Analysis of hepatitis C virus genotypes by a line probe assay and correlation with antibody profiles

Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e

We characterized the full-length genomes of nine hepatitis C virus genotype 3 (HCV-3) isolates: QC7, QC8, QC9, QC10, QC34, QC88, NE145, NE274 and 811. To the best of our knowledge, NE274 and NE145 were the first full-length genomes for confirming the provisionally assigned subtypes 3d and 3e, respectively, whereas 811 represented the first HCV-3 isolate that had its extreme 3' UTR terminus sequenced. Based on these full-length genomes, together with 42 references representing eight assigned subtypes and an unclassified variant of HCV-3, and 10 sequences of six other genotypes, a timescaled phylogenetic tree was reconstructed after an evolutionary analysis using a coalescent Bayesian procedure. The results indicated that subtypes 3a, 3d and 3e formed a subset with a common ancestor dated to ~202.89 [95% highest posterior density (HPD): 160.11, 264.6] years ago. The analysis of all of the HCV-3 sequences as a single lineage resulted in the dating of the divergence time to ~457.81 (95% HPD: 350.62, 587.53) years ago, whereas the common ancestor of all of the seven HCV genotypes dated to ~780.86 (95% HPD: 592.15, 1021.34) years ago. As subtype 3h and the unclassified variant were relatives, and represented the oldest HCV-3 lineages with origins in Africa and the Middle East, these findings may indicate the ancestral origin of HCV-3 in Africa. We speculate that the ancestral HCV-3 strains may have been brought to South Asia from Africa by land and/or across the sea to result in its indigenous circulation in that region. The spread was estimated to have occurred in the era after Vasco da Gama had completed his expeditions by sailing along the eastern coast of Africa to India. However, before this era, Arabians had practised slave trading from Africa to the Middle East and South Asia for centuries, which may have mediated the earliest spread of HCV-3.

Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant

We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.

Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark

The prevalence of hepatitis C virus (HCV) genotype 4 has increased throughout Europe. This is an epidemiological study of patients infected chronically with HCV genotype 4 in Denmark. The HCV strains analyzed originated from patient samples collected between 1999 and 2007 as part of the national Danish hepatitis B and C network, DANHEP. Sequence analyses were based on the envelope 1 region of HCV. Results from a total of 72 patients indicated a high degree of genetic heterogeneity. Fifty-six patients (78%) were infected with one of the three dominating subtypes: 4d, 4a, or 4r. The remaining 16 patients (22%) were infected with subtypes 4h, 4k, 4l, 4n, 4o, or 4Unclassified. Three epidemiological profiles were identified: (1) patients infected with HCV by intravenous drug use were infected solely with subtype 4d. They were all of European origin, and 15 of the 16 patients were ethnic Danes. No single transmission event could be confirmed, but the pairwise nucleotide identity within the patients of Danish origin was relatively high (∼95%), suggesting a recent introduction into Denmark. (2) The 21 patients infected with subtype 4a all came from Northern Africa, Egypt, Pakistan, or the Middle East. (3) Patients from Southern Africa dominated among patients infected with subtype 4r (10 of 12 patients). This study demonstrates that HCV genotype 4d has been introduced in and spread among Danish intravenous drug users. The remaining subtypes show restricted distribution, infecting almost exclusively patients from geographical areas with a relatively high prevalence of HCV genotype 4 infections.

Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t

In this study, we characterized the full-length genomic sequences of 13 distinct hepatitis C virus (HCV) genotype 4 isolates/subtypes: QC264/4b, QC381/4c, QC382/4d, QC193/4g, QC383/4k, QC274/4l, QC249/4m, QC97/4n, QC93/4o, QC139/4p, QC262/4q, QC384/4r and QC155/4t. These were amplified, using RT-PCR, from the sera of patients now residing in Canada, 11 of which were African immigrants. The resulting genomes varied between 9421 and 9475 nt in length and each contains a single ORF of 9018-9069 nt. The sequences showed nucleotide similarities of 77.3-84.3 % in comparison with subtypes 4a (GenBank accession no. Y11604) and 4f (EF589160) and 70.6-72.8 % in comparison with genotype 1 (M62321/1a, M58335/1b, D14853/1c, and 1?/AJ851228) reference sequences. These similarities were often higher than those currently defined by HCV classification criteria for subtype (75.0-80.0 %) and genotype (67.0-70.0 %) division, respectively. Further analyses of the complete and partial E1 and partial NS5B sequences confirmed these 13 'provisionally assigned subtypes'.

Replacement of hepatitis C virus genotype 1b by genotype 2 over a 10-year period in Venezuela

BACKGROUND

Changes in hepatitis C virus (HCV) genotype distribution with time have been reported in several countries.

GOALS

To explore eventual changes in HCV genotype distribution in Venezuela over a 10 years period.

STUDY

HCV genotype was determined by direct sequencing of the 5' noncoding region, in 236 isolates circulating in patients treated during years 2005 to 2006. Genotype distribution was compared with the one observed in 43 patients followed during years 1994 to 1996.

RESULTS

The prevalence HCV genotype 1 and 2 was 70% and 26%, respectively, in patients followed during years 1994 to 1996. The frequency of genotype 2 was significantly increased to 41% (P=0.04) in patients treated during years 2005 to 2006. A significant reduction in HCV genotype 1b prevalence (48% to 27%, P=0.01) was also observed after this 10 years period, whereas the prevalence of HCV genotype 1a did not change over time (22% vs. 27%, NS). Transfusion was more significantly associated with infection with HCV genotype 1b than with other genotypes (52% vs. 20%, P=0.002).

CONCLUSIONS

HCV subtype 1b seems to have been displaced by HCV genotype 2 in a relatively short period, without increase in the frequency of genotype 3. The low frequency of HCV genotype 3 in Venezuela might be due to the fact that intravenous drug use in Venezuela is less common than in other countries. The implementation of anti-HCV testing in blood banks since 1994 in Venezuela, might have contributed to the reduction in the frequency HCV genotype 1b infection.

Characterization of full-length hepatitis C virus genotype 4 sequences

Over 85% of the world's nearly 170 million hepatitis C virus (HCV)-infected subjects exist in regions of Africa, Southeast Asia and Middle Eastern countries where genotypes 4-6 are very common. In particular, HCV genotype 4 is highly prevalent in Egypt with more than 19% of the population infected and chronic HCV representing one of the top five leading causes of death, due in part to ineffective interferon alpha treatment against this genotype. Despite this, very little work has been carried out to characterize the sequence diversity of genotype 4, which will be critical to the development of effective vaccines and antiviral therapies against this genotype. As a result of the paucity of sequence data available for HCV genotype 4, for which only one full genome sequence is currently available, we were interested in characterizing additional genotype 4 sequences and to provide reagents for amplification of this genotype. Here we describe seven unique HCV genotype 4a full genomes, in addition to a single genotype 4d genome, and characterize their sequence diversity in relation to other more closely characterized HCV genotypes.

A real-time Taqman method for hepatitis C virus genotyping

BACKGROUND

There is the need for a rapid, inexpensive method for genotyping hepatitis C virus (HCV) to support clinical practice.

OBJECTIVES

To develop a real-time (Rotor-Gene 3000) Taqman assay for HCV genotyping in a single tube.

STUDY DESIGN

Seven type-specific probes, two for genotypes 1-3 and one for genotype 4 were designed around genotype-specific motifs in the 5' non-coding (NC) region to create two panels of probes. The first panel included two probes for genotype 1 detection and a single probe each for genotypes 2 and 3. The second panel had two probes for confirmation of genotypes 2 and 3 and a first line probe for genotype 4 detection. A comparative analysis of the Taqman assay against our in-house sequence-based method using 154 consecutive clinical samples, from HCV carriers in Cambridge, and four samples from the Quality Control for Molecular Diagnostics (QCMD) System was undertaken.

RESULTS

158 samples were analysed by conventional sequencing: 49% (n=78) were genotype 1, 11% (n=18) genotype 2, 30% (n=47) genotype 3 and 6% (n=10) genotype 4. For two samples, the sequence data was heterogeneous and difficult to analyse, suggesting mixed infection and for three samples, the viral load was insufficient for sequencing. Concordant results were obtained with the novel Taqman assay for 77/78 (99%) of genotype 1 isolates (positive with both genotype 1 probes), 17/18 (94%) of genotype 2 isolates, 43/47 (91%) of genotype 3 isolates and 10/10 (100%) genotype 4 isolates. One isolate, untypeable with sequencing was genotyped with the Taqman assay.

CONCLUSIONS

The Taqman assay was sensitive, specific and reliable over a wide range of viral loads and could identify mixed infections. These results highlight the potential of the Taqman assay as a fast, accurate and convenient method for routine HCV genotyping.

High frequency of gastric colonization with multiple Helicobacter pylori strains in Venezuelan subjects

Multiple Helicobacter pylori strains may colonize an individual host. Using enzyme-linked immunosorbent assay and line probe assay (LiPA) techniques, we analyzed the prevalence of mixed H. pylori colonization in 127 subjects from Venezuela, a country of high H. pylori prevalence, from three regions representing different population groups: the Andes (Merida), where Caucasian mestizos predominate, a major city near the coast (Caracas), where Amerindian-Caucasian-African mestizos predominate, and an Amazonian community (Puerto Ayacucho), where Amerindians predominate and mestizos reflect Amerindian and Caucasian ancestry. Among 121 H. pylori-positive persons, the prevalence of cagA-positive strains varied from 50% (Merida) to 86% (Puerto Ayacucho) by LiPA. Rates of mixed colonization also varied, as assessed by LiPA of the vacA s (mean, 49%) and m (mean, 26%) regions. In total, 55% of the individuals had genotypic evidence of mixed colonization. vacA s1c, a marker of Amerindian (East Asian) origin, was present in all three populations, especially from Puerto Ayacucho (86%). These results demonstrate the high prevalence of mixed colonization and indicate that the H. pylori East Asian vacA genotype has survived in all three populations tested.

Serological response to infection with different isolates of hepatitis C virus

Different isolates of hepatitis C virus (HCV) show nucleotide sequence variability throughout the genome. Detection of antibodies to recombinant proteins derived from hepatitis C virus genotype 1, the prototype HCV clone HCV-PT, constitutes the main method for screening HCV infection. The influence of the genomic variability on the serological diagnosis of HCV by enzyme immunoassay remains poorly defined. The aim of this study was to assess the serological reactivity of a panel of well characterized French HCV isolates typed by sequence analysis from patients with chronic hepatitis. The 73 sera samples were tested in three third generation EIA tests and three confirmatory assays. HCV isolates were determined by RT-PCR and sequencing in NS5B region of the genome. The 73 sera were positive in the three EIA tests. The three confirmatory tests showed a weaker reactivity with NS5 protein whatever the genotype, and a lower reactivity in NS4 antigens of non-type 1 sequences, particularly for genotype 3. Even though the reactivity of the antigens differed among the HCV isolates, the 73 isolates from genotype 1-6 were reactive with the three commercial screening assays. These results demonstrate that using a single test is adequate in the routine diagnosis of HCV infection in clinical laboratory, as recommended by the last French and European consensus conference.

Hepatitis C virus nonstructural protein NS4B transforms NIH3T3 cells in cooperation with the Ha-ras oncogene

Although the mechanism of carcinogenesis by hepatitis C virus (HCV) is not clearly known, core and NS3P protein have been shown to form tumors in specific cell lines. In this study, on the basis of the fact that the core and NS4B proteins of Kunjin virus translocate into the nucleus, we were prompted to investigate whether the HCV nonstructural protein NS4B has any function in tumor formation. First, we examined the location of the NS4B protein of HCV in transfected cells and then its oncogenic activity by transfection of NIH3T3 cells with the NS4B gene in the presence or absence of the Ha-ras gene. The NS4B protein was present only in the cytoplasm, particularly in the perinuclear region, different from the case of the Kunjun virus. The cells expressing HCV NS4B cooperatively with the Ha-ras gene showed loss of contact inhibition, morphological alterations, and anchorage-independent growth. These biological activities were confirmed by the transcription activation of the reporter gene from the AP1 promoter, by the NS4B protein in association with Ha-ras. Our results demonstrated that HCV NS4B protein in association with the Ha-ras gene played an important role in the malignant transformation of cells by HCV.

NS5A, a nonstructural protein of hepatitis C virus, binds growth factor receptor-bound protein 2 adaptor protein in a Src homology 3 domain/ligand-dependent manner and perturbs mitogenic signaling

Although hepatitis C virus (HCV) infection is an emerging global epidemic causing severe liver disorders, the molecular mechanisms of HCV pathogenesis remain elusive. The NS5A nonstructural protein of HCV contains several proline-rich sequences consistent with Src homology (SH) 3-binding sites found in cellular signaling molecules. Here, we demonstrate that NS5A specifically bound to growth factor receptor-bound protein 2 (Grb2) adaptor protein. Immunoblot analysis of anti-Grb2 immune complexes derived from HeLa S3 cells infected with a recombinant vaccinia virus (VV) expressing NS5A revealed an interaction between NS5A and Grb2 in vivo. An inactivating point mutation in the N-terminal SH3 domain, but not in the C-terminal SH3 domain, of Grb2 displayed significant diminished binding to NS5A. However, the same mutation in both SH3 regions completely abrogated Grb2 binding to NS5A, implying that the two SH3 domains bind in cooperative fashion to NS5A. Further, mutational analysis of NS5A assigned the SH3-binding region to a proline-rich motif that is highly conserved among HCV genotypes. Importantly, phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) was inhibited in HeLa S3 cells infected with NS5A-expressing recombinant VV but not recombinant VV control. Additionally, HeLa cells stably expressing NS5A were refractory to ERK1/2 phosphorylation induced by exogenous epidermal growth factor. Moreover, the coupling of NS5A to Grb2 in these cells was induced by epidermal growth factor stimulation. Therefore, NS5A may function to perturb Grb2-mediated signaling pathways by selectively targeting the adaptor. These findings highlight a viral interceptor of cellular signaling with potential implications for HCV pathogenesis.

Antibodies to hepatitis C virus envelope proteins correlate with hepatitis C viraemia after liver transplantation

BACKGROUND

Liver transplant recipients for hepatitis C virus (HCV)-related cirrhosis usually remain anti-HCV-seropositive after transplantation. The aim of this study was to characterize, longitudinally, the profile of HCV-specific antibodies and cryoglobulins in liver transplant recipients with recurrent HCV infection.

METHODS

Serial serum samples were collected prospectively before, at 1 month after, and at 12 months after transplantation for HCV cirrhosis in 30 patients infected with genotype 1. The antibodies against HCV envelope proteins (E1 and E2) were quantitated by enzyme-linked immunosorbent assay and antibodies against core, E2/hypervariable region I (HVRI), NS3, NS4, and NS5A antigens by a line immunoassay. Sera were also tested for cryoglobulins.

RESULTS

The titer of each anti-HCV antibody had fallen at 1 month after transplantation (P<0.05) with the exception of anti-E1 levels, which had risen in 16 patients with acute hepatitis C at that time (P=0.01). Anti-E1 and anti-E2 titers, but not antibodies against other HCV antigens, increased to pre-transplantation levels or higher at 12 months, which correlated with serum HCV RNA levels. Cryoglobulinemia was present in nine patients after transplantation (30%) and was associated with lower anti-E1 levels (P=0.04) and more severe graft damage.

CONCLUSIONS

The early increase in antibodies to HCV envelope proteins in correlation with viremia suggests that the envelope-specific humoral immune response may be directly stimulated by HCV replication. Anti-E1 levels may be a useful marker in monitoring patients with recurrent HCV infection.

Algorithmic approach to high-throughput molecular screening for alpha interferon-resistant genotypes in hepatitis C patients

This study was designed to analyze the feasibility and validity of using Cleavase Fragment Length Polymorphism (CFLP) analysis as an alternative to DNA sequencing for high-throughput screening of hepatitis C virus (HCV) genotypes in a high-volume molecular pathology laboratory setting. By using a 244-bp amplicon from the 5' untranslated region of the HCV genome, 61 clinical samples received for HCV reverse transcription-PCR (RT-PCR) were genotyped by this method. The genotype frequencies assigned by the CFLP method were 44.3% for type 1a, 26.2% for 1b, 13.1% for type 2b, and 5% type 3a. The results obtained by nucleotide sequence analysis provided 100% concordance with those obtained by CFLP analysis at the major genotype level, with resolvable differences as to subtype designations for five samples. CFLP analysis-derived HCV genotype frequencies also concurred with the national estimates (N. N. Zein et al., Ann. Intern. Med. 125:634-639, 1996). Reanalysis of 42 of these samples in parallel in a different research laboratory reproduced the CFLP fingerprints for 100% of the samples. Similarly, the major subtype designations for 19 samples subjected to different incubation temperature-time conditions were also 100% reproducible. Comparative cost analysis for genotyping of HCV by line probe assay, CFLP analysis, and automated DNA sequencing indicated that the average cost per amplicon was lowest for CFLP analysis, at $20 (direct costs). On the basis of these findings we propose that CFLP analysis is a robust, sensitive, specific, and an economical method for large-scale screening of HCV-infected patients for alpha interferon-resistant HCV genotypes. The paper describes an algorithm that uses as a reflex test the RT-PCR-based qualitative screening of samples for HCV detection and also addresses genotypes that are ambiguous.

Rapid genotyping of hepatitis C virus by direct cycle sequencing of PCR-amplified cDNAs and capillary electrophoresis analysis

There is an increasing demand for the genotyping of hepatitis C virus (HCV), since it has been shown that different HCV genotypes are associated with distinct profiles of pathogenicity and responses to antiviral treatment. Hence, there is a need for a simple and precise genotyping assay for routine diagnosis of HCV types and subtypes. Here we show that direct sequencing, considered as the reference method, can provide an accurate and rapid method for large-scale screening of HCV genotypes. PCR-amplified cDNAs of the HCV 5' non-coding region (5' NCR) were obtained from the widespread "Amplicor" HCV detection system. Semi-purified PCR products were directly cycle-sequenced in a single tube using multicolour dye terminator chemistry. Sample loading, electrophoresis and sequence analysis were automatically achieved by a capillary electrophoresis-based genetic analyser. Out of a total of 500 samples, HCV subtype 1b accounted for the majority of the infections (41%), followed by HCV 3 (31%) and HCV 1a (22%). This procedure failed to identify a genotype in only 3 samples. In addition, several cases of mixed HCV infection were also documented. The combination of direct cycle sequencing of PCR products with capillary electrophoresis provides a simple and rapid method convenient for routine HCV genotyping analysis.

Hepatitis C virus infections in dialysis centers in The Netherlands: a national survey by serological and molecular methods

A national survey of hepatitis C virus (HCV) infections among dialysis patients in The Netherlands was performed. The study involved 2,653 patients (2,108 hemodialysis patients and 545 chronic ambulatory peritoneal dialysis [CAPD] patients) from 39 of the 49 dialysis centers in the country. Patient sera were analyzed by both serological and molecular methods. Screening by a third-generation enzyme immunoassay (EIA) yielded 79 reactive sera. The presence of anti-HCV antibodies was confirmed in 70 patients by a line immunoassay. All seropositive samples were tested by reverse transcriptase PCR, and 57 samples were found to contain HCV RNA. Of the nine EIA-positive and line immunoassay-negative or indeterminate samples, four were HCV RNA positive. All seronegative samples were screened for the presence of HCV RNA in pools of five sera. Of 2,576 antibody-negative samples, 6 contained HCV RNA. All antibody-positive and RNA-positive samples were also tested by a second serological assay. The prevalence of HCV infections among Dutch dialysis patients as determined by serology or the presence of HCV RNA was 3% (80 of 2,653), i.e., 3.5% (73 of 2,108) in patients treated on hemodialysis and 1.3% (7 of 545) in patients on CAPD. Of these 80 HCV-infected dialysis patients, 67 (84%) were HCV RNA positive. Serological screening alone would have diagnosed only 70 infected patients. Therefore, antibody screening combined with detection of HCV RNA should be considered as the "gold standard" for diagnosing HCV infection in dialysis patients. The prevalence of HCV-infected patients in Dutch dialysis centers ranged from 0 to 8%, suggesting the existence of local risk factors for acquiring HCV infection. Genotyping analysis by reverse hybridization line probe assay revealed the presence of genotypes la (23%), 1b (46%), 2 (3%), 2a (13%), 2b (1%), 3a (7%), and 4a (4%). In four (6%) samples multiple genotypes were detected. The genotype distribution of HCV isolates among Dutch dialysis patients was similar to the distribution among nondialysis patients from the Benelux, except for subtype 1a, which was significantly more prevalent among dialysis patients. In only one center, a high prevalence of an uncommon genotype was suggestive of infection from a common source.

[Biology of hepatitis C viruses: clinical implications]

Infection by hepatitis C virus is characterized by a high rate of chronicity and low viremia. The virus has only been recently identified; it is a positively stranded RNA virus which shows homology in its genetic organisation with the pestiviruses and flaviviruses. There is not yet an efficient culture system available. Evidence indicates that the genetic variability of the HCV genome might have important clinical implications.

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.

Reduced antibody reactivity to hepatitis C virus antigens in hemodialysis patients coinfected with hepatitis B virus

Antibody reactivities to hepatitis C virus (HCV) antigens and to synthetic peptides derived from different parts of the HCV genome (core, NS4, and NS5) were evaluated in HCV-infected hemodialysis patients. In the RIBA 3 assay, NS5 was significantly less recognizable by sera of hemodialysis patients compared to other HCV-infected subjects. Among hemodialysis patients, those coinfected with hepatitis B virus (HBV) (positive for hepatitis B surface antigen [HBsAg+]) showed a reduction in reactivity to C33 and C100. Sera of only 23% of the hemodialysis patients (37 of 161) reacted with more than three of eight peptides tested, significantly fewer than the 60% (12 of 20) of the sera of other HCV-infected patients tested (P = 0.001). This immunosuppression was also manifested by a reduced frequency of recognition of additional peptides on follow-up. An even more reduced reactivity was observed among the HBV-coinfected patients (HBsAg+). The low-responder hemodialysis patients were not infected with any particular genotype of HCV, and the same HCV genotypes observed in the whole group of hemodialysis patients (1a, 1b, 2a, and 3a) were found circulating in the low-responder group. Even in this low-responder population, the good performance of two peptides (peptide 716, corresponding to a portion of the core, and peptide 59, corresponding to a portion of NS4) corroborates the immunodominance of the conserved epitopes within these peptides.

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.

Serum interleukin 4 and interleukin 10 levels in patients with chronic hepatitis C virus infection

BACKGROUND/AIMS

Immune-mediated mechanisms are believed to play an important pathogenetic role in chronic hepatitis C virus infection. Interleukin 4 (IL-4) and IL-10 are secreted by T helper-2 type cells (Th2) which may downregulate cell-mediated immune effector mechanisms important in the host defense against intracellular pathogens. This study aimed to determine Th2 cytokine levels in chronic hepatitis C virus infection.

METHODS

Serum IL-4 and IL-10 levels were measured in 74 patients with chronic hepatitis C virus infection and 20 healthy controls. The expression of CD30 in liver, a marker that is preferentially expressed in Th2 cells, was also determined by immunohistochemical staining in 37 patients.

RESULTS

Serum IL-4 and IL-10 were below the detection limit (5 pg/ml) in all 20 healthy controls. However, 36 patients (49%) had elevated serum IL-4 levels (range 5-106 pg/ml, p<0.001) and 23 patients (31%) had elevated serum IL-10 levels (range 5-37 pg/ml, p<0.05). There was no correlation between serum IL-4 and IL-10 levels. There was also no correlation between serum IL-4 and IL-10 levels and any of the clinical (age, gender, mode of acquisition), biochemical (serum alanine transaminase levels), virologic (viremia level, genotype), and histological parameters examined. Twenty of 37 liver biopsy specimens from patients with chronic hepatitis C virus infection showed occasional CD30+ lymphocytes, suggestive of Th2 phenotype. However, in 20 of the 37 patients with paired cryostat liver sections, IL-4 was not detected in any of these patients, suggesting that IL-4 was not produced in the liver in patients with chronic hepatitis C virus infection.

CONCLUSIONS

This study showed that serum Th2 cytokines are elevated (but at a low level) in a proportion of patients with chronic hepatitis C virus infection. However, the elevated Th2 cytokine levels may represent a systemic response and not a result of increased local production within the liver.

Hepatitis C virus genotypes in a cohort of Australian blood donors and haemophiliac and liver transplant patients

The aim of the present study was to characterize hepatitis C virus (HCV) genotypes using the INNO-LiPA HCV line probe assay and direct sequencing from three different HCV-RNA-positive (serum) groups: (i) blood donors (n = 59); (ii) haemophiliacs (n = 43); and (iii) patients undergoing liver transplantation (n = 26). Of 128 HCV-RNA-positive samples, 74 (58%) were genotype 1. Of these, 41 were genotype 1a, 32 were genotype 1b and one was genotype 1 indeterminate. Of the remaining 54 samples, seven (5%) were genotype 2a, two (2%) were genotype 2b, 26 (20%) were genotype 3a, three (2%) were genotype 4a, while 16 (12.5%) were of a mixed genotype. There was no significant difference between the three groups with regard to the prevalence of any specific genotype. However, in blood donors and haemophiliac patients there was a statistically significant difference in the occurrence of genotype 3a in patients with elevated alanine aminotransferase (ALT) levels (30.3%) compared with those patients with persistently normal ALT levels (5.6%; P = 0.004; chi 2). Genotype 3a was also uncommon in liver transplant patients (one of 14) with "sporadic' HCV infection. Genotype 4a was detected only in liver transplant patients. These patients had originated from Egypt (n = 1), Italy (n = 1) and Romania (n = 1).

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.

HCV viraemia is more important than genotype as a predictor of response to interferon in Sicily (southern Italy)

BACKGROUND/AIMS

To investigate host- and virus-related factors predictive of early and sustained alanine aminotransferase normalization after interferon therapy for HCV-related chronic liver disease, in an area where genotype 1 is highly prevalent.

METHODS

We studied 100 patients with HCV-RNA positive chronic liver disease (73 chronic hepatitis and 27 cirrhosis) undergoing alpha-interferon treatment. Thirty-four patients had an early response but relapsed, 15 patients remained into sustained response for at least 12 months after therapy, and 51 patients did not respond. Serum HCV-RNA levels were assessed by bDNA (Chiron), and genotype by LiPA (Innogenetics) and by sequencing of the 5' non-coding region.

RESULTS

Mean pre-treatment HCV-RNA level (x 10(3) genome equivalents/ml +/- SD) was lower in sustained responders (3854 +/- 7142) than in relapsers (9587 +/- 10163) or in non-responders (5709 +/- 6618). HCV subtype 1b was highly prevalent (82%), while types 1a, 2a, 3 and 4 were rare (about 5% each). However, the prevalence of 1b was much lower (31%) under 40 years of age. The prevalence of subtype 1b among sustained responders (74%) was similar to that observed among relapsers (82%) or non-responders (84%), but some nucleotide substitutions in the putative RNA loop of the 5' non-coding region were seen only among relapsers or non-responders. Multiple logistic regression model showed that early response to interferon was predicted by absence of cirrhosis and a pre-treatment HCV-RNA level below 350. Sustained response to interferon was predicted by pre-treatment HCV-RNA level below 350 and a low fibrosis score.

CONCLUSIONS

Among patients with hepatitis C from an area where subtype 1b is highly prevalent, absence of cirrhosis and low pre-treatment serum HCV-RNA level are the most important predictors of response to IFN. Some nucleotide substitutions found in the 5' non-coding region of subtype 1b are associated with non-response or relapse.

Hepatitis C virus genotypes in northern Italy: clinical and virological features

We analyzed the characteristics of subjects from the same area who were infected with hepatitis C virus genotypes 1 through 4 and subtypes 1a and 1b. Our data are consistent with a rapid evolution in the epidemiology of HCV genotypes and argue against different pathogenic potentials for genotypes 1b and 2.

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%).

Accurate quantification of hepatitis C virus (HCV) RNA from all HCV genotypes by using branched-DNA technology

In studies monitoring disease progression and therapeutic response, it is essential that the method used for hepatitis C virus (HCV) quantification not be influenced by genotypic variability. The branched DNA assay provides a reliable method for the quantification of HCV RNA. A modified set of oligonucleotide probes for the branched DNA assay was developed to enhance the efficiency of binding to genotypic variants of HCV. The improved branched DNA assay (HCV RNA 2.0) yielded highly reproducible quantification of hepatitis C virus RNA and displayed a nearly 600-fold dynamic range in quantification up to 120 Meq of HCV RNA per ml. The quantification limit was set at 0.2 Meg of HCV RNA per ml to ensure a specificity of > or = 95%. With this lowered quantification limit and the enhanced hybridization of the probes, the HCV RNA 2.0 assay exhibited a high level of sensitivity (96%) and was virtually unaffected by the genotypic variability of HCV. The HCV RNA 2.0 assay may be a useful tool for following HCV RNA levels throughout the course of disease, selecting patients for therapy, and evaluating therapeutic response.

Hepatitis C plasma viral load is associated with HCV genotype but not with HIV coinfection

The influence of human immunodeficiency virus (HIV) coinfection and hepatitis C virus (HCV) genotype distribution on HCV viral load and alanine amino transferase (ALT) levels in chronically infected patients remains unclear. In the present study, serum samples from a group of haemophiliac patients were investigated retrospectively. HCV geno- and subtyping was carried out using the Inno line probe assay (Inno LIPA, Innogenetics, Zwijnaarde, Belgium) in 87 patients positive by HCV RT PCR. Of these patients, 31 (35.6%) were HIV coinfected. HCV RNA was quantified with the HCV Monitor kit (Roche, Basel, Switzerland) in 43 patients (22 HIV-negatives, 21 HIV-positives). The most prevalent genotypes were 1 (n = 52) and 3a (n = 16) followed by genotype 2 (n = 9) and 4 (n = 3). Mixed infections were detected in 7 patients. Of genotype 1 positive samples, 24 and 23 were classified as subtype a and b, respectively. Five samples could not be subtyped. Although higher mean values of ALT were observed in genotype 1 infected patients, there was no statistically significant association between HCV genotype or subtype and liver enzymes (P > 0.05). On the other hand, statistically significant higher HCV RNA titres were observed in haemophiliacs infected with HCV genotype 1 in comparison to those infected with other genotypes (P < 0.01). No relationship was found between the presence of HIV coinfection and viral load of HCV RNA. There was no evidence that HCV infection had a more severe outcome in HIV-positive patients who had been infected with HIV and HCV more than ten years ago, even in those with very low CD4+ cell counts. No clear association between high ALT levels and large amounts of viral RNA was observed. In conclusion, a large viral load is associated with HCV genotype 1 infection; HIV coinfection has no clear effect on the intensity of HCV replication. An ongoing prospective study will evaluate the respective role of viral load, genotype, HIV coinfection and ALT level in the response to interferon therapy.

Long-term outcome of hepatitis C infection after liver transplantation

BACKGROUND

End-stage cirrhosis related to hepatitic C virus (HCV) is a common reason for liver transplantation, although viremia ia known to persist in most cases. We investigated the impact of persistent HCV infection after liver transplantation on patient and graft survival and the effects of the HCV genotype and the degree of HLA matching between donor and recipient on the severity of recurrent hepatitis.

METHODS

A group of 149 patients with HCV infection who received liver transplants between January 1982 and April 1994 were followed for a median of 36 months; 623 patients without HCV infection who underwent liver transplantation for end-stage chronic liver disease were used as a control group. A total of 528 liver-biopsy specimens from the HCV-infected recipients were reviewed, including 82 obtained one year after transplantation as scheduled and 39 obtained at five years as scheduled. In addition, biopsy specimens were obtained from 91 of the HCV-negative patients five years after transplantation.

RESULTS

Cumulative survival rates for the 149 patients with HCV infection were 79 percent after one year, 74 percent after three years, and 70 percent after five years, as compared with rates of 75 percent, 71 percent, and 69 percent, respectively, in the HCV-negative transplant recipients (P=0.12). Of the 130 patients with hepatitis C infection who survived more than 6 months after transplantation, 15 (12 percent) had no evidence of chronic hepatitis on their most recent liver biopsy (median followup, 20 months), 70 (54 percent) had mild chronic hepatitis (median, 35 months), 35 (27 percent) had moderate chronic hepatitis (median, 35 months), and 10 (8 percent) had cirrhosis (median, 51 months). Graft loss occurred after a median of 303 days in 27 of the 149 patients, including 5 with HCV-related cirrhosis and 3 with HCV-related cholestatic hepatitis. Infection with HCV genotype 1b was associated with more severe graft injury, whereas the primary immunosuppressive regimen used and the extent of HLA mismatching between donors and recipients had no significant effect on this variable.

CONCLUSIONS

After liver transplantation for HCV-related cirrhosis, persistent HCV infection can cause severe graft damage, and such damage is more frequent in patients infected with HCV genotype 1b than with other genotypes. After five years, the rates of graft and overall survival are similar between patients with and those without HCV infection.

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.

Evaluation of a reverse hybridization assay for genotyping of hepatitis C virus

BACKGROUND/AIMS

Several strains of the hepatitis C virus exist; distinct genotypes and subtypes can be identified by sequence comparison of the viral genomes. Recent evidence that the genotype/subtype of hepatitis C virus may influence the clinical course of chronic hepatitis C and the response to interferon-alpha therapy for this disease suggests that methods to identify the genotype may become clinically useful. In the present study we evaluated a recently introduced reverse hybridization assay.

METHODS

HCV-RNA was isolated from serum samples from 61 consecutive patients attending our out-patient clinic and subsequently sequenced in the 5'-noncoding and the nonstructural-5 region by the dideoxynucleotide chain termination method. HCV-genotyping was performed by phylogenetic analysis of nonstructural-5 sequences. The amplification product for the reverse hybridization assay was obtained by "nested" polymerase chain reaction using biotinylated primers corresponding to the 5'-noncoding region. The assay is based on hybridization of the resulting polymerase chain reaction product with oligonucleotide probes immobilized as parallel lines on membrane strips.

RESULTS

According to the phylogenetic analysis of the nonstructural-5 region the prevalence of hepatitis C virus subtypes was as follows: 1a 18%, 1b 51%, 2a 3%, 2b 3%, 2c 7% and 3a 18%. The reverse hybridization assay correctly identified each hepatitis C virus genotype (1, 2, and 3). However, differentiation of hepatitis C virus subtypes was insufficient. 1/11 HCV-1a isolates was incorrectly classified by the reverse hybridization assay as HCV-1b and vice versa 3/31 HCV-1b isolates as HCV-1a. Classification of hepatitis C virus subtypes 2a, 2b and 3a was correct, but 4/4 HCV-2c isolates were misinterpreted by the assay as HCV-2a.

CONCLUSIONS

The reverse hybridization assay can differentiate between hepatitis C virus genotypes 1, 2, and 3, but is not completely reliable for hepatitis C virus subtyping.

Hepatitis C virus replication in hepatocellular carcinoma

Hepatitis C virus (HCV) replication is reported in both tumour and non-tumour tissue in a case of hepatocellular carcinoma. Viral replication was established by showing the presence of minus strand HCV RNA by PCR amplification, after excluding residual reverse transcriptase activity of Taq polymerase. No minus strand was found in serum derived virion RNA. PCR amplified products from both tumour and non-tumour parenchyma were sequenced in the 5' non-coding region and shown to be identical. The genotype of this Indonesian patient was found to be 1b (or II), the most prevalent type in the Far East.

Rapid genotyping of hepatitis C virus RNA-isolates obtained from patients residing in western Europe

Two rapid genotyping methods for hepatitis C virus (HCV), the line probe assay (Inno-LiPA) and the subtype-specific core amplification system [Okamoto et al., (1992b) Journal of General Virology 73:673-679], were applied to 58 HCV isolates which were typed as type 1 (n = 37) and type 2 (n = 21) by sequence analysis of the 5' untranslated region (5'UTR). The line probe assay targets the 5'UTR and recognized 12 subtype 1a, 25 subtype 1b, 18 subtype 2a, 2 subtype 2b and 1 subtype 2d in accordance with sequence analysis of this region. Subtype-specific core amplification revealed 7 discrepancies among the 37 type 1 isolates when compared to LiPA. A different subtype was observed in 3 isolates (1a versus 1b), 2 isolates remained untyped and 2 isolates showed a coinfection of subtype 1a and 1b. The first 5 discrepancies were confirmed by sequence analysis of the core region whereas the coinfection could not be confirmed. Of the 21 type 2 isolates only one could be typed by subtype-specific core amplification. HCV RNA was detected in all 21 cases after the general first round of polymerase chain reaction (PCR). Direct sequencing of the core region indicated sequence variation as a source of failure. It is concluded that LiPA results are conclusive for typing of HCV. However, LiPA is hampered occasionally for subtyping by lack of subtype-specific sequence variation in 5'UTR. Subtyping results by subtype-specific core amplification were accurate. However, it seems that this assay is not suitable for the identification of genotype 2 isolates that circulate in patients living in Western Europe.

Influence of hepatitis C virus (HCV) genotypes on HCV recombinant immunoblot assay patterns

Ninety-six patients with chronic hepatitis C were studied. A second-generation recombinant immunoblot assay detected anti-NS4 antibodies significantly more often in patients infected by hepatitis C virus genotype 1 than in patients infected by other types. By a third-generation recombinant immunoblot assay, the prevalences of the four antibodies measured did not differ according to the hepatitis C virus genotype.

Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes

Genotyping of hepatitis C virus-positive sera by means of a line probe assay indicated that < 3% of European samples, but up to 30% of Gabonese sera, could not be classified as either 1a, 1b, 2a, 2b, 3a, 3b, 4c, 5a, or 6a. Such samples were analyzed in the 5' untranslated region and in the nonstructural 5 (NS5) region. Classification based on phylogenetic analysis of the commonly used 222-bp-long NS5B region was possible for most but not all of the selected sera. Therefore, the core/envelope 1 region (579 bp) and a larger NS5B (340 bp) region were also analyzed. Only the phylogenetic analysis of the 340-bp NS5B region of these newly identified and published isolates provided unambiguous classification into types and subtypes. Furthermore, unequivocal evidence for four subtypes in type 2 and eight subtypes in type 4 was provided. A specific recognition sequence in the 5' untranslated region was observed for every newly identified subtype. Based on 1830 pair-wise comparisons in NS5B, isolates belonging to the same subtype showed evolutionary distances of < 0.127 and isolates of the same type exhibited evolutionary distances of < 0.328. These phylogenetic border distances can be conveniently used for classification of hepatitis C virus isolates into types and subtypes.