Molecular epidemiology of HCV genotypes among injection drug users in Taiwan: Full‐length sequences of two new subtype 6w strains and a recombinant form_2b6w

Human immunodeficiency virus type 1 (HIV‐1) circulating recombinant form (CRF) 07_BC strain has caused serious outbreaks among injection drug users in Taiwan since 2004. The objective of this study was to conduct a molecular epidemiological study of HCV genotypes in intravenous drug users in Taiwan. Blood samples and questionnaires from 591 intravenous drug users infected with HIV‐1 were collected nationwide. In total, 180 samples were selected for HCV genotyping using multiplex PCR and phylogenetic analysis of the core, E1 and NS5B regions. The Inno‐Lipa assay was used to confirm multiple infections with different genotypes. Eighty percent had a single infection with subtype 1b being the most common subtype (24%), 12% had double infections and two had triple infections. In addition, three recombinant forms (RFs)‐2a1a, 3a1b, and 2b6w were identified. Phylogenetic analyses showed that the 3a, 6a, and 6n strains were clustered with strains present in Thailand and mainland China. Full‐length sequence analysis showed that two 6w strains shared 89.4–90.2% sequence homology with the 6(r) strain from the Guangdong Province, China. Bootscan analysis revealed that the recombination breakpoint of RF_2b6w was located at the NS2‐NS3 junction. In summary, the distribution of HCV genotypes among Taiwanese intravenous drug users was complex and more than 12% of the drug users were infected with more than one genotype of HCV. J. Med. Virol. 82:57–68, 2010. © 2009 Wiley‐Liss, Inc.     

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.     

High prevalence of HBV and HCV infection among intravenous drug users in Korea

Although intravenous drug users are a well-known route of hepatitis C virus (HCV) and hepatitis B virus (HBV) transmission, there is no data on the prevalence of HBV and HCV infection among intravenous drug users in Korea. In order to describe the prevalence of HBV and HCV infection, and to determine HCV genotypes in the population, serum samples were collected from 107 intravenous drug users during 2005-2006. Fifty-seven percent (n = 61) were HCV RNA positive and 51% (n = 55) were HBV DNA positive. Co-infection of HBV and HCV were found in 23% (n = 25). HCV genotypes 1b, 2a/2c, 2, 2b, and 3a were found in 38% (n = 23), 44% (n = 27), 8% (n = 5), 2% (n = 1), and 3% (n = 2), respectively. Moreover, mixed infections of genotypes 1b and 2a/2c were found in 5% (n = 3). When the number of patients with HCV genotype 1b compared with that of patients with genotype 2a/2c, HBV DNA titer was not significantly different by independent t-test (t = -0.881, P = 0.392 > 0.05) between the two patient groups. These results suggest that the prevalence of HBV and HCV infection among intravenous drug users is high showing over 50% in Korea and a strategic prevention program should be performed in this group to prevent further infection into local community.     

Distribution of hepatitis C virus genotypes among injecting drug users in contact with treatment centers in Belgium, 2004-2005

The aim of this study was to determine the current prevalence of HCV genotypes in injecting drug users recruited at treatment centers all over Belgium, and to analyze if the distribution of genotypes was correlated with demographic characteristics, at-risk behaviors, and co-infection with other viruses. Therefore 147 anti-HCV-positive serum samples were selected for subsequent HCV RNA detection and genotyping. HCV RNA could be detected in 98 (67%) of the 147 serum samples. Genotype 1 (38%) and 3 (49%) were the most common genotypes followed by genotype 4 (9%) and genotype 2 (2%). One mixed infection (1%) was detected. The subtype could be determined in 80 cases: genotype 3a was the most prevalent (49%), followed by genotype 1a (16%) and genotype 1b (15%). No significant difference was found between the distribution of genotypes and the location of treatment centers, at-risk behaviors and co-infection with other viruses. Nevertheless, a slight variation over time could be identified (P = 0.06): one in two genotype 3 drug users started with their injecting drug use in the last 10 years (33% in the period 1995-1999 and 21% in the period > or =2000) compared to only one in four genotype 1 drug users (20% in the period 1995-1999 and 9% in the period > or =2000).     

Anti-HCV RIBA/LiaTek reactivity and HCV genotype in EIA-negative patients with viremia.

Individuals infected with hepatitis C virus (HCV) usually produce anti-HCV antibodies detectable by enzyme immunoassay (EIA); however, in certain viremic cases this antibody does not appear. To investigate whether anti-HCV in these cases is detectable by Western blot (WB), 38 HCV RNA positive/anti-HCV EIA-negative sera were tested by RIBA 3.0 or LiaTek III. The HCV genotypes (INNO-LiPA) were analyzed to determine whether the variance in these genotypes can be the reason for the late, weak antibody production or its absence. As the control group, 282 EIA-positive/HCV RNA-positive patients were examined. A single band reactivity of various intensities by RIBA or LiaTek was observed in 16/38 EIA negative sera. Positive results with NS3 were detected in 4 sera and weak positive (+/-) with core, NS3, and NS5 in 5, 6, and 1 sera, respectively. In 3 cases with anti-NS3, the seroreversion was observed in follow-up. The distribution of genotypes in anti-HCV-negative versus anti-HCV-positive groups was: 1b alone, 50.0% vs. 78.0%; 3a alone, 13.2% vs. 15.6%; and mixed (1b+3a), 36.8% vs. 5.0%, respectively. The follow-up studies showed that viremia was lost spontaneously in 12/35 patients. In some patients infected with two genotypes, the spontaneous loss of the 3a genotype was observed. The study showed that WB tests are useful for serological confirmation of HCV infection in some EIA negative/HCV RNA-positive patients but, because seroreversion may occur, sequential sera samples should be tested. No unusual HCV genotype was detected in anti-HCV-negative/HCV RNA-positive cases, but the frequency of mixed infection with the 1b+3a genotypes in this group was found to be higher than that in anti-HCV-positive hepatitis patients.     

Molecular and epidemiological aspects of hepatitis C virus infection among crack cocaine users

The aim is to investigate the prevalence, risk factors, and hepatitis C virus (HCV) genotypes/subtypes among crack users in-treatment in Central Brazil. A cross-sectional survey in which 600 in-treatment crack users were interviewed and tested for anti-HCV Ab by enzyme-linked immunosorbent assay was conducted between August 2012 and April 2013. Anti-HCV-positive samples were also submitted for HCV RNA detection by polymerase chain reaction. Positive HCV RNA samples were genotyped by direct sequencing analysis of the NS5B region of the viral genome, followed by phylogenetic analysis. Of the total, 3.7% (95.0% CI, 2.4%-5.6%) were anti-HCV positive. Age over 40 years and history of injecting drugs were risk factors for HCV, while snorting cocaine was a protector variable. HCV RNA was detected in 14 of 22 anti-HCV-positive samples, and the genotypes 1 (n = 10) and 3 (n = 2), subtypes 1a (n = 7), 1b (n = 3), and 3a (n = 2) were identified. The HCV prevalence found among crack users is almost threefold that observed in the general population in Brazil supporting that this population is at higher risk for HCV. The findings of cocaine insufflation as a protective behavior for HCV infection in this population should be explored.     

High prevalence of genotype 4 among hepatitis C virus-infected intravenous drug users in north-eastern Poland

The aim of this study was to describe the distribution of hepatitis C genotypes among intravenous drug users in north-eastern Poland. The study group included intravenous drug users recruited at a drug treatment center and a clinic for HIV-infected patients. HCV infection was confirmed by qualitative nested RT-PCR to test for the presence of HCV RNA. Genotypes were determined by 5'UTR sequencing and comparing the results with known genotype sequences. Among 111 HCV-infected and HCV-RNA-positive intravenous drug users, the most prevalent genotypes were 1 (38.7%), 3 (37.8%), and 4 (23.4%). Most infections with genotype 4 (88.5%) were found among HCV-HIV-coinfected drug users. The study demonstrated a high prevalence of genotype 4 (23.4%) among HCV-infected Polish drug users.     

Hepatitis C virus recombinants are rare even among intravenous drug users

Systematic studies of the circulation of hepatitis C virus (HCV) recombinants in different parts of the world have been initiated only recently, and no detailed information on this subject is available. The aim of the current investigation was to determine the frequency of HCV recombinants in intravenous drug users (IVDU) from two European countries. HCV RNA from serum samples was tested by RT‐PCR with primers derived from the core and NS5B regions with subsequent sequencing and genotype assignment. The 118 samples from Germany (100%) and 45 out of 47 (96%) sera from Russia demonstrated concordant genotyping results. In the two genotype discrepant sera from Russia 2k/1b recombinants were identified. In order to test the hypothesis that the individuals from the IVDU group might be multiply exposed to various genotypes, 145 out of 165 genotyped serum samples, which were found to be positive for anti‐NS4 antibodies, were serotyped with the Murex HCV serotyping kit that is based on detection of antibodies to type‐specific peptides derived from the NS4 proteins of different HCV genotypes. Discrepancy in genotype and serotype attributions was observed in 11% cases. Retesting of 99 type 1a or 3a samples with a set of type‐ and subtype‐specific primers revealed the presence of a mixed infection only in one case (1a/3a). Thus, the cases of the mixed infection with different HCV genotypes as well as the recombinant forms of HCV are very rare even in such a highly exposed group as IVDU. J. Med. Virol. 82:232–238, 2010. © 2009 Wiley‐Liss, Inc.     

Molecular epidemiology of hepatitis C among drug users in Flanders, Belgium: association of genotype with clinical parameters and with sex- and drug-related risk behaviours

The aim of this study was to determine the genotypic variation of hepatitis C among drug users in Flanders and to relate the distribution of genotypes to the characteristics of the population. Hepatitis C virus RNA (HCV-RNA) quantification and genotyping was performed on stored samples from 161 anti-HCV-positive injecting and non-injecting drug users. Information on sociodemographic status, drug-related risk behaviour and sexual risk behaviour was available for each drug user. HCV-RNA was present in 152 of 161 samples (94.4%). Genotype 1 was predominant (48.7%), followed by genotype 3 (41.2%), genotype 4 (8.8%) and genotype 2 (1.4%). In the multivariate analysis, lack of a history of injecting drug use was confirmed as a statistically significant predictor for infection with genotype 1. Predictors for infection with genotype 3 were the presence of anti-HBc antibodies and a history of injecting drug use. Being tattooed emerged as a statistically significant predictor for infection with genotype 4. The 94.4% prevalence of HCV-RNA among anti-HCV-positive drug users was considerably higher than the 54–86% chronicity rate found globally among HCV-infected patients. The results of this study suggest the existence of separate transmission networks for injecting drug users and non-injecting drug users. Finally, the results suggest that tattooing practices play a role in the spread of HCV among drug users.     

Antigenic heterogeneity of the hepatitis C virus NS4 protein as modeled with synthetic peptides

The effect of sequence heterogeneity on the immunologic properties of two strong antigenic regions of the hepatitis C virus (HCV) NS4 protein was studied by using a set of 443 overlapping 20-mer synthetic peptides. One antigenic region comprising the cleavage site between NS4a and NS4b (region 5-1-1) was modeled with peptides derived from 73 different known sequences, representing HCV genotypes 1-6. The other antigenic region, designated region 59 and located at the C-terminus of the NS4b protein, was modeled with peptides from 7 known sequences representing genotypes 1-3. All peptides were tested for antigenic reactivity by enzyme immunoassay with a panel of anti-HCV-positive serum specimens representing genotypes 1-5. The data demonstrated that immunoreactive peptides fell into two groups. One group, represented by N-terminal peptides, demonstrated genotype-independent immunoreactivity; the other group, from the central part of region 5-1-1, showed strict genotype specificity. Nineteen peptides from the genotype-independent group strongly immunoreacted with a wide range of serum samples containing antibodies to all 5 HCV genotypes. Twenty-five peptides from the genotype-specific group were found to strongly react with serum containing antibodies only to the genotype from which the peptides were derived. Similar to the N-terminal part of region 5-1-1, peptides derived from region 59 did not show genotype-specific immunoreactivity. Some peptides derived from the central part of region 59 showed very strong and broad antigenic reactivity. Thus, after examining two antigenic regions of the NS4 protein, we identified short sequences that can be used for the efficient detection of either genotype-independent or genotype-specific HCV antibodies.     

Hepatitis C virus genotypes in French blood donors

The prevalence of different hepatitis C virus (HCV) genotypes in HCV infected individuals and the relation between the HCV genotypes and the source of the infection are controversial. The aim of this study was to determine the HCV genotypes in French blood donors. Fifty-one anti-HCV positive blood donors were studied with detectable serum HCV RNA by nested polymerase chain reaction (PCR) using primers derived from the 5′ non-coding region. For genotyping HCV, we used a method based on analysis of the restriction fragment length polymorphisms (RFLP) after amplification by PCR of the HCV non-structural 5 (NS5) genome domain. Using this technique, the genotypes of 39 of the 51 blood donors (76%) were determined. Three previously described genotypes were found: 19 blood donors were infected by HCV genotype I (37%), 14 were infected by HCV genotype II (27%), 3 were infected by HCV genotype III (6%), and 3 were coinfected by two genotypes (6%). All three blood donors infected with two different genotypes were intravenous drug abusers. A past history of intravenous drug abuse was more frequent in blood donors with HCV genotype I. However, there was no difference in alanine transaminase (ALT) levels, histological lesions, and RIBA-2 patterns in blood donors infected with either HCV genotype I or HCV genotype II. These findings indicate that most HCV genotypes isolated from French blood donors belong to HCV genotype I and HCV genotype II, and that risk factors for HCV infection may differ for different genotypes of HCV. © 1995 Wiley-Liss, inc.     

Molecular epidemiology of hepatitis C infection in cyprus: Evidence of polyphyletic infection

The genetic diversity of the hepatitis C virus (HCV) in Cyprus is investigated for the first time in this study. Nucleotide sequence analysis of the CORE‐E1 and NS5B regions of the HCV genome was performed on blood plasma samples obtained from 77 HCV patients in Cyprus, collected during 2005–2008. The amplified products were sequenced and compared to reference HCV strains of known genotype and subtype in order to classify the isolates found in this study. Genotype could be determined for all strains, and subtype for all but four isolates. Phylogenetic analysis revealed that 51 patients were genotype 1, of which 38 were subtype 1b, 9 were 1a, and 1 was unclassified, one patient was genotype 2c, 13 were genotype 3a, nine were genotype 4, of which six were subtype 4a, and three were of unclassified subtype, one was genotype 5a, two patients seem to carry a possible 2k/1b recombinant strain, and no genotype 6 strains were found. This study demonstrated a genetic heterogeneity of HCV infection in Cyprus, with five of the six known HCV genotypes on the island, including unclassified isolates in genotypes 1 and 4, and also the apparent introduction of the 2k/1b recombinant strain in intravenous drug users. J. Med. Virol. 81:238–248, 2009. © 2008 Wiley‐Liss, Inc.     

Hepatitis C infection among intravenous drug users attending therapy programs in Cyprus

The most high‐risk population for HCV transmission worldwide today are intravenous drug users. HCV genotypes in the general population in Cyprus demonstrate a polyphyletic infection and include subtypes associated with intravenous drug users. The prevalence of HCV, HBV, and HIV infection, HCV genotypes and risk factors among intravenous drug users in Cyprus were investigated here for the first time. Blood samples and interviews were obtained from 40 consenting users in treatment centers, and were tested for HCV, HBV, and HIV antibodies. On the HCV‐positive samples, viral RNA extraction, RT‐PCR and sequencing were performed. Phylogenetic analysis determined subtype and any relationships with database sequences and statistical analysis determined any correlation of risk factors with HCV infection. The prevalence of HCV infection was 50%, but no HBV or HIV infections were found. Of the PCR‐positive samples, eight (57%) were genotype 3a, and six (43%) were 1b. No other subtypes, recombinant strains or mixed infections were observed. The phylogenetic analysis of the injecting drug users' strains against database sequences observed no clustering, which does not allow determination of transmission route, possibly due to a limitation of sequences in the database. However, three clusters were discovered among the drug users' sequences, revealing small groups who possibly share injecting equipment. Statistical analysis showed the risk factor associated with HCV infection is drug use duration. Overall, the polyphyletic nature of HCV infection in Cyprus is confirmed, but the transmission route remains unknown. These findings highlight the need for harm‐reduction strategies to reduce HCV transmission. J. Med. Virol. 82:263–270, 2010. © 2009 Wiley‐Liss, Inc.     

The effects of widespread methadone treatment on the molecular epidemiology of hepatitis C virus infection among injection drug users in Hong Kong

The distribution of HCV genotypes among injection drug users in Hong Kong was assessed in context of methadone treatment availability. Three time periods were defined by the year of initiating injection-on or before 1980, 1981-1994, and 1995-2006-with methadone becoming widely available since the second period. Of the 273 HCV RNA-positive cases, the most prevalent subtype was HCV 6a (52.4%), followed by HCV 1b (38.5%). The new variants of HCV subtypes 6e and 6h were detected. Both subtypes 1b and 6a were prevalent among older injectors, while subtype 3a was more common in young injectors and those initiating injection recently during the third time period. Age (P < 0.05) and recent injection frequency (P < 0.01) were independently associated with HCV 6a infection. Subtype 1b was predominant in the first period, whereas 6a was more common in the second and third. Subtype 1b sequences appeared to have originated at two positions on the phylogenetic tree, while 6a showed a more disperse distribution suggestive of multiple introductions. Phylogenetic analysis on the NS5B region did not reveal specific clustering of any subtype/genotype. Overall, there was no suggestion of outbreaks of HCV. The extensive use of methadone may have protected Hong Kong from the emergence of HCV clusters among injection drug users.     

Determining the source of nosocomial transmission in hemodialysis units in Tunisia by sequencing NS5B and E2 sequences of HCV

Hepatitis C virus infection is a significant problem in hemodialysis units. HCV is very variable genetically with six genotypes. Clinical and epidemiological investigation of a new infection requires the determination of both the genotype and the strain of the HCV involved. A prospective, epidemiologic study of 395 dialysis patients in Tunisia was conducted from November 2001 to November 2003 to identify the source of nosocomial transmission using phylogenetic analysis of NS5b and E2 sequences. Hepatitis C infection was diagnosed by screening for anti-HCV antibodies and HCV RNA in sera using third generation ELISA and a qualitative RT-PCR assay. HCV strains were genotyped by sequencing the NS5b region. The genetic relatedness of the HCV strains was studied by sequencing the NS5b and the HVR-1 regions of the HCV genome. Two de novo cases of HCV infection were detected during the follow-up. One of them has been described previously. The case described in this study occurred in a center in which 12 patients were already infected with HCV strains belonging to genotypes 1b (n = 8) and 1a (n = 4). Phylogenetic analysis of the NS5b region from the HCV strains circulating in this center disclosed four clusters, confirmed by analysis of the HVR-1 region, providing strong evidence for nosocomial infection. Epidemiological data showed that these patients were dialyzed during the same shift and in the same area. Phylogenetic analysis of NS5b sequences is useful for determining the HCV genotype and providing evidence of nosocomial transmission.     

Predominance of HCV type 2a in saliva from intravenous drug users

Paired serum and saliva samples were collected simultaneously from 50 intravenous drug users with serologically proven hepatitis C virus infection. The oral health of the volunteers was also assessed. Hepatitis C virus RNA was detected by nested PCR, employing primers from the 5′ non-coding region. Positive PCR products were sequenced using the Sequenase PCR Product Sequencing Kit (Amersham Life Sciences). HCV RNA was detected in 33 (66%) of the 50 serum samples. HCV RNA was detected in 19 (57.6%) of the corresponding 33 saliva samples. There was no correlation between oral health status or HIV seropositivity and the detection of HCV in saliva. However, subjects with HCV in their saliva were significantly more likely to complain of xerostomia (P < 0.05). Isolate genotypes were identified in paired serum and saliva of 15 intravenous drug users. HCV genotypes 1, 2, 3 and 6 were detected in both specimens. In seven cases, a differing HCV genotype was found in serum compared to the paired saliva specimen. The distributions of genotypes in serum and saliva were very different, with genotype 2a more common in saliva than serum (P < 0.005). These data suggest that in some cases the source of salivary HCV may not be serum transudation along the periodontal membrane or across damaged mucosa, and that an alternative local source, possibly the salivary glands themselves, should be considered. J. Med. Virol. 54:271–275, 1998. © 1998 Wiley-Liss, Inc.     

Evaluation of a multiple peptide assay for typing of antibodies to the hepatitis C virus: Relation to genomic typing by the polymerase chain reaction

A panel of 16 type-specific synthetic peptides corresponding to variable antigenic regions within the hepatitis C virus (HCV) core, nonstruc-tural 4 (NS4), and NS5 proteins was synthesised. The peptide panel was used to develop an enzyme immunoassay (EIA) for the detection of antibodies directed to HCV type 1 (genotypes I/1a and II/1 b), type 2 (genotypes III/2a and IV/2b), and type 3 (genotype V/3). The peptides corresponded to residues 68–81 of the HCV core (types 1,2, and 3), residues 1692–1705 and 1710–1728 of HCV NS4 (types 1 a, 1 b, 2a, 2b, and 3), and residues 2303–2319 of HCV NS5 (types 1a, 1b, 2a, and 2b). The 16-peptide panel was evaluated using human sera from 46 carriers of HCV, which were genotyped in parallel by the polymerase chain reaction (PCR) using primers specific for types I, II, III, IV, and V of HCV core. Of the 46 carriers, 14 (30%) were infected by HCV genotype I, 7 (15%) by genotype II, 16 (35%) by HCV genotype IV, and 6 (13%) by HCV of genotype V. Two carriers had double infections of types I and II, and the HCV strain of one carrier could not be genotyped. Using the serotyping system, 40 (89%) out of the 45 genotyped carriers were found to contain type-specific antibodies corresponding to the genotypes identified by PCR. In 5 of the 23 carriers infected by genotypes I and/or II, antibodies specific for HCV type 1 could not be detected, whereas all 16 carriers infected by genotype IV were serologically typed as type 2. Out of the six carriers infected by HCV of genotype V, all were found to have antibodies of serotype 3, but in most cases together with antibodies to NS5 type 1, indicating sequence homologies between types 1 and 3 of this NS5 region. In the one patient serum where the HCV strain could not be genotyped, a mixture of types 1, 2, and 3 antibodies were found. In conclusion, a serotyping system with a sensitivity and specificity of 89% was developed. It is confirmed that at least three distinct serotypes of antibodies to HCV exist. The major advantage of using four different antigenic regions is that we often obtain high absor-bance values which are easily interpreted, or multiple reactions which confirm each other. © 1995 Wiley-Liss, Inc.