Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai, Thailand

Hepatitis C virus genotype analysis in patients with chronic hepatitis in North Eastern Bulgaria

Background: The main objective of this study was to analyse the spread of hepatitis C virus (HCV) genotype in patients with chronic liver disease; commenting on the molecular characterization of HCV and gender and age in Varna, Bulgaria. Across Europe and the world, HCV is a significant economic concern and public health crisis. Defined by genotype variations, HCV is the leading cause of chronic liver disease, liver related morbidity, and mortality worldwide. Active examination for asymptomatic patients is essential, initiating early treatment aimed at the specific HCV genotype, effective outcomes, and reducing transmission and mortality in Bulgaria. Methods and materials: Nucleic acid extraction and amplification were performed with commercially available test kits on 115 patients blood samples collected from March 2018 to October 2018. Male (n = 58) (50.43%, 95% CI = 41.29%-59.57%) and female (n = 57) (49.57%, 95% CI = 41.29%-59.57%) samples were equally distributed (mean age = 51.4 years; SD = ±16.5 years; range = 17-87 years old). Results: Genotype 1b predominated (73%, 95% CI = 64.89%-81.11%), followed by high prevalence of 1a (13.9%, 95% CI = 7.58%-20.22%) and 3 genotypes (11.3%, 95% CI = 5.51%-17.09%). Genotypes 2 and 4 were equally the least prevalent (0.9%, 95% CI = -0.83%-2.63%). In genotype 1b, 60.7% were women and 39.3% were men; in genotype 1a, 25% were women and 75% were men; and in genotype 3, only 7.7% were women and 92.3% were men. Males were most prevalent in genotypes 1a (75%) and 3 (92.3%), while women were most prevalent in genotype 1b (60.7%). Conclusions: HCV genotype lb is the predominant variant within the epidemiological pattern of HCV genotypes in patients with chronic liver diseases in North Eastern Bulgaria.

Molecular evolution of hepatitis C virus in China: A nationwide study

The evolutionary and epidemic history and the regional differences of hepatitis C virus (HCV) are complex and remain unclear in the vast territory China. Here we recruited 1540 HCV-RNA positive patients sampled in 29 provinces across whole China, which is the largest sample capacity and the most comprehensive geographic coverage of China to our knowledge. 1b, 2a, 3b, 6a and 3a were the major subtypes in China. 1b was the most predominant subtype which presented in every province. The second most predominant subtype, 2a, appeared to concentrate in the north of China. Subtypes 3a and 3b were mainly found in the Southwest region, while 6a was restricted in the South region. We further estimated the origins of the dominating subtypes and discovered for the first time that a Chinese-specific transmission pattern for some strains of subtype 2a which was restricted in north China, and Chinese subtype 3b originated from Thailand.

Epidemiology of hepatitis C virus genotypes in northeastern Thai blood samples

BACKGROUND

Hepatitis C virus (HCV) infection is an important cause of liver cancer in Thailand. The highest prevalence of anti-HCV positive among Thai blood donors is found in the northeastern region. The present analysis of the genotype distribution among anti-HCV positive northeastern-Thai blood donors was conducted to provide a base for the epidemiological pattern of HCV infection in this region.

MATERIALS AND METHODS

A total of 112 HCV seropositive healthy blood donors were randomly selected and tested for the presence of HCV-RNA by RT-PCR. HCV-RNA positive samples were genotyped by direct sequencing at core region genomes and confirmed by phylogenetic analysis.

RESULTS

HCV viremia was found in 94.6% (106/112) of HCV seropositive blood donors. There were 3 major genotypes distributed among this population. HCV genotype 3a was the most prevalent (71.7%) followed by genotypes 1a (7.5%), 1b (7.5%), 6i (3.8%), 6f (2.8%) and 6n (1.9%).

CONCLUSIONS

HCV genotype 3a in asymptomatic infections in northeastern Thailand is significantly higher than other previous reports. Subgenotype 6 prevalence is less than in neighboring countries and distribution patterns differ. The findings are relevant as predictors for using interferon therapy in this population.

High rate of seronegative HCV infection in HIV-positive patients

Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) is a significant global health problem. The two viruses are transmitted with high efficacy via blood-to-blood contact, mainly intravenous drug use (IVDU), whereas HCV is less easily transmitted sexually. Antibody testing is the main screening method for HCV infection, although it may not be the optimal option for HIV infection. The aim of this study was to investigate HCV infection in HIV-positive patients, with and without a detectable anti-HCV antibody response. A total of 187 plasma samples were obtained from HIV-positive patients in Surabaya, Indonesia and examined for anti-HCV [HCV enzyme immunoassay (EIA) 3.0], HCV genotype/subtype [reverse transcription-polymerase chain reaction (RT-PCR) using primers targeting a part of NS5B/5'UTR followed by sequencing] and HCV viral load (quantitative RT-PCR). A total of 119 patients (63.6%) were found to be anti-HCV-positive and, among these, HCV RNA was detected in 73 (61.3%), with HCV-1a as the predominant subtype (31.5%). Of the 68 anti-HCV-negative samples, HCV RNA was detected in 26/68 (38.2%) mostly as the HCV-3a subtype (50%). High HCV viral loads were more common among the HCV-seropositive patients. The HCV-seropositive samples with detected HCV RNA were mostly obtained from HIV-positive patients with parenteral transmission (IVDU) (76.7%); however, the HCV-seronegative samples with detected HCV RNA were mostly from patients who had acquired HCV through heterosexual transmission (61.5%). In conclusion, HIV-positive patients were at high risk of becoming co-infected with HCV and several remained HCV-seronegative. Furthermore, there may exist differences in HCV seropositivity and subtypes between HIV-positive patients who acquired HCV sexually and those who acquired HCV parenterally.

An overview about hepatitis C: a devastating virus

Hepatitis C (HCV) is the disease that has affected around 200 million people globally. HCV is a life threatening human pathogen, not only because of its high prevalence and worldwide burden but also because of the potentially serious complications of persistent HCV infection. Chronicity of the disease leads to cirrhosis, hepatocellular carcinoma and end-stage liver disease. HCV positive hepatocytes vary between less than 5% and up to 100%, indicating the high rate of replication of viral RNA. HCV has a very high mutational rate that enables it to escape the immune system. Viral diversity has two levels; the genotypes and Quasiaspecies. Major HCV genotypes constitute genotype 1, 2, 3, 4, 5 and 6 while more than 50 subtypes are known. All HCV genotypes have their particular patterns of geographical distribution and a slight drift in viral population has been observed in some parts of the globe.

Complete genome analysis of hepatitis C virus subtypes 6t and 6u

Hepatitis C virus (HCV) genomes exhibit high nucleotide sequence diversity. In this study, we performed complete genome sequence analysis of 11 HCV genotype 6 samples from Vietnam and Thailand. We identified nine HCV complete genomes belonging to subtypes 6a (D9), 6e (D42 and D88), 6f (TH52), 6i (TH24), 6l (D33), 6n (TH22 and TH31) and 6o (D85). Phylogenetic analysis of the core/E1 and NS5B regions from unclassified genotype 6 isolates from Asian immigrants in Canada revealed that two other viruses (D49 and D83) could be classified as novel candidates of HCV subtypes 6t and 6u.

Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6

Five hepatitis C virus (HCV) complete genome sequences (Th846, 537796, QC227, QC216 and QC99) from a blood donor in Thailand and three Asian immigrants and one Caucasian in North America were determined. Phylogenetically, they represent the first complete genomes for subtypes 6c, 6l, 6o, 6p and 6q, respectively. Similarity analysis showed no evidence of inter- or intrasubtype recombination. Further analysis in conjunction with partial sequences from the Los Alamos HCV database led to the identification of other closely related isolates from south-eastern Asia or immigrants from that region. However, Th846 did not cluster with any reference sequence and is the sole isolate of subtype 6c reported so far. This study completes the full genome sequencing of all 17 assigned HCV genotype 6 subtypes (6a-6q). The utility of this panel of complete sequences for accurate detection and classification of infection, and for estimating the origin of this genotype of HCV, is discussed.

Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses

In this study, the first complete genome sequences for hepatitis C virus (HCV) subtypes 6f, 6i, 6j and 6m, obtained from infected blood donors in Chiang Mai, Thailand, are reported. Pairwise genome-wide nucleotide similarities between some of these isolates were higher than the 75-80% value used previously to define different HCV subtypes. To investigate further, the entire genomes of four prototype isolates, Th602 (6i), Th553 (6j), B4/92 (6m) and D86/93 (6n), were sequenced. Pairwise comparison of these sequences gave a similar range of nucleotide similarities, thereby providing new information for HCV subtype classification. In order to study the hypothesis of interspousal HCV transmission, four additional complete HCV genome sequences were obtained from two infected Thai blood donors and their spouses, C-0044 and C-0046 (6f), and C-0192 and C-0185 (6m). Pairwise comparison of the sequences revealed that C-0044 and C-0046 share a nucleotide similarity of 98.1%, whilst C-0185 and C-0192 have a similarity of 97.8%. Several other studies of partial HCV sequences of different genomic regions from HCV-infected couples have shown nucleotide similarities ranging from 96.3 to 100%. The similarities of the complete genome sequences from the two couples in the current study are consistent with HCV transmission between spouses.

Hepatitis C virus genotype distribution in Myanmar: Predominance of genotype 6 and existence of new genotype 6 subtype

AIM

This study was performed to determine the prevalence and distribution of hepatitis C virus (HCV) genotypes in Myanmar.

METHODS

A total of 1333 peripheral blood samples were collected from four different border cities of Myanmar. The anti-HCV antibody-positive serum samples were identified. HCV was genotyped by reverse transcriptase polymerase chain reaction, direct DNA sequencing and phylogenetic analysis on the partial core genome.

RESULTS

The overall prevalence of HCV infection was 11.6% (154/1333). Regionally, it was 13.5% (47/349) in the north-eastern city, 12.8% (64/501) in the north-western city, 4.2% (16/380) in the southern city and 26.2% (27/103) in the western city. HCV was genotyped in 145/154 (94.2%) samples. Genotype 6 was the most prevalent genotype in this study (71/145, 49%), followed by genotype 3 (57/145, 39.3%), genotype 1 (16/145, 11%), and genotype 2 (1/145, 0.7%). Genotype 6 was mostly found in the northern cities and genotype 3 in the southern and western cities of Myanmar. Multiple HCV genotypes/subtypes were successfully characterized as 1a, 1b, 2a, 3a, 3b, 6m, 6n, and a new 6 subtype. Among them, subtype 6n was the most predominant subtype (38.6%), followed by subtype 3b (29.7%), 3a (9.6%), 6m (9%), 1b (6.9%), 1a (4.1%), new 6 subtype (1.4%) and 2a (0.7%). Subtype 6n was more widely distributed in the northern cities whereas subtype 3b was more common in the western city. The newly discovered genotype 6 subtype was from the northern cities.

CONCLUSIONS

The results indicate there are regional differences of HCV genotype distribution in Myanmar. There is a distinct geographic variation from other South-East Asian countries in terms of the existence of the new genotype 6 subtype.

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.

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.

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.

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.

Hepatitis C virus core protein selectively inhibits synthesis and accumulation of p21/Waf1 and certain nuclear proteins

By using a vaccinia virus-T7 expression system, possible effects of hepatitis C virus (HCV) core protein on synthesis and accumulation of host cellular proteins transiently expressed in cultured cells were analyzed. Immunoblot and immunofluorescence analyses revealed that synthesis and accumulation of certain nuclear proteins, such as p21/Waf1, p53, proliferating cell nuclear antigen and c-Fos, were strongly inhibited by HCV core protein. On the other hand, synthesis and accumulation of cytoplasmic proteins, such as 2'-5'-oligoadenylate synthetase (2'-5'-OAS), RNase L and MEK1, were barely affected by HCV core protein. Northern blot analysis showed that the degrees of mRNA expression for those proteins did not differ between HCV core protein-expressing cells and the control, suggesting that the inhibition occurred at the post-transcription level. Pulse-labeling analysis suggested that HCV core protein strongly inhibited synthesis of p21/Waf1 at the translation level. Once being accumulated in the nucleus, p21/Waf1 stability was not significantly affected by HCV core protein. Mutants of HCV core protein C-terminally deleted by 18 or 41 amino acids (aa), which were localized almost exclusively in the nucleus, lost their ability to inhibit synthesis/accumulation of p21/Waf1 whereas another mutant C-terminally deleted by 8 aa still maintained the same properties (subcellular localization and the inhibitory effect) as the full-length HCV core protein of 191 aa. Taken together, our present results suggest that expression of HCV core protein in the cytoplasm selectively inhibits synthesis of p21/Waf1 and some other nuclear proteins at the translation level.

Inhibition of protein synthesis by the nonstructural proteins NS4A and NS4B of hepatitis C virus

Possible inhibitory effects of hepatitis C virus (HCV) proteins on cellular protein synthesis were analyzed using transient expression system. The core protein, the nonstructural protein 4A (NS4A) and NS4B, but not NS3, NS5A or NS5B, inhibited p21/Waf1 expression post-transcriptionally. Further analysis revealed that the inhibition by NS4A and NS4B was mediated at least partly, if not entirely, at the translation level. NS4A-mediated translational inhibition was counteracted to some extent by NS3 co-expressed either in trans or cis. Co-expression of NS4A and NS4B exerted an additive effect on the translational inhibition. The N-terminal two-thirds of NS4A (amino acids 1-40) was shown to be involved in the translational inhibition. We also tested possible inhibitory effects of NS4A and NS4B on synthesis of other cellular proteins in parallel with p21/Waf1. NS4A and NS4B inhibited p21/Waf1 most strongly, followed by RNase L, p53, a C-terminally truncated form of CREB-RP and 2'-5' oligoadenylate synthetase. p21/Waf1, RNase L and p53 are known to have the PEST (proline-glutamic acid-serine-threonine) motif with relatively high scores in their sequences and considered to be sensitive to intracellular degradation. Taken together, our results suggest that NS4A and NS4B each mediate translational inhibition and, probably, increased degradation of certain cellular proteins.

Comparative sequence analysis of the core protein and its frameshift product, the F protein, of hepatitis C virus subtype 1b strains obtained from patients with and without hepatocellular carcinoma

The core protein of hepatitis C virus (HCV) has been implicated in hepatocarcinogenesis. In order to determine whether there is a correlation between mutations of the core protein and the development of hepatocellular carcinoma (HCC), the core protein-coding sequence of the viral genome of HCV subtype 1b (HCV-1b) obtained from patients with and without HCC was analyzed. We found that 12 (40.0%) of 30 HCV-1b isolates from patients with HCC but none of 29 isolates from patients without HCC had a point mutation(s) in an N-terminal region of 20 residues. Similarly, 10 (33.3%) of 30 isolates from patients with HCC had mutations in a limited region between residues 141 and 160, whereas only 2 (6.9%) of 29 isolates from patients without HCC did. The differences between the two groups were statistically significant. The mutations were found in isolates from both cancerous and adjacent noncancerous tissues of patients with HCC, suggesting that the mutations were present before the development of HCC. The other regions of the core protein of some isolates also had mutations, but no significant difference was observed between isolates from patients with HCC and those from patients without HCC. The F protein, a frameshift product that is still hypothetical for HCV-1b strains, showed more sequence diversity than the core protein among the isolates analyzed, but there were no significant differences in the mutation rates or positions between isolates from patients with HCC and isolates from patients without HCC, except for a short N-terminal sequence of approximately 11 residues that is shared with the core protein.

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.

Nuclear localization and intramolecular cleavage of N-terminally deleted NS5A protein of hepatitis C virus

The full-size NS5A (NS5A-F) of hepatitis C virus is localized in the cytoplasm despite the presence of a functional nuclear localization signal (NLS) in its C-terminal region (amino acids (aa) 354-362). In the present study, we demonstrated that a short stretch of sequence near the N-terminus of NS5A (aa 27-38) masked the functional NLS, preventing NS5A from being transported to the nucleus. This sequence, referred to as an NLS-masking sequence, was distinct from a nuclear export signal, as it did not actively target a protein to the cytoplasm. We also found that other sequences located at either an N- (aa 1-21) or a C-terminal region (aa 353-447) were responsible for targeting NS5A to the cytoplasm. Western blot analysis of the transfected cells revealed that NS5A mutants that had been N-terminally deleted by 66 aa or more were cleaved at a certain cleavage site, generating a common fragment of ca. 40 kDa. This result implies the possible presence of a cleavage site in the NS5A sequence around aa 150, which is exposed through conformational alteration upon the N-terminal deletions.

A novel hepatitis C virus (HCV) subtype from Somalia and its classification into HCV clade 3

Hepatitis C virus (HCV) sequences from throughout the world have been grouped into six clades, based on recently proposed criteria. Here, the partial sequences and clade assignment are reported for three HCV isolates from chronic hepatitis C patients from Somalia, for whom conventional assays failed to identify the genotype. Phylogenetic analysis of the sequences of the core, envelope 1 and part of the non- structural 5b regions suggests that all three isolates belong to a distinct HCV genetic group, tentatively classified as subtype 3h. This novel HCV subtype shows the highest sequence similarity with HCV isolates from Indonesia. Despite the fact that these patients were infected with HCV clade 3, none of them responded to standard interferon treatment.

Prevalence of GB virus C/Hepatitis G virus infection among various populations in Surabaya, Indonesia, and identification of novel groups of sequence variants

A molecular epidemiological study was performed to investigate the prevalence of GB virus C/hepatitis G virus (GBV-C/HGV) infection among various populations in Surabaya, Indonesia. The prevalence of GBV-C/HGV RNA, determined by reverse transcription-PCR for a portion of the NS3 region of the viral genome, was 2.7% (4 of 150) among randomly collected blood donor sera, which were all negative for both hepatitis B virus surface antigen and antibodies against hepatitis C virus (HCV). On the other hand, the prevalence among anti-HCV-positive blood donors was 17.8% (13 of 73), with the ratio being significantly higher than that observed with the anti-HCV-negative blood donors (P < 0.001). A high prevalence of GBV-C/HGV infection was also observed among patients with chronic liver disease, such as chronic hepatitis (5.7%), liver cirrhosis (11. 5%), and hepatocellular carcinoma (7.0%), and patients on maintenance hemodialysis (29.0%). No correlation was observed between GBV-C/HGV viremia and serum alanine aminotransferase levels in the populations tested, suggesting the possibility that GBV-C/HGV does not cause apparent liver injury. Phylogenetic analysis of sequences of a portion of the 5' untranslated region and the E1 region of the viral genome identified, in addition to a previously reported then novel group of GBV-C/HGV variants (group 4), another novel group of variants (group 5). This result suggests that GBV-C/HGV can be classified into at least five genetic groups. GBV-C/HGV isolates of group 4 and group 5 were each shown to comprise approximately 40% of the total Indonesian isolates.

Hepatitis C virus genotypes: epidemiological and clinical associations. Benelux Study Group on Treatment of Chronic Hepatitis C

In a cohort of 292 chronic hepatitis C patients living in the Benelux countries the relationship between viral genotype and geographical origin, route of transmission, clinical characteristics and severity of liver disease was analyzed. HCV-RNA isolates could be classified by the Line Probe Assay (LiPA) as 1a, 1b, 2, 3, 4 or 5 in 286 (98%) cases. Patients of European origin were predominantly infected with HCV subtype 1b (164/254, 65%, CI 58-70%), as were patients of Asian origin (7/13, 54%). Patients originating from Surinam (South America) had predominantly type 2 (9/10, 90%), whereas Africans were mainly infected with type 4 (7/9, 77%). Blood transfusion was the mode of transmission in 142 (50%) patients, intravenous drug abuse (IVDA) in 40 (14%), occupational needle accident or tattoo in 11 (4%); no obvious source of infection was found in 93 (33%). In patients infected by blood transfusion, subtype 1b was predominant (70%, CI 61-77%), whereas subtypes la and 3 were predominant in those infected by IVDA (25% and 45%, respectively, p<0.001). Cirrhosis was observed in 68 (24%) patients; in multivariate analysis, factors independently related to cirrhosis were: the duration of infection, age and prior hepatitis B. No significant relationship was found between the severity of fibrosis or liver inflammation and the HCV (sub)types. In summary, in this large cohort of patients in the Benelux countries the hepatitis C virus (sub)type present was clearly related to the country of origin and the route of transmission, but not to the severity of liver disease.

Follow-up study of hypervariable region sequences of the hepatitis C virus (HCV) genome in an infant with delayed anti-HCV antibody responses

An infant born prematurely and infected with hepatitis C virus (HCV) one month after birth was followed for 4.5 years. The patient did not produce detectable anti-HCV antibodies until two years after the onset of hepatitis. Before seroconversion, a single clone of HCV, as determined by quasispecies of the hypervariable region (HVR) of the HCV genome, was almost exclusively found in the serum. After seroconversion, however, another distinct lineage of HCV clones replaced it within half a year. As HCV infection persisted further in the presence of anti-HCV antibodies, many derivatives of both sequence lineages emerged to exhibit the typical quasispecies feature of HVR sequences. Neither seroconversion nor the changes in HVR sequences influenced the serum aminotransferase titers.

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.

Hepatitis C virus (HCV) genotypes and chronic liver disease in Pakistan

Hepatitis C virus (HCV) is classified into different types depending on nucleotide sequence variability. Detailed information on the distribution of various HCV genotypes in some geographical areas is available but little is known about Pakistan. In this study, a 5' non-coding region (NCR)-based restriction fragment length polymorphism (RFLP) genotyping assay was used to investigate the genotype distribution in a large series of HCV-infected patients in Karachi, Pakistan. Serum samples from 74 hepatitis B surface antigen (HBsAg)-negative patients with a clinical diagnosis of chronic liver disease (60 patients) and hepatocellular carcinoma (HCC) (14 patients) were assayed for anti-HCV antibody by second generation enzyme immunoassay and 48 were confirmed anti-HCV-positive (33 males, 15 females). Other causes of chronic liver disease (e.g. haemochromatosis, Wilson's disease and immune-mediated injury) were ruled out. Liver biopsy was done in 27/48 anti-HCV-positive patients and in all HCC patients. Genotypes were determined for 45/48 anti-HCV-positive study patients; 39/45 (87%) were type 3; four (9%) were type 1; one was type 2; and one was type 5. Past blood transfusion was the main identifiable risk factor found in 10 patients, all type 3. Seven of the 14 HCC patients were anti-HCV positive, (six were type 3). Most patients with hepatitis C presented with established cirrhosis and complications of portal hypertension and liver failure.

IN CONCLUSION

(i) genotype 3 is the most common isolate in HCV-associated chronic liver disease in Pakistan; (ii) a significant proportion of HBsAg-negative cirrhotics are non-B, non-C in aetiology; and (iii) half of the patients with HCC have serological evidence of HCV infection.

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.

Nuclear localization of the NS3 protein of hepatitis C virus and factors affecting the localization

Subcellular localization of the NS2 and NS3 proteins of hepatitis C virus was analyzed. In stable Ltk transfectants inducibly expressing an NS2-NS3 polyprotein (amino acids [aa] 810 to 1463), processed full-size NS2 (aa 810 to 1026) was detected exclusively in a cytoplasmic membrane fraction. On the other hand, the other processed product, carboxy-truncated NS3 (NS3 deltaC1463; aa 1027 to 1463), was present in both cytoplasmic and nuclear fractions. To further analyze subcellular localization of NS3, NS3 deltaC1459 (aa 1027 to 1459), full-size NS3 (NS3F; aa 1027 to 1657), and both amino- and carboxy-truncated NS3 (NS3 deltaNdeltaC; aa 1201 to 1459) were expressed in HeLa cells by using a vaccinia virus-T7 hybrid expression system. NS3 deltaC1459 and NS3F accumulated in the nucleus as well as in the cytoplasm, exhibiting a dot-like staining pattern. On the other hand, NS3 deltaNdeltaC was localized predominantly in the cytoplasm, suggesting the presence of a nuclear localization signal(s) in the amino-terminal sequence of NS3. NS4A, a viral cofactor for the NS3 protease, inhibited nuclear transport of NS3 deltaC1459 and NS3F, with the latter inhibited to a lesser extent than was the former. Interestingly, wild-type p53 tumor suppressor augmented nuclear localization of NS3 deltaC1459 and NS3F, whereas mutant-type p53 inhibited nuclear localization and augmented cytoplasmic localization of NS3 deltaC1459. However, subcellular localization of NS3 deltaNdeltaC was not affected by either type of p53. Wild-type p53-mediated nuclear accumulation of NS3 deltaC1459 and NS3F was inhibited partially, but not completely, by coexpressed NS4A, with NS3F again affected less prominently than was NS3 deltaC1459.

Differential prevalence of hepatitis C virus subtypes in healthy blood donors, patients on maintenance hemodialysis, and patients with hepatocellular carcinoma in Surabaya, Indonesia

Determination of the prevalence of liver disease caused by hepatitis C virus (HCV) of various genotypes helps provide an understanding of the virulences of these genotypes. Differences in the prevalences of these genotypes are known to exist in the various geographical regions of the world. Hence, we performed seroepidemiological and molecular epidemiological analyses of HCV in Surabaya, Indonesia. The prevalences of anti-HCV antibodies were 2.3, 76.3 and 64.7% in healthy blood donors, patients on maintenance hemodialysis, and patients with hepatocellular carcinoma (HCC), respectively. HCV-2a was the most common (52%) among the HCV clones obtained from blood donors; this was followed by HCV-1b (15%), HCV-1a (7%), and HCV-1d (7%), a unique Indonesian subtype. The high prevalence of HCV-2a in blood donors was further supported by serotyping analysis that could discriminate HCV type 2 (HCV-2a and -2b) from HCV type 1 (HCV-1a, -1b, and -1d). HCV-1a, -1b, and -1d were strongly associated with elevated serum alanine aminotransferase (ALT) levels in blood donors, suggesting a possibly more pathogenic feature of those subtypes than HCV-2a. In patients on maintenance hemodialysis, HCV-1a and -1b (each 31%) were among the most common subtypes, and in contrast to the case with blood donors, HCV-1a, -1b, and -1d were found in those with normal ALT as well as those with elevated ALT levels. Impaired immune responses of hemodialyzed patients might be responsible for the apparently decreased hepatocytic injury caused by infection with HCV type 1. In patients with HCC, HCV-1b (57%) was the most common; this was followed by HCV-1d (19%) and HCV-2a (5%). Subtype prevalence was not different between HCC patients with advanced liver cirrhosis and those without advanced cirrhosis.

Heterogeneity of hepatitis C virus

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

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

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

Hepatitis C virus infection-associated markers in sera from blood donors in Surabaya, Indonesia

Among 2,233 sera obtained from volunteer blood donors, 259 (11.6%) showed elevated alanine aminotransferase (ALT) levels. A second-generation enzyme-linked immunosorbent assay (ELISA) revealed that 23 (8.9%) of the 259 sera were positive for antibodies against hepatitis C virus (HCV), whereas only 9 (1.4%) of 646 sera randomly collected from blood donors with normal ALT levels were positive (P < 0.001). The overall prevalence of anti-HCV antibodies among blood donors was estimated to be 2.3%. HCV RNA was detected in 19 (83%) of the 23 anti-HCV-positive sera with elevated ALT levels, and 8 (89%) of the 9 sera with normal ALT levels. Among the anti-HCV-positive sera, IgM anti-HCV was detected in 5 (22%) of 23 sera with elevated ALT levels and in 2 (22%) of 9 sera with normal ALT levels. All of the IgM anti-HCV-positive sera were positive for HCV RNA, irrespective of ALT levels.

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

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

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

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

Hepatitis C virus genotyping by means of 5'-UR/core line probe assays and molecular analysis of untypeable samples

To test the theoretical possibility of 5'-UR mistyping between hepatitis C virus subtypes 1a and 1b, we combined a 5'-UR/Core line probe assay (LiPA) with a nested PCR system and retested 183 sera, previously genotyped as type 1a or 1b and originating mainly from Western Europe. Eight percent of these were found to be wrongly subtyped. Based on this method, 3 additional subtypes of type 1 were discovered (1d-1f). Randomly selected European type 2 sera (n = 18) were tested with a similar type 2 5'-UR/Core LiPA. They were unexpectedly found to belong to subtype 2c in the majority of cases. Among serum samples originating from South-East Asia, several additional genotypes (7a, 7c, 7d, and 9a) were detected which had 5'-UR sequence motifs indistinguishable from genotype 1. Based on 13,203 pairwise comparisons in the 340-bp NS5B region, classification into types, subtypes, and isolates was obtained in 99.8% of all cases by using the phylogenetic border value of 0.328 for subtypes/types and 0.127 for isolates/subtypes; and evidence for a 10th major type of HCV was provided. Combination of all available HCV sequence data from the 447-bp Core/E1 region and the NS5B 340-bp and 222-bp regions provided evidence for the existence of 10 types, including 50 subtypes. Previously, extensive studies involving genotypes 1a, 1b, 2a, and 2b indicated the importance of HCV subtyping in interferon treatment and progression of chronic liver disease. The herein described expansion in the number of HCV types and subtypes should help improve diagnosis, treatment and possibly prophylaxis of hepatitis C liver disease.

Frequent detection of hepatitis C virus subtype 3a (HCV-3a) isolates in Thailand by PCR using subtype-specific primers

By means of a polymerase chain reaction (PCR) method using subtype-specific primers for hepatitis C virus (HCV) subtypes 1a, 1b, 2a, 2b and 3a, the prevalence of each subtype among HCV isolates in Chiang Mai, Thailand, was determined. HCV-3a appeared to be the most common subtype in blood donors, and was also frequently found in patients with liver disease. HCV-1b, but not HCV-2a or -2b, was also commonly found in this area, while a considerable percentage of the total HCV isolates still remained unclassifiable by the above methods. Serotype analysis of the HCV isolates using C14-1 and C14-2 recombinant peptides revealed that HCV-3a was likely to carry an antigenic determinant(s) different from those of the major types 1 (HCV-1a and -1b) and 2 (HCV-2a and -2b).