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

Hepatitis C virus infection and genotypes in Antananarivo, Madagascar

The prevalence of hepatitis C virus (HCV) genotypes in Madagascar is not well known. Serum samples were obtained from 2,169 individuals selected by random sampling in the population living in Antananarivo city. Using HCV antibody test (Monolisa anti-HCV Plus version 2), 36 (1.7%) of the 2,169 samples were positive. The presence of HCV RNA was determined by using reverse transcription polymerase chain reaction amplifying the 5'-untranslated region (UTR): HCV RNA was detected in 17 of the 36 HCV antibodies positive samples. The genotype was determined using BLAST tool with another 5'-UTR fragment. The phylogenetic analysis of the polymerase (NS5b) and envelope (E1/E2) fragment sequences showed a low level of diversity compared to the high diversity in other African countries: subtype 1b (nine cases, 52.9%) and genotype 2 (eight cases, 47.1%) including subtype 2b (six cases), subtype 2k (one case), and one unclassified subtype. BLAST search with the 5'-UTR fragment sequence of this unclassified subtype identified that strain as subtype 2a.

Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5' untranslated regions

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5' untranslated region (5'UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5'UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5'UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5'UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5'UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5'UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information.

Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection

In one of our recent studies, two HCV genotype 6 variants were identified in patients from Hong Kong and Guangxi in southern China, with injection drug use and HIV-1 co-infection. We report the complete genomic sequences for these two variants: GX004 and HK6554. Their entire genome lengths were 9,468 and 9,462 nt; the 5' UTRs were 338 nt followed by single ORFs of 9,069 nt; the 3' UTRs were 61 and 55 nt including 29 and 23 nt poly(U) tracks. Phylogenetic analysis using a maximum likelihood method showed that HK6554 was classified into subtype 6g and GX004 represented the first complete genome sequence for subtype 6e. Further analysis with reference sequences in three different genomic regions revealed that GX004 closely clustered with a group of subtype 6e variants, which were previously exclusively found in Vietnam and recently increasingly identified in injection drug users from the Guangxi province in southern China that borders Vietnam. This suggests that subtype 6e could become epidemic in southern China by network transmission among injection drug users.

Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently classified into six genotypes and an increasing number of subtypes. Most likely, this heterogeneity is caused by genetic drift; evidence for recombination is scarce. To study the molecular heterogeneity of HCV in Vietnam, we analyzed 58 HCV RNA-positive sera from Vietnamese blood donors by sequence analysis of the CORE and NS5B regions. Phylogenetic analyses revealed the presence of genotype 1 (38%), genotype 2 (10.3%), and genotype 6 viruses (51.7%). All samples showed concordant results except for two (D3 and D54). Sample D54 was a mixed infection of genotype 2i and 6h viruses. Whole-genome analysis and bootscan analysis of sample D3, on the other hand, revealed a recombinant virus with genotype 2i and genotype 6p sequences at the 5' and 3' ends, respectively. The crossover point was located between nucleotide positions 3405 to 3464 (numbering according to prototype strain HCV-H, M67463) at the NS2/NS3 junction. The identification of this naturally occurring recombinant virus strengthens the concept that recombination may play a role in HCV epidemiology and evolution. Furthermore, the location of the recombination breakpoint may be relevant for constructing infectious chimeric viruses.

Hepatitis C virus genotype distribution among intravenous drug user and the general population in Hong Kong

This study describes the distribution of hepatitis C genotypes among 106 intravenous drug users and 949 non-drug users in Hong Kong. Genotypes were identified by multiplex RT-PCR targeting the core region of viral genome. The accuracy of this typing system in identifying genotypes 1b and 6a was assessed by phylogenetic analysis. The distribution of hepatitis C virus (HCV) genotypes amongst non-drug users was 63.6% for genotype 1b, 23.6% for 6a, 4.5% for 1a, 3.9% for 3a, and 3.1% for 2a; whereas amongst the intravenous drug users, it was 58.5% for genotype 6a, 33.0% for 1b, 5.7% for 3a, 0.9% for 1a, and 0.9% for 2a. The proportion of genotype 6a was significantly higher (P < 0.001), whereas that for genotype 1b was significantly lower (P = 0.001) for the intravenous drug user group. Multivariate analysis revealed significant independent associations for the distribution of HCV genotypes 1b and 6a with age, sex, and intravenous drug user status. The co-circulation of a common (1b) and a rare (6a) HCV genotype in Hong Kong provides a unique opportunity for future studies to compare their transmission efficiency, clinical course, and response to treatment.

Chronic hepatitis C virus infection: genotyping and its clinical role

Chronic hepatitis C virus (HCV) infection is a worldwide public health problem with a global prevalence of 2%. A high proportion of those infected are at risk of developing cirrhosis and hepatocellular carcinoma and modeling data predicts that the burden of disease could soon increase substantially. The liver disease associated with chronic infection has led investigators to look for correlates between viral properties and disease progression, severity of disease and the response to antiviral therapy. HCV has been classified into six genotypes but genotype does not appear to influence disease presentation or severity of disease. However, genotype has been identified as a major predictor of response to interferon-based antiviral therapy. Antiviral regimens have been optimized for infections with HCV genotypes 1-4, although treatment strategies for genotypes 5 and 6 have yet to be developed. The molecular basis for the differences in response of HCV genotypes has yet to be determined.

Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6

Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5' untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3' UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.

Distribution of hepatitis C virus genotypes in the Middle East

It is well established that hepatitis C develops into cirrhosis of the liver and hepatocellular carcinoma (HCC) both of which are fatal diseases. The World Health Organization estimates that there are at least 21.3 million hepatitis C virus (HCV) carriers in the Eastern Mediterranean countries, which is close to the number of carriers estimated in the Americas and Europe combined. With such a high disease burden of HCV infection in this part of the world, and in light of the new evidence that genotypes may influence the outcome of antiviral therapy, the focus of this review is on the epidemiology and distribution of HCV genotypes in the Eastern Mediterranean countries. Accumulated data show that there are two main patterns for the distribution of HCV genotypes in the Middle East: in the first pattern, genotype 4 is prevalent in most of the Arab countries, and in the second pattern, genotype 1a or 1b predominates in the non-Arab countries. Results from the limited number of clinical trials on the treatment of chronic HCV genotype 4 using peginterferon alfa-2b in combination with ribavirin are encouraging. However, efforts to develop more effective antiviral therapies and the establishment of an effective HCV vaccine remain the largest challenges for the near future.

Drug interactions between psychoactive substances and antiretroviral therapy in individuals infected with human immunodeficiency and hepatitis viruses

The liver disease characteristic of alcohol dependence encompasses three main related entities: steatosis, alcoholic hepatitis, and cirrhosis. Alcoholic cirrhosis is a leading cause of global morbidity and mortality. Alcohol intake among injecting drug users is a major contributor to transmission of viral infections, such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C viruses (HCV). HIV and HCV coinfected patients develop liver diseases earlier and more severely than the monoinfected individuals, including hepatocellular carcinoma. Interactions exist between the therapeutic drugs used to minimize and control the drug and alcohol dependence. Furthermore, drug-drug interactions occur between the highly active antiretroviral therapy (HAART) and alcohol, different HAART components and methadone, or each one of the therapies with the other, thus contributing to a higher toxicity level. With the evolution of effective antiretroviral therapy, survival of persons with HIV, and the syndrome it causes, acquired immunodeficiency syndrome (AIDS) has increased dramatically. Drug-drug interactions may appear between alcohol and anti-HBV or anti-HCV, therapy in the presence or absence of anti-HIV therapy. Several other medical-, social-, and drug-related factors of this population have to be considered when providing HAART. Because many coinfected patients also have problems with substance use, dealing with their drug dependence is an important first step in an attempt to improve adherence to and tolerance of antiviral therapy. It is necessary to minimize the risk of liver disease acceleration and/or reinfection with hepatitis viruses. Knowledge of potential drug interactions between methadone, antiretroviral therapy, psychoactive drugs, and antipsychotics and the role of coinfection with HBV or HCV and the drugs used in eradicating viral hepatitis permits suitable antiretroviral combinations.

Response to combined interferon and ribavirin is better in patients infected with hepatitis C virus genotype 6 than genotype 1 in Hong Kong

Data on the treatment efficacy of interferon (IFN)-alpha and ribavirin in patients with chronic hepatitis infected with hepatitis C virus (HCV) of genotype 6 are lacking. A study has been reported from Hong Kong which compared the treatment efficacy of IFN-alpha and ribavirin in the treatment of chronic HCV infection with genotypes 1 and 6. Twenty-four patients with HCV genotype 1 and 16 patients with HCV genotype 6 were studied. The baseline demographic data including median age, gender ratio, alanine aminotransferase levels, bilirubin levels, HCV RNA levels and histological scores were comparable between the two groups of patients. All patients received IFN-alpha 5 million units three times per week and ribavirin (1,000 mg for those weighing </=75 kg and 1,200 mg for those weighing >75 kg) for 1 year. Patients infected with HCV genotype 6 achieved virological response significantly higher than those with HCV genotype 1 (67 vs. 33% at week 24, p = 0.02; 75 vs. 42% at the end of treatment, p = 0.05; 63 vs. 29% at 6 months after completion of treatment, p = 0.04). Histological improvement in inflammatory activity and fibrosis in the liver were observed in 25% and 25% of patients infected with HCV genotype 6 in contrast to only 13 and 8% in patients infected with HCV genotype 1; however, the differences were not statistically significant. In conclusion, patients with HCV genotype 6 gain a better response to combined treatment with IFN-alpha and ribavirin than those with HCV genotype 1 and achieve a significantly higher rate of sustained virological response.

Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes

International standardization and coordination of the nomenclature of variants of hepatitis C virus (HCV) is increasingly needed as more is discovered about the scale of HCV-related liver disease and important biological and antigenic differences that exist between variants. A group of scientists expert in the field of HCV genetic variability, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re-examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised criteria for the assignment of new genotypes as they are discovered in the future. A comprehensive listing of all currently classified variants of HCV incorporates a number of agreed genotype and subtype name re-assignments to create consistency in nomenclature. The paper also contains consensus proposals for the classification of new variants into genotypes and subtypes, which recognizes and incorporates new knowledge of HCV genetic diversity and epidemiology. A proposal was made that HCV variants be classified into 6 genotypes (representing the 6 genetic groups defined by phylogenetic analysis). Subtype name assignment will be either confirmed or provisional, depending on the availability of complete or partial nucleotide sequence data, or remain unassigned where fewer than 3 examples of a new subtype have been described. In conclusion, these proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future.

Changes in epidemiological patterns of HCV infection and their impact on liver disease over the last 20 years in Greece

The aim of this study was to investigate the relative frequency of hepatitis C virus (HCV) genotypes in Greek patients with chronic infection as well as possible secular changes in their distribution in relation to modes of transmission, age and time at acquisition of the infection and other variables. We evaluated 434 unselected patients, 241 males and 193 females with a median age of 46.2 years (18-75), with chronic HCV infection presenting during the period 1996-2000. HCV infection was confirmed by the detection of HCV-RNA by polymerase chain reaction (PCR), while HCV genotyping was performed by the Inno-LiPA assay. Liver biopsies were evaluated according to Ishak's scoring system. Of 434 patients, 167 had a history of blood transfusion [post-transfusion hepatitis (PTH)], 80 were i.v. drug users and in 187 the route of infection remained unknown. The overall distribution of HCV genotypes 1, 2, 3 and 4 was 47, 8.3, 27 and 15.2%, respectively. Genotype 3 was common in younger adults and i.v. drug users, whereas genotype 1 predominated in older people and PTH patients (P < 0.001 for both). Infection acquired before 1981 (group A) was related to transfusion and genotype 1, while after 1981 (group B) with i.v. drug use and genotype 3 (P < 0.01). Biopsy was available in 369 (85%) patients, of whom 22.5% had cirrhosis; 29.8% in group A and 9.9% in group B. In a multivariate analysis, cirrhosis was strongly associated with the duration of infection (P = 0.013). Our study revealed a change of HCV genotype distribution in the last 20 years among Greek patients with chronic HCV infection as a result of epidemiological changes in HCV transmission. The presence of cirrhosis was associated only with the duration of infection. These observations have impact both on prevention and treatment.

Chronic hepatitis C: genotypes 4 to 9

Infection with hepatitis C virus (HCV) genotypes 1, 2, or 3 is widely distributed throughout the world and has been the focus of the majority of studies on the epidemiology and treatment of chronic hepatitis C. Infection with HCV genotypes 4 through 9 is prevalent in some geographic areas where the disease burden of chronic hepatitis C approaches endemic levels (eg, HCV genotype 4 in Egypt where there is an HCV infection prevalence of approximately 18%). This article reviews the existing literature, which suggests that chronic hepatitis C with genotypes 4 through 9 may exhibit epidemiologic, clinical, and treatment outcome differences from infection with genotypes 1, 2, or 3.

Hepatitis C virus genotype distribution in China: predominance of closely related subtype 1b isolates and existence of new genotype 6 variants

To determine hepatitis C virus (HCV) genotype distribution in China, a total of 148 HCV RNA positive serum samples were collected from nine geographic areas and subjected to RT-PCR followed by direct DNA sequencing and phylogenetic analysis of the core, E1, and NS5B regions. HCV was genotyped in 139 (93.9%) samples. Among them subtype 1b was the most predominant [66% (92/139)] followed by 2a [14% (19/139)]. Of 92 subtype 1b isolates, 35 (38%) and 30 (33%) formed two clusters, designated groups A and B. Group A was prevalent throughout China, while group B was predominant in the central and southern regions. In three cities in the Pearl River Delta, subtype 6a replaced 2a as the second most predominant subtype, and in Kunming (southwest) multiple HCV genotypes/subtypes were present. New variants of HCV genotype 6 were discovered in three samples from Kunming and one in Guangzhou in the Pearl River Delta.

New combination test for hepatitis C virus genotype and viral load determination using Amplicor GT HCV MONITOR test v2.0

AIM

To develop a new sensitive and inexpensive hepatitis C virus (HCV) combination test (HCV Guideline test) that enables the determination of HCV genotypes 1, 2 and 3, and simultaneous determination of HCV viral load using commercial Amplicor GT HCV MONITOR test v2.0 (microwell version).

METHODS

The HCV Guideline test used the PCR product generated in commercial Amplicor GT HCV Monitor test v2.0 for viral load measurement using microwell plate version of Amplicor HCV Monitor and also captured on separate plates containing capture probes and competitive oligonucleotide probes specific for HCV genotypes 1, 2 and 3, The HCV genotype was subsequently determined using the biotin-labeled PCR product and five biotin-labeled HCV-specific probes.

RESULTS

The sensitivity of the HCV Guideline test was 0.5 KIU/mL. Specificity of the HCV Guideline test was confirmed by direct sequencing of HCV core region and molecular evolutionary analyses based on a panel of 31 samples. The comparison of the HCV Guideline test and an in-house HCV core genotyping assay using 252 samples from chronic hepatitis C patients indicated concordant results for 97.2% of samples (59.5% genotype 1, 33.7% genotype 2, 6.0% genotype 3, and 0.8% mixed genotypes). Similarly, the HCV Guideline test showed concordance with a serological test, and the serological test failed to assign any serotype in 12.7% of the samples, indicating a better sensitivity of the HCV Guideline test.

CONCLUSION

Clinically, both viral load and genotypes (1, 2 and 3) have been found to be major predictors of antiviral therapy outcome regarding chronic hepatitis C based on guidelines and they are, in normal circumstances, performed as separate stand-alone assays. The HCV Guideline test is a useful method for screening large cohorts in a routine clinical setting for determining the treatment regimen and for predicting the outcome of antiviral therapy of chronic hepatitis C.

Molecular epidemiology of hepatitis B and C virus infections in Asia

The present paper provides a review of the current literature regarding the molecular-based epidemiology of hepatitis B virus (HBV) and hepatitis C virus (HCV), which are very important viruses underlying the etiology of blood-borne infectious diseases worldwide. Particularly, both HBV and HCV are widespread on the Asian continent and are associated with acute and chronic liver diseases, including hepatocellular carcinoma. HBV has been classified into genotypes A through G and shown to have a distinct geographic distribution. In Asia, genotypes B and C of HBV prevail, and genotype C has been shown to cause more serious liver disease than genotype B. High prevalence of HBV mutants with various forms, such as the pre-S mutant, basal core promoter mutant, YMDD motif mutant and vaccine escape mutant, were seen in Asia and these were found to be related to the severity of liver disease and sensitivity to therapy. HCV has also been classified into multiple genotypes and associated with geographic distribution. HCV genotype 1 is less sensitive to interferon therapy and may be associated with the presence of more serious liver disease than the other genotypes. Data on the relation among the HBV/HCV genotypes, their pathogenicity in chronic liver diseases including hepatocellular carcinoma and their effect on therapy are awaited with great interest, especially in Asia, which is an endemic region of blood-borne hepatitis viruses.

Comparative study of different methods to genotype hepatitis C virus type 6 variants

Hepatitis C virus (HCV) genotype 6a is found frequently in Southeast Asia. In Thailand, however, genotype 6 variants may exist which posses a genotype 1 like sequence in the 5' non-coding region. In order to genotype correctly these viruses, four different methods; INNO-LiPA assay, two RFLP assays on the core region (using different restriction enzymes) and phylogenetic analysis of the core sequences were compared. Samples from 17 chronic HCV patients from the Netherlands and Thailand and 18 anti-HCV positive blood donors recruited from Thailand were tested. The INNO-LiPA could not distinguish genotype 6 variants. The RFLP methods used could not, or only in combination with 5'NCR genotyping methods, identify type 6 variants. In conclusion, for identification of type 6 variants at least two different regions of the HCV genome have to be analyzed (both 5'NCR and core).

Hepatitis C virus genetic variability: pathogenic and clinical implications

HCV is variable because of the properties of the viral RdRp, high levels of replication, and large population sizes. The Darwinian evolution of HCV has been characterized by the emergence of the HCV genotypes, including six main types and a large number of subtypes. The study of HCV genotype epidemiology provides useful information on the worldwide HCV epidemics. The HCV genotype is an important predictor of the response to IFN-alpha-based antiviral therapy, and genotype determination is currently used to tailor treatment indications. In addition, HCV circulates and behaves in infected individuals as mixtures of closely related but distinct viral populations referred to as quasispecies. This particular nature of the virus influences its transmission, the pathogenesis of liver disease and extra-hepatic manifestations, and the outcome during and after antiviral therapy or after transplantation for HCV-related end-stage liver disease. Further studies are needed to understand better the implications of HCV quasispecies diversity in the pathophysiology of HCV infection.

Southeast Asian patients with chronic hepatitis C: the impact of novel genotypes and race on treatment outcome

Hepatitis C virus (HCV) genotype and other host and viral factors influence treatment outcome in chronic HCV infection. We evaluated the effect of race and genotype on interferon and ribavirin treatment outcome in 70 Southeast Asian (SEA) and 50 white patients. Genotype was based on the 5' untranslated region (5'UTR) with a commonly used line probe assay (INNO-LiPA HCV II) that may mistype genotype 7, 8, or 9 as 1b. HCV core region sequencing resulted in reclassification of 8 genotype 1 and 25 genotype 1b SEA subjects as genotype 7, 8, or 9. Twenty-six SEA genotype 7, 8, and 9 (79%) and 10 SEA true genotype 1b (59%) patients achieved a sustained virologic response (SVR) compared with 15 (34%) white genotype 1b patients. Logistic regression analysis showed that SEA patients with genotype 7, 8, or 9 were more likely to achieve a SVR than white genotype 1b patients (OR 16.56; 95%CI 4.16, 65.91) as were SEA true genotype 1b patients compared with white genotype 1b patients (OR 4.63; 95%CI 1.19, 18.04). In conclusion, a proportion of SEA patients classified by INNO-LiPA as genotype 1b were in reality genotype 7, 8, or 9. In comparison with white genotype 1b patients, both SEA genotype 1b and SEA genotype 7, 8, and 9 patients showed a significantly greater SVR. HCV core sequencing was necessary to determine genotype accurately in persons potentially exposed to HCV genotypes 7, 8, or 9. This study also supports the concept that race and ethnicity are important determinants of treatment outcome in HCV infected patients.

Infection with hepatitis C virus among intravenous-drug users: prevalence, genotypes and risk-factor-associated behaviour patterns in Thailand

Hepatitis C virus (HCV) infection, a major problem worldwide, is usually transmitted parenterally or by use of contaminated needles among intravenous-drug users (IVDU). In a cross-sectional study, demographic data were collected and behaviour patterns investigated in interviews with 453, consenting IVDU. Blood samples were collected from each interviewee and checked for anti-HCV antibodies and, in a PCR-based assay, for the RNA of HCV. Almost all (92.5%) of the IVDU investigated were found positive for anti-HCV and/or the viral RNA. Most (73.5%) of those positive for HCV RNA were found to be infected with genotype 3a alone, the rest being infected with 1b (17.9%), 6a (3.5%), 3b (1.4%), 1a (1.0%), or both 3a and 6a (2.1%) or having non-typable infections (0.6%). Curiously, 26.0% of those who appeared seronegative for anti-HCV were positive for HCV RNA. The longer an interviewee had been using intravenous drugs, the more likely he or she was to be infected with HCV. Among the IVDU, the sharing of needles, syringes and/or other drug-related paraphernalia appeared to be the behaviour carrying the highest risk of HCV infection, giving an adjusted odds ratio and (95% confidence interval) of 4.84 (1.88-12.43). Programmes of needle and syringe exchange should probably be implemented among IVDU in Thailand and elsewhere, to slow the transmission of HCV.

Molecular testing in the diagnosis and management of hepatitis C virus infection

OBJECTIVES

To review hepatitis C virus (HCV), describe the types of molecular-based tests available for the diagnosis and management of HCV infection, and discuss the appropriate utilization of these tests.

DATA SOURCES

Current information is presented from the published literature, as well as new information where available.

STUDY SELECTION

A major cause of posttransfusion and community-acquired non-A, non-B hepatitis worldwide is HCV. Approximately 4 million people in the United States are infected with HCV, resulting in 8000 to 10,000 deaths annually. Because HCV is not readily cultured, in vitro molecular-based tests have been developed for use in the diagnosis and treatment of HCV-infected patients. Molecular tests include qualitative and quantitative nucleic acid amplification tests, branched DNA tests, and HCV genotyping assays. Qualitative HCV nucleic acid amplification tests are used routinely in association with serologic tests to help make a diagnosis of infection with HCV. Quantitative HCV testing and genotyping methods have been found to be valuable tools in the treatment of infected patients. A patient's pretreatment HCV viral load and the rate of virus decline during therapy have been shown to correlate with the likelihood of long-term response to antiviral therapy. Information pertaining to the genotype of HCV infecting patients has been shown to be helpful in making recommendations regarding treatment. Certain genotypes of HCV are much more responsive to therapy, allowing a shorter course of treatment.

CONCLUSIONS

Molecular tests are valuable tools for use in the diagnosis and treatment of patients infected with HCV.

HCV infection in northeastern Brazil: unexpected high prevalence of genotype 3a and absence of African genotypes

The genomic diversity of HCV embraces 6 genotypes and at least 52 subtypes with clinical and epidemiological correlations. There is a paucity of studies assessing HCV genotypes and biomolecular epidemiology in Brazil. We studied genotype distribution and epidemiological aspects in 232 HCV carriers, 133 (57.9%) males and 99 (42.1%) females, followed in the liver disease referral unit in Salvador, BA, northeastern Brazil. All of them were anti-HCV positive by 3rd generation ELISA assay, and HCV-RNA positive by RT-PCR. Genotyping was performed by INNOLIPA. Assessment of risk factors for HCV infection showed that 93 (40%) had past blood transfusion, 14 (6%) intravenous drug use, 19 (8%) inhalation of cocaine, 28 (12%) tattooing, 15 (7%) were health care workers, 5 (2%) had reused disposable syringes, 5 (2%) had multiple risk factors and in 53 (23%) no risk factor was determined. Genotype 1a was observed in 75 (32%), 1b in 72 (31%), 3a in 61 (26%), 2ab in 14 (6%); 5 (2.5%) had mixed genotypes and 5 (2.5%) were undetermined. Patients with genotype 1 had a higher mean age (P < 0.05) and no particular risk factors were associated with a specific genotype. Genotype 1 largely predominates in northeast Brazil followed by genotype 3 which, in this population, does not seem to be related to intravenous drug abuse, in contrast to some European studies. Although 80% of the Salvador population comprises African-Brazilians, no African genotype was identified, which may mean that HCV was introduced into this region via European immigration. This study demonstrated some peculiarities of HCV epidemiology in Brazil and strongly suggests that HCV introduction to this region was probably related to European immigration.

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.

Molecular epidemiology of hepatitis C infection in U.S. veteran liver transplant recipients: evidence for decreasing relative prevalence of genotype 1B

OBJECTIVE

The U.S. Veteran population represents a unique patient group to study different HCV genotypes because of geographically diverse exposures. The aim of this study was to characterize the distribution of HCV genotypes in U.S. veterans undergoing liver transplantation (OLT), trace genotypes to modes of acquisition (risk behavior and location), and evaluate the relative prevalence of HCV genotypes according to the time of acquisition.

METHODS

Between 10/88 and 12/95, 110 primary OLTs were performed in U.S. Veterans at our center. Forty-nine (45%) patients had detectable HCV-RNA by PCR at the time of OLT. Determination of HCV genotypes was performed by restriction fragment length polymorphism of the 5' noncoding region and classified according to Simmonds et al.

RESULTS

Twenty-three of 49 (47%) veterans had 1a, 17 (35%) 1b, two (4%) 2a, three (6%) 2b, two (4%) 3a, two (4%) mixed (1a/2a, 1b/2a). This distribution of HCV genotypes was comparable to the genotypic distribution of a contemporary cohort of nonveteran OLT recipients at the University of Washington. There was a statistically significant association between illicit injection drug use (IDU) and 1a, with 63% of 1a patients having IDU whereas only 14% of 1b patients admitted to IDU (p = 0.03). All patients in whom the mode of acquisition was unknown had genotype 1b (p = 0.04). Intranasal cocaine use was strongly correlated with IDU (p = 0.002). Patients who had tattoos but no history of blood transfusion (BT) or recreational drug use had genotype 1 (2 had 1a, 2 had 1b; p = NS). Twenty-two (45%) patients had serological evidence of prior hepatitis B (HBV) infection. Patients who had genotype 2a, 2b, 3a, or mixed were much more likely to have had HBV (seven of nine, 78%) than patients with genotype 1a or 1b (15 of 40, 37.5%) (p = 0.03). There was no significant correlation between BT, dates, or military branch of service, high risk behavior in Southeast Asia, level of education, ethnicity, and particular genotype(s). Whereas the proportion of 1b accounting for HCV infection in patients with a first exposure before 1968 was 50%, all patients with a first exposure post-1975 were non-1b (p = 0.04), suggesting a change in the epidemiology of HCV in our cohort.

CONCLUSIONS

In U.S. Veterans undergoing OLT: 1) 45% had PCR-confirmed HCV infection, 2) 1a was the predominant genotype and was associated with IDU, and 3) a significant decrease in the prevalence of genotype 1b from the pre-Vietnam era to post-1975 suggests a changing epidemiology of HCV genotypes.

A serotyping assay for hepatitis C virus in Southeast Asia

A serotyping assay for hepatitis C virus (HCV) was evaluated with samples from Thailand, where the distribution of HCV genotypes was different from that in Western countries where the assay was designed and validated. The sensitivity of the assay was low (58%) for HCV RNA-positive samples compared to that of the genotyping assay (95%, P < 0.01). In addition, only 36% of anti-HCV-positive but HCV RNA-negative samples could be serotyped. The serotypes and genotypes were identical in 96% of the samples that could be typed by both methods. Most of the samples with genotype 6, which was common in Southeast Asia, were nontypeable by this serotyping assay.

High prevalence of hepatitis C virus genotype 6 among certain risk groups in Hong Kong

The genotype of hepatitis C virus (HCV) of 172 HCV-RNA positive serum specimens taken from patients with chronic liver diseases, thalassaemia major, chronic renal failure (CRF), haemophilia and intravenous drug abusers (IVDA) was determined by analysis of the amplified 5'UTR region by genotype-specific oligonucleotide probes and restriction fragment length polymorphism (RFLP). Six different genotypes and subtypes (1a, lb, 2, 3, 4 and 6) were found. Genotype lb was the predominant genotype among patients with chronic liver diseases (69.6%), followed by genotype 6 (18.8%), which was similar to that reported for blood donors in earlier studies. Pronounced differences in the distribution of genotypes were seen between the four risk groups. Patients with CRF had a similar distribution to those with chronic liver diseases, whilst the greatest diversity of genotypes was seen in patients with haemophilia, which was expected since they were given factor VIII manufactured overseas. Genotype 6 was particularly prominent in patients with thalassaemia major (50%) and IVDA (62.5%). It is possible that clonal spread of HCV genotype 6 has taken place among a closed subset of the population in Hong Kong through intravenous drug abuse.

Hepatitis C genotyping by direct sequencing of the product from the Roche AMPLICOR test: methodology and application to a South Australian population

The Roche AMPLICOR RT-PCR amplifies a 244 nucleotide sequence within the 5' non coding region (5'NCR) of the viral genome and is a widely used commercial test for the qualitative determination of hepatitis C RNA from sera. This paper describes a routine procedure for the purification of the PCR product, and its use in automated DNA sequencing, for determining the genotype of hepatitis C virus (HCV) isolates. Direct sequencing of the purified product was possible for 86% of samples, whilst 14% required additional amplification using a nested PCR method in order to read the resulting electropherogram. This method of genotyping is considerably less expensive than currently available commercial kits, and is convenient for the increasing number of laboratories that have access to automated DNA sequencers. The highly conserved nature of the 5'NCR limited differentiation of types and subtypes to an extent comparable to commercial HCV typing methods. Using this method on available laboratory samples and on patients about to commence interferon therapy, we found a predominance of genotype 1 (59%) and 3a (31%). Analysis of data on the interferon patients showed the median length of time from first exposure to diagnosis to be significantly longer for patients with genotype 1 than genotype 3a.

Hepatitis C virus heteroduplex tracking assay for genotype determination reveals diverging genotype 2 isolates in Italian hemodialysis patients

A heteroduplex tracking assay (HTA) was developed for genetic analyses of the hepatitis C virus (HCV) using single-stranded probes from the core (C)/E1 region. Nucleotide sequencing of reverse transcriptase (RT)-PCR products from 15 Italian dialysis patients confirmed the specificity and accuracy of the HTA genotyping method, which identified 5 of 15 (33.3%) 1b, 7 of 15 (46.7%) 3a, and 3 of 15 (20%) type 2 infections. The genotypes of an additional 12 HCV antibody-positive blood donors from different geographical locations were also in agreement with the genotypes determined by the Inno-LiPA HCV II kit (Innogenetics) and/or restriction fragment length polymorphism (RFLP). Isolates which had between 35 to 40% nucleotide divergence from control subtype 1a, 1b, 2a, 2b, or 3a standards could be typed. Surprisingly, HTA detected one 1b-2 coinfection which was missed by DNA sequencing. Three samples that were designated non-2a or 2b type 2 by HTA were found to be type 2a by both RFLP and direct nucleotide sequencing of the 5' untranslated region. The genetic distance between patient type 2 and control 2a, 2b, and 2c isolates indicated that a new subtype was present in the population being studied. Serotyping (RIBA serotyping strip immunoblot assay kit) of 23 dialysis patients showed that the genotype could be determined in 6 of 8 (75%) C/E1 RT-PCR-negative and 15 of 23 (65.2%) RT-PCR-positive samples, indicating that the two tests complement each other.

Distribution of hepatitis C virus genotypes among blood donors in Taiwan

The aim of this study was to investigate the prevalence and distribution of hepatitis C virus (HCV) genotypes of blood donors in Taiwan. RNA was extracted from the serum of anti-hepatitis C virus-positive carriers and this was followed by reverse transcriptase-polymerase chain reaction (RT-PCR) using type-specific primers for the presence of HCV genotypes, 1a, 1b, 2a, 2b, 3a and 6a. Of the 604 anti-HCV-positive specimens, the PCR demonstrated that 93.0% (562/604) were positive for at least one HCV genotype. The remaining 42 specimens (7%) were HCV negative. Among the 562 HCV-positive specimens, 505 (89.8%) contained HCV 1a, 1b, 2a, 2b and 3a as the only genotype, with a prevalence of 0.4% (2/562), 60.1% (338/562), 15.5% (87/562), 11.9% (67/562), and 2.0% (11/562), respectively. No HCV genotype 6a was found. Thirty-seven specimens (6.6%) exhibited mixed infections with multiple HCV genotypes that included types 1b, 2a and 2b, while 20 (3.5%) HCV RNA-positive sera remained unclassified. These results confirm that the predominant HCV genotype in Taiwan is 1b. In addition, genotypes 1a and 3a can also be found in Taiwan at low frequency.

The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa

Hepatitis C virus (HCV) genotype 5a is the predominant genotype in southern Africa with a high prevalence amongst infected blood donors from areas in South Africa. We have determined the nucleotide sequence corresponding to the complete coding region of an HCV isolate, EUH1480, previously classified as genotype 5a, from an Edinburgh haemophiliac. The sequence contained a single open reading frame (ORF) coding for a polyprotein of 3014 amino acids. Comparison with the polyprotein sequences from other HCV genotypes, where the ORF varies from 3008 to 3037 amino acids, showed the observed variation in size was due to differences in lengths of the envelope 2 and the nonstructural 5A proteins. The sequence divergence of HCV genotype 5 ranged from 29.4% nucleotide differences (24.91% amino acid differences) compared with genotype 1c to 32.5% nucleotide differences (30.3% amino acid differences) compared with 2a. Phylogenetic analysis of the available full length nucleotide sequences showed EUH1480 to form a branch distinct from the other HCV types, confirming the classification of type 5a as a separate genotype.

Genotypic distribution of hepatitis C virus in different regions of Thailand

The genotypic distribution of hepatitis C virus (HCV) isolated from blood donors from four major regions of Thailand was studied by reverse hybridization assays. PCR-amplified products from the 5' noncoding and core regions of the viral genome were hybridized to genotype- and subtype-specific probes which were immobilized on the nitrocellulose membrane. Of 332 anti-HCV-positive plasma samples studied, 71% contained HCV RNA. HCV genotype 3a was the most prevalent genotype (39%), followed by genotype 1b (20%) and genotype 6 group variants (18%). HCV genotype 1a was identified among 9% of all isolates. Other genotypes (genotype 1 which was neither 1a nor 1b, genotype 3b, and an unclassified genotype) were uncommon. There was no difference in the mean age of the donors infected with different HCV genotypes. The genotypic distribution pattern of HCV was similar among HCV isolates from different regions of Thailand.

Review: molecular epidemiology of hepatitis C virus

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

Genotyping hepatitis C virus isolates from Spain, Brazil, China, and Macau by a simplified PCR method

An improved and simplified method of genotyping was developed for classifying hepatitis C virus (HCV) isolates into the five common genotypes, i.e., I/1a, II/1b, III/2a, IV/2b, and V/3a, by PCR with genotype-specific primers deduced from the core gene. Sense and antisense primers, specific for each of the five common genotypes, were designed by comparison of 319 core gene sequences from HCV isolates of various genotypes from genetic groups 1 to 9. In the first round of PCR, a sequence of 433 bp representing nucleotides 319 to 751 was amplified with universal primers. The second round of PCR was performed with respective sense and antisense primers in two separate reactions, one for the amplification of genotypes I/1a and II/1b and the other for the amplification of genotypes III/2a, IV/2b, and V/3a. The specificity of genotyping was confirmed with a panel of 191 serum samples containing HCV isolates whose core gene sequences were known: 110 serum samples infected with HCV of the five common genotypes and 81 serum samples infected with HCV of other genotypes. The use of sense and antisense primers for genotype II/1b (primers 389 and 492) abolished the cross-reaction of the antisense primer for genotype II/1b (primer 133) with some HCV isolates of genotype I/1a found by our original method. The new method was used for genotyping 130 HCV isolates from Spain, 53 from Brazil, 106 from China, and 30 from Macau. A total of 329 bp of the NS5b region (nucleotides 8279 to 8607) of five isolates from Spain and five isolates from Macau which could not be classified as any of the five common HCV genotypes or genotype 2c were sequenced, and the sequences were compared with those of HCV isolates of known genotypes; two isolates from Spain were deduced to be of genotype 4d and one was deduced to be of genotype 1d, while the remaining two isolates from Spain had novel genotypes in genetic group 2; however, all five isolates from Macau were of genotype 6a.

Heterogeneity of hepatitis C virus

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