremia (< 10(6) copies/ml) could be genotyped by the PCR (P < 0.00001), and these patients showed the genotype-specific antibody responses (P < 0.00001). These findings suggest that low levels of hepatitis C virus replication may reduce the efficiency of genotyping by serological assay as well as by PCR.

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.

Comparison of hepatitis C virus serotyping and genotyping in French patients

BACKGROUND

Hepatitis C virus (HCV) serotyping has been proposed as an alternative assay to determine the respective genotype as it is more rapid, simple and less expensive than polymerase chain reaction (PCR) based typing methods.

OBJECTIVES

A serotyping assay was compared with a genotyping assay to determine the infecting hepatitis C virus type in chronically HCV infected patients eligible for interferon therapy.

STUDY DESIGN

An enzyme immunoassay (HC01, Murex) was tested to identify HCV types 1, 2 and 3 specific antibodies in 134 PCR-positive sera from chronically infected patients which had been previously genotyped by a reverse hybridization assay (INNO-LiPA HCV I, Innogenetics). Respectively nine and seven sera were from HIV-seropositive and hemodialysis patients. Unreactive sera and those with discrepant results were retested by a new version (HC02) extended to types 4, 5 and 6.

RESULTS

The distribution frequency of HCV genotypes was subtype 1a, 16.4%; subtype 1b, 46.3%; subtype 2a, 7.5%; subtype 3a, 20.9%; type 4, 4.5%; type 5, 0.7%; and co-infections, 3.7%. Among all the patients, 95% were of type 1, 2 or 3. The antibody reactivities of hemodialysis (1/7; P < 0.05) and HIV-seropositive patients (4/9; P = 0.06) were lower than for the patients seen at the hepatology unit (87/118). For these latter patients, the serotyping assay was interpretable in 71% and concordant in 64% of the samples with the genotyping assay. Out of the 84 samples with interpretable results, 75 sera were correctly serotyped (89% specificity). The two mixed results obtained by serotyping did not correspond to genotype co-infections (n = 3) and reciprocally. Six discrepancies were ruled out by the new assay, but the 2 untypeable sera remained unsolved, and four out of six sera with genotype 4 were serotyped as type 5.

CONCLUSIONS

Serotyping could be an attractive approach if the reactivity was improved and the subtyping possible.

Investigation of the pattern of diversity of hepatitis C virus in relation to times of transmission

The rate of sequence change of HCV in vivo was used to date the spread of HCV genotype 1b in European, USA and Japanese populations. Silent substitution rates of 0.0011 and 0.0017 substitutions per site per year were observed in the NS5 and E1 regions by sequence comparisons from a cohort of individuals infected from a common source of infection 17 years previously. Mean silent substitution frequencies of 0.169 and 0.224 in NS5 and E1, respectively, were observed amongst type 1b variants infecting epidemiologically unrelated individuals from several countries. This predicted a time of divergence from a common ancestor of 64-69 years. The absence of country-specific groupings by phylogenetic analysis of these sequences suggested that the spread of this genotype occurred on a worldwide basis at a similar time. Dates for the spread of other genotypes varied from around 80 years (type 2a) to 54 years (type 3a), suggesting that different variants spread into communities at different times this century. By extrapolating the silent substitution rate, the time of divergence of type 1a from 1b can be estimated at 200-300 years, but even this is likely to be an underestimate of the true time due to inequalities on the transition and transversion ratios, and the greater frequency of G <--> A transitions, compared with C <--> U, which are not considered in the current analysis. Thus, the diversity of the globally distributed genotypes such as type 1b and 3a suggests a relatively recent origin for HCV in Western countries and Japan, and contrast with the much greater diversity of specific genotypes in Central Africa (type 4) and South East Asia (type 6). These data may assist in understanding the global epidemiology of HCV and the mechanisms by which it has spread.

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.

Analysis of hepatitis C virus isolates by serotyping and genotyping

Hepatitis C virus (HCV)-positive sera from 106 chronically infected patients which had previously been genotyped were characterized by serotyping. Genotypes were determined by a first-generation line probe assay (INNO-LiPA HCV) and by sequence analyses of the core, core-E1, and NS5B regions. HCV serotypes were determined by measuring type-specific antibodies to NS4-derived peptide antigens (Murex HCV serotyping 1-6 assay). Of 106 serum samples, serotype-specific antibodies were detected in 88 (sensitivity, 83.0%), and 77 (specificity, 87.5%) of these serotypeable samples revealed a corresponding serotype (total concordance, 72.6%). Eleven samples revealed discrepant results as follows. (i) Five serum samples in which only a single genotype was detected contained an additional serotype. (ii) In one sample with two genotypes only one serotype was detected. (iii) In five isolates the serotype (all serotype 1) was completely different from the genotype. Double infections, as determined by genotyping, were confirmed by serotyping in two of four cases. Of 11 serum samples from chronically infected hemodialysis patients, 7 (64%) were reactive in the serotyping assay. In conclusion, genotyping allows discrimination between (sub)types but requires the relatively complex reverse transcriptase PCR. The novel serotyping assay offers an alternative method to distinguish the major types of HCV, although the sensitivity of the assay may be limited by the immunocompetence of the infected host.

Distribution of HCV genotypes among blood donors, patients with chronic liver disease, hepatocellular carcinoma, and patients on maintenance hemodialysis in Korea

Hepatitis C virus (HCV) is a single-stranded RNA virus related to the Flaviviridae family, and striking nucleotide sequence diversity has been reported among HCV isolates from different geographic areas. To study the distribution HCV genotypes among disease group in Korea, we subtyped HCV using the method of Okamoto et al. [(1992a): Journal of General Virology 73:673-679] and the reverse hybridization method (INNO-LiPA) on 138 patients who were HCV polymerase chain reaction (PCR)-positive: 30 blood donors, 30 with hepatocellular carcinoma (HCC), 33 with chronic hepatitis, 15 with liver cirrhosis, and 30 patients on maintenance hemodialysis in Korea. In 30 blood donors, HCV genotype 1b was most dominant (80%), followed by genotype 2a (13.3%), and 2b (6.7%). In 30 HCC cases, HCV genotype 1b was less frequent (60%), compared to blood donors, followed by genotype 2a (33.3%), and unclassified (6.7%). In 33 chronic hepatitis cases, HCV genotype 1b was also dominant (63.6%), followed by genotype 2a (30.3%), and 1a (6.1%). In 15 patients with liver cirrhosis, HCV genotype 1b was also dominant (60%), followed by genotype 2a (33.3%), and 1a (6.7%). In 30 patients on maintenance hemodialysis, HCV genotype 1b was dominant (86.7%), followed by genotype 2a (13.3%). In conclusion, among 138 HCV PCR-positive patients, type 1b was the prevailing type (71%), followed by type 2a (23.9%), type 1a (2.1%), type 2b (1.5%), and unclassified (1.5%) in Korea. The prevalence of type 1b in blood donors (80%) was higher than in patients with liver disease (61.5%) and the prevalence of type 1b was the lowest in patients with HCC (60%).

Comparative evaluation of two serologic typing methods for hepatitis C virus

Serologic methods of typing for hepatitis C virus offer advantages over PCR-based typing methods in terms of speed and simplicity of sample preparation and in the use of standard laboratory equipment. We examined the sensitivities and specificities of two hepatitis C virus serotyping assays which use sets of type-specific antigenic peptides derived from the core or the nonstructural 4 (NS4) regions and compared the results with those of molecular typing with type-specific primers from the core region. Although there was a good concordance between serotyping by either assay and genotyping, we found that the sensitivities of both serologic assays were less than optimal compared with that of molecular typing, with only about 50% of samples being unequivocally typed. Moreover, amino acid sequence similarities within the regions of the genome used for serotyping preclude differentiation into subtypes, which may have important clinical and therapeutic implications.

Characterization of the antibody reactivity to synthetic peptides from different parts of the hepatitis C virus genome

Infection by hepatitis C virus (HCV)*, the aetiologic agent responsible for the majority of non-A-non-B posttransfusion hepatitis, is detected by assaying for antibodies against structural and nonstructural recombinant proteins or synthetic peptides. The aim of this study was to characterize the antibody reactivity of selected sera against antigenic peptides spanning immunodominant regions of the core, NS4 and NS5 HCV proteins. Reactivity to synthetic peptides was determined by enzyme immunoassay (EIA) for 11 selected sera from blood donors (good responders), for 27 selected sera from hemodialysis patients (poor responders), all positive for HCV antibodies (tested by different second and third-generation assays), and for 7 negative sera. Some peptides from the core and the NS4 region were widely recognized by the tested sera. Sera not reactive with core, NS4, or NS5 region by some immunoblot assays exhibited reactivity against peptides from these proteins. Autoimmune reactivity associated with HCV infection was evaluated by using a synthetic peptide derived from the GOR peptide; 8/11 HCV-positive sera were found reactive against this peptide. No correlation was found between reactivity to any of the peptides tested and the presence of HCV RNA in the serum or with HCV genotype. The EIA reactivity of peptides from the core region suggested a multideterminant antigenic structure, where reactivity of each epitope may be differentially affected by neighboring amino acids depending on individual sera. This situation was particularly evidenced in selected sera from poor responder specimens where a more restricted antibody response to core peptides was observed. Reactivity of sera from HCV-infected patients with synthetic peptides from the core, NS4, and NS5 regions indicated the presence of multiple linear epitopes (particularly in the core region) that may be used in a mixture for immunodiagnosis; however, the length and exact position of the synthetic peptides must be chosen carefully.

Genomic characterization of hepatitis C virus isolates from Argentina

Thirty-three Argentinian patients infected with hepatitis C virus (HCV) were studied for viral genotyping. The patients included 10 hemophiliac and 4 polytransfused children and 19 adults: 3 polytransfused, 7 dialyzed and 9 sporadic cases. Core-based genotyping permitted the classification of 31 samples. Genotypes II, I and V were the most frequent: 21 (63.6%), 16 (48.4%) and 10 (30.3%) of the 33 patients, respectively. Only one polytransfused patient carried genotype IV. Genotype II was detected in 7 out of 9 sporadic cases. Thirteen patients (39.3%) were coinfected with two genotypes, and 2 others were coinfected with three genotypes. The remaining 2 samples which could not be typed were characterized following the restriction fragment length polymorphism (RFLP) method, and were classified as type 1. One of these had two consecutive transitional mutations in the 5' untranslated region (5' UTR).