Shift in predominating subtype of HCV from 1b to 3a in St. Petersburg mediated by increase in injecting drug use

Epidemiology and Genotype Distribution of Hepatitis C Virus in Russia

The hepatitis C virus (HCV) causes both acute and chronic infection of the liver that can lead to liver cirrhosis, cancer, and liver failure. HCV is characterized by high genetic diversity and substantial variations in the prevalence of specific HCV genotypes throughout the world. Many effective regimens of direct-acting antivirals (DAAs), including pan-genotypic, can successfully treat HCV infection. Additionally, genotype-specific treatments for HCV are being actively employed in national plans for eliminating HCV infection around the world. The evaluation of HCV genotype prevalence in a given country is necessary for the successful implementation of the HCV elimination plans and for allocating financial resources to the DAAs which are the most effective against those specific HCV genotypes prevalent in a given country. Here, we analyzed HCV genotypes, subgenotypes, and recombinants in 10,107 serum samples collected in 2015-2017 from patients with chronic HCV infection living in all federal districts of Russia. This is the first and largest evaluation of HCV genotypes performed on samples from all territories of Russia, from its Central federal district to the Far East. Moreover, we have updated retrospective epidemiological analysis of chronic and acute HCV infection in Russia from 2001 to 2021. We demonstrate that the incidence of acute HCV (AHC) infection in Russia decreased from 16.7 cases per 100,000 people in 2001 to 0.6/100,000 in 2021. The number of cases of chronic HCV (CHC) infection also decreased from 29.5 to 16.4 per 100,000 people during this period. The HCV genotype analysis indicated that HCV genotype 1 dominates in Russia (53.6%), while genotypes 3 and 2 were detected in 35.4% and 7.8% of patients, respectively. These proportions are virtually identical in all regions of Russia except for the Far East, where HCV genotype 2 was detected in only 1% of the samples. HCV genotypes 1 and 2 are more widespread in women, and HCV genotype 3 in men. Genotype 3 was the most prevalent in 31-40-year-olds (44.9%), and genotype 1 was most prevalent in those over 70 years of age (72.2%). HCV genotype 2 was predominant among HCV-infected persons older than 40 years. Discriminating between HCV genotype 2 and recombinant RF1_2k/1b, which are frequently misclassified, is important for successful antiviral treatment. For the first time, we demonstrate, here, countrywide prevalence of HCV RF1_2k/1b in different regions of Russia. HCV RF1_2k/1b makes up 3.2% of HCV genotypes, reaching 30% among samples classified as genotype 2 by some commercial genotyping tests. The highest proportion of HCV RF1_2k/1b was detected in the North-West (60%), Southern (41.6%), and Central (31.6%) federal districts; its frequency in the Far Eastern and North Caucasus districts was ~14.3%. HCV RF1_2k/1b, and it was not detected in the Volga, Ural, or Siberian districts. To conclude, this is the first and most complete evaluation of HCV epidemiology and genotype/subgenotype distribution in Russia.

Frequency of Hepatitis C Virus Genotypes in Patients Who Had Hepatocellular Carcinoma in Gastroenterological Hospitals of Tabriz

BACKGROUND

Generally, hepatitis C has been identified as one of the major health issues that about 3% of the world's population have been threatened and affected by it (about 170 million people), and also, it can be considered a factor in acute and chronic hepatitis.

METHODS

The aim of this study is to determine the prevalence of HCV genotypes in Azerbaijan patients. In this study, sampling was done on the referred patients to the hospitals (Mahallati and Behbud Hospital). RNA was extracted after isolation of plasma, and then, after the synthesizing of cDNA, the sample was carried out to the laboratory for performing the real-time PCR in order to determine the genotypes.

RESULTS

The evaluation of HCV genotypes in positive plasma samples showed that dominant subsets were remarkable and the mean age of the patients was 37/3 ± 11/8 (in the age range of 2-63). Among the 235 patients,139 of them (59%) were male. Statistically, the average number of women was more than men (T test, P < 0/05). 1b genotype was reported 70% in the patients above 40 years old, and also, it was reported as 71/6% in the patients under 40 years old that was not statistically significant. The incidence of serotype 3a was higher among the patients younger than 40 years old (3a was 18.1% vs. 15%), and this serotype was prevalent among men (3a was 18.7% vs. 14.6%), which was statistically significant.

CONCLUSION

The findings indicate that among Azerbaijan's patients with chronic hepatitis C, genotypes 1b (71.1%) and 3a (17%) were dominant.

Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage

Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n = 109) sampled in ninteen countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.

Glecaprevir/pibrentasvir in patients with chronic HCV and recent drug use: An integrated analysis of 7 phase III studies

BACKGROUND

Injection drug use is the primary mode of transmission for hepatitis C virus (HCV), and treatment guidelines recommend treating HCV-infected people who use drugs; however, concerns about adherence, effectiveness, and reinfection have impeded treatment uptake.

METHODS

Data were pooled from seven phase III trials that evaluated the efficacy and safety of 8 or 12 weeks of glecaprevir/pibrentasvir (G/P) in patients chronically infected with HCV genotypes 1-6. Patients had compensated liver disease, with or without cirrhosis, and were HCV treatment-naïve or -experienced with interferon or pegylated interferon ± ribavirin, or sofosbuvir plus ribavirin ± pegylated interferon. Patients were grouped into recent drug users (injection drug use ≤12 months before screening, positive urine drug screen [UDS], and/or drug-related adverse event), former drug users (>12 months before screening and negative UDS), or non-drug users. Assessments included sustained virologic response at 12 weeks posttreatment (SVR12), treatment adherence, and safety.

RESULTS

Among 1819 patients, 5%, 34%, and 61% were recent, former, and non-drug users, respectively. Treatment adherence and completion were high (≥96%) regardless of drug use status. SVR12 was achieved by 93% (n/N = 91/98), 97% (n/N = 591/610), and >99% (n/N = 1106/1111) of recent, former, and non-drug users, respectively (intention-to-treat analysis). The overall rates of virologic failure were ≤1.5% across all three subpopulations, with no HCV reinfections among recent drug users. Drug-related serious adverse events and adverse events leading to treatment discontinuation were experienced by ≤1% of patients.

CONCLUSIONS

G/P is a well-tolerated and efficacious pangenotypic regimen for chronic HCV-infected people with recent or active drug use.

Management of acute HCV infection in the era of direct-acting antiviral therapy

The management of acute HCV infection has not been standardized following the availability of direct-acting antiviral agents (DAAs) for chronic HCV infection, and substantial uncertainty exists regarding the optimal treatment regimen and duration. Despite the lack of direct evidence, the 2016 American Association for the Study of Liver Diseases (AASLD)-Infectious Diseases Society of America (IDSA) guidelines supported "the same regimens for acute HCV as recommended for chronic HCV infection … owing to high efficacy and safety", whereas the 2016 European Association for the Study of the Liver (EASL) guidelines recommended sofosbuvir-ledipasvir, sofosbuvir-velpatasvir or sofosbuvir plus daclatasvir for 8 weeks in acute HCV infection, with a longer duration of 12 weeks recommended for those infected with HIV and/or baseline HCV RNA levels >1,000,000 IU/ml. This Review outlines the epidemiology, natural history and diagnosis of acute HCV infection and provides contemporary information on DAAs for acute and recent HCV infection. The Review also discusses the 2016 AASLD-IDSA and EASL recommendations for acute HCV infection management in light of available evidence and highlights key differences in study populations and design that influence interpretation. We focus on populations at high risk of HCV transmission and acquisition, including people who inject drugs and HIV-positive men who have sex with men, and highlight the potential effects of diagnosis and treatment of acute HCV infection in contributing to HCV elimination.

Hepatitis C virus subtype 3a was introduced in the USSR in the early 1980s

A total of 2120 nucleotide sequences of the NS5b region of HCV subtype 3a were analysed, including 310 strains derived from former republics of the USSR (Azerbaijan, Estonia, Lithuania, Russia, Tajikistan and Uzbekistan). Among the viral isolates collected from former regions of the Soviet Union, 294 strains formed 3 sustained phylogenetic clusters, with each having a common origin. Phylodynamic analysis demonstrated that the most recent common ancestors of the current strains inside the three clusters were introduced into the USSR population in 1981±1, 1984±2 and 1985±2, respectively (the confidence intervals were calculated using Student's t-distribution, P<0.05). The time estimation obtained for HCV subtype 3a correlated well with the historical and epidemiological context of this period, and in particular with the start of widespread injection drug use in the USSR in the first half of the 1980s.

Hepatitis C virus genotype 3A in a population of injecting drug users in Montenegro: Bayesian and evolutionary analysis

Few reports are available on HCV molecular epidemiology among IDUs in Eastern Europe, and none in Montenegro. The aim of this study was to investigate the HCV genotype distribution in Montenegro among IDUs and to perform Bayesian and evolutionary analysis of the most prevalent HCV genotype circulating in this population. Sixty-four HCV-positive IDUs in Montenegro were enrolled between 2013 and 2014, and the NS5B gene was sequenced. The Bayesian analysis showed that the most prevalent subtype was HCV-3a. Phylogenetic data showed that HCV-3a reached Montenegro in the late 1990s, causing an epidemic that exponentially grew between the 1995 and 2005. In the dated tree, four different entries, from 1990 (clade D), 1994 (clade A) to 1999 (clade B) and 2001 (clade C), were identified. In the NS5B protein model, the amino acids variations were located mainly in the palm domain, which contains most of the conserved structural elements of the active site. This study provides an analysis of the virus transmission pathway and the evolution of HCV genotype 3a among IDUs in Montenegro. These data could represent the basis for further strategies aimed to improve disease management and surveillance program development in high-risk populations.

Enhancing the detection and management of acute hepatitis C virus infection

Acute HCV infection refers to the 6-month period following infection acquisition, although this definition is somewhat arbitrary. While spontaneous clearance occurs in approximately 25%, the majority will develop chronic HCV infection with the potential for development of cirrhosis, end stage liver disease and hepatocellular carcinoma. Detection of acute HCV infection has been hampered by its asymptomatic or non-specific presentation, lack of specific diagnostic tests and the inherent difficulties in identifying and following individuals at highest risk of transmitting and acquiring HCV infection, such as people who inject drugs (PWID). However, recognition of those with acute infection may have individual and population level benefits and could represent an ideal opportunity for intervention. Despite demonstration that HCV treatment is feasible and successful in PWID, treatment uptake remains low with multiple barriers to care at an individual and systems level. Given the burden of HCV-related disease among PWID, strategies to enhance HCV assessment, treatment and prevention in this group are urgently needed. As the therapeutic landscape of chronic HCV management is revolutionised by the advent of simple, highly effective directly-acting antiviral (DAA) therapy, similar opportunities may exist in acute infection. This review will discuss issues surrounding improving the detection and management of acute HCV infection, particularly in PWID.

Mixed HCV infection and reinfection in people who inject drugs--impact on therapy

The majority of new and existing cases of HCV infection in high-income countries occur among people who inject drugs (PWID). Ongoing high-risk behaviours can lead to HCV re-exposure, resulting in mixed HCV infection and reinfection. Assays used to screen for mixed infection vary widely in sensitivity, particularly with respect to their capacity for detecting minor variants (<20% of the viral population). The prevalence of mixed infection among PWID ranges from 14% to 39% when sensitive assays are used. Mixed infection compromises HCV treatment outcomes with interferon-based regimens. HCV reinfection can also occur after successful interferon-based treatment among PWID, but the rate of reinfection is low (0-5 cases per 100 person-years). A revolution in HCV therapeutic development has occurred in the past few years, with the advent of interferon-free, but still genotype-specific regiments based on direct acting antiviral agents. However, little is known about whether mixed infection and reinfection has an effect on HCV treatment outcomes in the setting of new direct-acting antiviral agents. This Review characterizes the epidemiology and natural history of mixed infection and reinfection among PWID, methodologies for detection, the potential implications for HCV treatment and considerations for the design of future studies.

Genotyping of hepatitis B and C virus Russian isolates for reference serum panel construction

Approximately 2% and 5% of the world human population is estimated to be infected with HCV and HBV, respectively. Reference panels of HCV and HBV serum samples with defined genotypes and serotypes is necessary for monitoring of the specificity and sensitivity of diagnostic test kits. The aim of this study was to determine genotypes/serotypes of HBV and HCV circulating in Russia in order to construct a panel of reference sera containing these HCV genotypes and HBV serotypes. A total of 343 HBsAg-positive and 207 anti-HCV positive serum samples were collected from patients with HBV and HCV infection from different cities between years 2002 and 2010 in St. Petersburg, Krasnodar, Nizhny Novgorod, Novosibirsk, Barnaul, Gorno-Altaisk, and Khabarovsk. HBV DNA was found in 76.4% of HBsAg positive samples by PCR for the S gene and HCV RNA was found in 71.5, 70.0, and 64.7% of anti-HCV positive samples in the 5'UTR, Core, and NS5B regions, respectively. The prevalence and proportion of HBV genotype/serotype associations were as follows: A/adw2, 2.1%; D/ayw2, 54.0%; D/ayw3, 43.1%; D/adw2, 0.7%. A new combination of genotype D and adw2 serotype was discovered. The distribution of HCV genotypes was the following: 43.6%, b; 3.8%, 2a; and 52.6%, 3a. Russian National reference panels of HBV and HCV lyophilized sera were developed to monitor specificity and sensitivity of approved kits and for the certification of newly developed assays.

Phylogenetic analysis of hepatitis C virus strains and risk factors associated with infection and viral subtypes among Iranian patients

Hepatitis C virus (HCV) has infected approximately 170 million people worldwide. While the seroprevalence of anti-HCV antibody among Iranian blood donors is 0.13%, HCV infection is prevalent in 59-80% of Iranian injecting drug users. One hundred seventy-eight anti-HCV positive patients were referred to the Gastroenterology Department at the Taleghani Hospital (Tehran, Iran) between June 2007 and June 2012. Out of 178 samples, 142 were positive for HCV-RNA. HCV subtypes were determined using phylogenetic analysis of the NS5B or 5'UTR/core regions. Of 142 viremic patients, 71 (50%) were infected with HCV subtype 1a, 43 (30.3%) with subtype 3a, 20 (14.1%) with subtype 1b, 3 (2.1%) with subtype 4d, 2 (1.4%) with subtype 4a, 1 (0.7%) with subtype 2b, and 1 (0.7%) with subtype 6a. Interestingly, genetic analysis of a sub-genomic fragment from one patient identified a non-subtypeable HCV genotype-3 strain. There was a significant association between HCV subtype and a history of injecting drug use (P = 0.003). Subtype 3a was predominant among patients with such a history. Injecting drug use was associated with younger age (P < 0.001). HCV subtype was also significantly associated with a history of upper gastrointestinal endoscopy (P = 0.02). Subtype 1a was more frequent among patients with such a history. In addition, history of upper gastrointestinal endoscopy was significantly associated with older age (P = 0.002). In conclusion, while HCV subtype 1a is predominant among infected Iranian individuals, subtype 3a is predominant among Iranian injecting drug users.

Acute hepatitis C: management in the rapidly evolving world of HCV

The acute phase of hepatitis C (HCV) infection is typically defined as the initial 6 months following exposure to the virus; however, in some individuals, the acute phase of the infection can last much longer (Orland et al. Hepatology 33:321-27, 2001). Although some patients have symptoms of acute hepatitis, most infected individuals are entirely asymptomatic. As a result, many patients are unaware of the infection until it progresses to chronic infection, and may not develop symptoms until decades later with the onset of decompensated cirrhosis or hepatocellular carcinoma (HCC). A substantial proportion (20-40%) of infected patients clear the virus during the acute phase. Interferon-based treatment is also much more likely to be successful in the acute phase of infection but is relatively poorly tolerated. Therefore, recognition of acute HCV infection is critical to prioritize those patients who do not spontaneously clear the infection for immediate therapy. However, the promise of highly effective well-tolerated all-oral therapies in development may alter the management approach. This review will focus on the epidemiology, natural history, diagnosis, and treatment of acute HCV infection.

Distribution of hepatitis C virus genotypes among azerbaijani patients in capital city of iran-tehran

BACKGROUND

Determination of the Hepatitis C virus (HCV) genotype distributed in a particular area has an important role on public health throughout the world.

OBJECTIVES

The aim of this study was to determine the frequency of HCV genotypes in Azerbaijani patients.

PATIENTS AND METHODS

From March 2010 until March 2012, 235 Azerbaijani patients with established chronic hepatitis C, referred to Hospitals related to Iran University of Medical Sciences and Tehran Hepatitis Center, Clinical department of Baqiyatallah Research Center for Gastroeneterology and Liver Disease, were enrolled in this cross sectional study. About 5 mL of peripheral blood was collected from patients and after separation of plasma, viral RNA extracted. HCV-RNA were amplified by RT-nested PCR using primers from the 5´-UTR and genotyped by RFLP assay, and then HCV genotypes were confirmed using sequencing of cloned PCR products into pJET1.2/blunt cloning vector.

RESULTS

HCV genotyping of positive plasma samples demonstrated that predominant HCV subtype was noted for 1b (71.1%) followed by subtype 3a (17.0%), genotype 2 (6.8%), 1a (1.7%), and mixed infection (3.4%). The mean ± SD age of patients was 37.3 ± 11.8 (range: 2-63) years. Out of 235 patients, 139 (59.1%) were male. The frequency of HCV subtype 3a was higher in patients under 40 years old (3a: 18.1% vs. 15.0%), and subtype 3a was higher in male patients (3a: 18.7% vs. 14.6%).

CONCLUSIONS

The current study shows that the predominant HCV genotype among Azerbaijani patients with established chronic hepatitis C is subtype 1b (71.1%) followed by subtype 3a (17.0%).

Prevalence of hepatitis C virus genotypes in risk groups in the Republic of Macedonia: a 5 years survey

The prevalence of hepatitis C virus (HCV) genotypes depends on geographical location. HCV genotyping is important for epidemiological investigations and treatment management. The aim of this study was to determine the HCV genotype prevalence in the most prominent risk groups in the Republic of Macedonia in the last 5 years and to evaluate its association with patient's age, gender, and mode of transmission. A total of 1,167 HCV positive patients, divided into three risk groups (intravenous drug use, chronic hemodialysis, and other risk factor), were genotyped using an in-house ASO hybridization method with genotype-specific oligonucleotide probes. The genotypes 1, 2, and 3 were present with 52.2%, 0.6%, and 47.0%, respectively. Genotype 1 was most prevalent in hemodialysis (89.0%) and other risk factor group (53.8%). It was found associated independently with hemodialysis, age >40 and female gender. Genotype 3 predominated in intravenous drug users (64.0%) and was associated significantly also with age ≤40 and male gender. Multivariable logistic regression analysis pointed out hemodialysis (P < 0.0001, Exp (B) = 12.0) as a positive predictor factor for genotype 1 and age ≤40 (P = 0.021, Exp (B) = 1.8) and intravenous drug use (P < 0.0001, Exp (B) = 8.4) as a positive predictor factors for genotype 3. In conclusion, the main transmission route of HCV infection in the Republic of Macedonia is intravenous drug use, followed by hemodialysis. HCV genotypes 1 and 3 dominate in these two most prominent risk groups in the Republic of Macedonia.

A new subtype of hepatitis C virus genotype 3: analysis of available evidence

BACKGROUND

Hepatitis C virus (HCV) is one of the leading causes of chronic liver disease. Seven genotypes and more than 80 subtypes have been identified for HCV so far. To date, 10 subtypes (3a to 3i; and 3k) of HCV genotype 3 have been identified. In 2006, two HCV isolates were reported from Iran that belonged to a new subtype of genotype 3. However, considering the consensus proposal for HCV genotype nomenclature, the available sequences of the new subtype did not correspond to the regions that are required to be analyzed prior to subtype assignment. During a study on the molecular epidemiology of HCV in Iran, an HCV isolate (FSM165) which seemed to belong to a new subtype of genotype 3 was obtained from a patient residing in Tehran, Iran.

OBJECTIVES

The aim of this study was to assess the relatedness of isolate FM165 together with several sequences retrieved from the database to the new HCV-3 subtype reported from Iran in 2006.

MATERIALS AND METHODS

Various parts of the genome including the core/E1 region and two segments of the NS5B region were amplified and sequenced for isolate FSM165. Furthermore, using the Basic Local Alignment Search Tool (BLAST), the HCV database was searched for sequences that had a high level of similarity with sequences of FSM165 isolate and such sequences were retrieved from the database. To investigate the relatedness of isolate FSM165 and also the retrieved sequences to a new HCV-3 subtype reported previously, phylogenetic analyses were performed using the Kimura two-parameter model and the neighbor joining method.

RESULTS

Phylogenetic analysis of the partial NS5B region demonstrated the relatedness of isolate FSM165 to the new subtype reported from Iran in 2006. Moreover, some core/E1 and NS5B sequences that had a high level of similarity with FSM165 isolate were found through searching the HCV database. These sequences were previously either misclassified or could not be accurately classified. Phylogenetic analyses showed that all of the described sequences belonged to the new subtype of HCV genotype 3.

CONCLUSIONS

Data suggests that the new subtype has a vast geographical distribution in Iran. The core/E1 and the NS5B sequences described in this paper can be used as references for the new HCV-3 subtype in future studies.

Prevalence and associated clinical characteristics of hepatitis B, C, and HIV infections among injecting drug users in Korea

Injecting drug use is associated with an increased risk of blood-borne viral infections, such as hepatitis B and C viruses (HBV and HCV, respectively) and human immunodeficiency virus (HIV). However, their prevalence, virological characteristics, and associated factors are not clear among the injecting drug users in Korea. The aim of this study was to determine the prevalence of HBV, HCV, and HIV infection, as well as their virological and clinical characteristics of injecting drug users in South Korea. Between 2007 and 2010, 318 injecting drug users (89.3% male; mean ± age 41.9 ± 8.15 years) were participated. While HIV infection was not found, the seroprevalence of anti-HCV and HBV surface antigen (HBsAg) was 48.4% (n = 154) and 6.6% (n = 21), respectively. HBV/HCV co-infection was found in 4.1% (n = 13). Occult HBV infection was suggested in 5.0% (n = 16). Among the HCV genotypes, 1b (37.7%) and 2a/2c (35.7%) were mostly often detected. HCV RNA was detected in 98.1% (n = 151/154) and high-level viremia (HCV RNA level, ≥400,000 IU/ml) were observed in 59.6% (n = 90/151). In multiple logistic regression analysis, old age (OR 1.18 per year, 95% CI = 1.09-1.27) and ever-sharing injecting equipment (OR 4.17, 95% CI = 1.39-12.45) independently predicted HCV mono-infection. The prevalence of HBV and HCV infection were high but largely undiagnosed in the present sample of Korean injecting drug users. Strategic prevention, screening, and treatment are needed to reduce further transmission and morbidity.

Molecular epidemiology of hepatitis C virus among injection drug users in Iran: a slight change in prevalence of HCV genotypes over time

Injecting drug users (IDUs) are the main at-risk population for hepatitis C virus (HCV) transmission. We studied HCV infection, risk factors, and genotype distribution in relation to the year of first injection among Iranian IDUs. Of a total of 126 specimens positive for HCV antibody, 93 (74 %) had detectible HCV RNA, and the NS5B gene was sequenced for 83, with genotype 3a (n = 48, 58 %) being predominant, followed by 1a (n = 35, 42 %). Tattooing was an independent predictor for HCV infection. No significant difference was found between HCV genotypes and IDU characteristics. Although there was no change in the distribution of prevalent genotypes before and after 1997, a slight variation in the prevalence was observed (p = 0.71). The difference in the prevalence of subtypes 1a and 3a (9.1 % in the period 1984-1996 and 18.2 % in the period 1997-2009) during 25 years was 9.1 %. These findings indicate a high prevalence of HCV infection among Iranian IDUs and highlights HCV-3a as the most prevalent subtype for the past 25 years. Harm-reduction strategies appear to be the most important measures to reduce the transmission of HCV in Iran.

Origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b

Since its initial identification in St. Petersburg, Russia, the recombinant hepatitis C virus (HCV) 2k/1b has been isolated from several countries throughout Eurasia. The 2k/1b strain is the only recombinant HCV to have spread widely, raising questions about the epidemiological background in which it first appeared. In order to further understand the circumstances by which HCV recombinants might be formed and spread, we estimated the date of the recombination event that generated the 2k/1b strain using a Bayesian phylogenetic approach. Our study incorporates newly isolated 2k/1b strains from Amsterdam, The Netherlands, and has employed a hierarchical Bayesian framework to combine information from different genomic regions. We estimate that 2k/1b originated sometime between 1923 and 1956, substantially before the first detection of the strain in 1999. The timescale and the geographic spread of 2k/1b suggest that it originated in the former Soviet Union at about the time that the world's first centralized national blood transfusion and storage service was being established. We also reconstructed the epidemic history of 2k/1b using coalescent theory-based methods, matching patterns previously reported for other epidemic HCV subtypes. This study demonstrates the practicality of jointly estimating dates of recombination from flanking regions of the breakpoint and further illustrates that rare genetic-exchange events can be particularly informative about the underlying epidemiological processes.

Prevalence and risk factors of HCV infection in Poland

BACKGROUND

According to small studies carried out in preselected populations, the estimated prevalence of anti-hepatitis C virus (HCV) antibodies in Poland ranges from 0.6 to 2.1%.

AIMS

The aim of this study was to evaluate the prevalence of anti-HCV and HCV RNA among patients and healthcare workers.

METHODS

Anti-HCV antibodies were measured (Elecsys, Roche) in serum samples from 26,057 adults, consecutive patients or healthcare workers, from hospitals and out patient clinics not involved in the management of liver diseases. The majority of them (18,233) consented to fill out an anonymous questionnaire related to possible risk factors for HCV infection. Anti-HCV-positive samples were assessed for HCV RNA (Cobas Amplicor, Roche). A multivariate logistic regression model and the χ² test or the Fisher's exact test were applied.

RESULTS

Anti-HCV antibodies were detected in 1.9% of individuals, and 31% of them demonstrated HCV RNA, which varied from 26% in hospitals to 66% in specialistic out-patient clinics. Prevalence of anti-HCV was significantly lower in healthcare workers (1.42%) than in patients (1.92%). Significant independent risk factors for anti-HCV positivity were as follows: male sex, more than three hospitalizations in a lifetime, blood transfusions before 1992, and intravenous drug use. The only significant risk factor for HCV RNA was intravenous drug use. An analysis carried out for multispecialistic hospitals demonstrated significantly lower prevalence of HCV RNA positivity in healthcare workers.

CONCLUSION

Prevalence of anti-HCV in the Polish population studied was up to 1.9%, but active infection could be diagnosed in only 31% of them. Intravenous drug use, blood transfusions before 1992, multiple hospitalizations, and male sex increase the risk of HCV infection.

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.

Molecular analysis of hepatitis C virus infection in Bulgarian injecting drug users

Intravenous drug users constitute a group at risk for hepatitis C virus (HCV) infection. Today, no data are available on the molecular epidemiology of HCV in Bulgaria despite the fact that in recent years the incidence of acute hepatitis C infection among Bulgarian intravenous drug users increased sixfold and about 2/3 of them developed a chronic infection. The aim of this study was to determine the circulation of hepatitis C genotypes among drug users and to study the evolution and transmission history of the virus by molecular clock and Bayesian methods, respectively. Sequencing of NS5B gene showed that the genotype 3a was the most prevalent type among intravenous drug users. In the Bayesian tree, the 3a subtypes grouped in one main clade with one small cluster well statistically supported. The root of the tree was dated back to the year 1836, and the main clade from Bulgaria was dated 1960. The effective number of infections remained constant until about years 1950s, growing exponentially from the 1960s to the 1990s, reaching a plateau in the years 2000. The not significant intermixing with isolates from other countries may suggest a segregated circulation of the epidemic between 1940s and 1980s. The plateau reached by the epidemic in the early 2000s may indicate the partial success of the new preventive policies adopted in Bulgaria.

Hepatitis C virus infection among drug injectors in St Petersburg, Russia: social and molecular epidemiology of an endemic infection

AIMS

To understand the epidemiology and transmission patterns of hepatitis C virus (HCV), the predominant blood borne-pathogen infecting injection drug users (IDUs), in a part of the former Soviet Union.

DESIGN

Cross-sectional respondent-driven sample of IDUs.

SETTING

St Petersburg, Russia.

PARTICIPANTS

A total of 387 IDUs were recruited in late 2005 and throughout 2006.

MEASUREMENTS

Participants were surveyed to collect demographic, medical and both general and dyad-specific drug injection and sexual behaviors. A blood sample was collected to detect antibodies to hepatitis C and to amplify viral RNA for molecular analysis. The molecular data, including genotypes, were analyzed spatially and linkage patterns were compared to the social linkages obtained by respondent-driven sampling (RDS) for chains of respondents and among the injection dyads.

FINDINGS

HCV infection was all but ubiquitous: 94.6% of IDUs were HCV-seropositive. Among the 209 viral sequences amplified, genotype 3a predominated (n = 119, 56.9%), followed by 1b (n = 61, 29.2%) and 1a (n = 25, 11.9%). There was no significant clustering of genotypes spatially. Neither genotypes nor closely related sequences were clustered within RDS chains. Analysis of HCV sequences from dyads failed to find associations of genotype or sequence homology within pairs.

CONCLUSIONS

Genotyping reveals that there have been at least five unique introductions of HCV genotypes into the IDU community in St Petersburg. Analysis of prevalent infections does not appear to correlate with the social networks of IDUs, suggesting that simple approaches to link these networks to prevalent infections, rather than incident transmission, will not prove meaningful. On a more positive note, the majority of IDUs are infected with 3a genotype that is associated with sustained virological response to antiviral therapy.

Changes in the prevalence of hepatitis C virus genotype among Italian injection drug users-relation to period of injection started

BACKGROUND

Chronic hepatitis C is a worldwide health problem. Intravenous drug users are the main risk group.

OBJECTIVES

To determine the prevalence of HCV genotypes in Italian injecting drug users and the distribution of genotypes in relation to the period when the infection was acquired.

STUDY DESIGN

Two hundred sera from patients with chronic hepatitis C and a history of intravenous drug use were assayed for HCV-RNA and genotyped by a commercial line probe assay.

RESULTS

Genotypes 1 (45.5%) and 3 (35%) were the most common genotypes, followed by genotypes 4 (15%) and 2 (3%). One genotype 5 (0.5%) was found. Two mixed infections (1%) were detected. Subtype could be determined in 160 cases (80%): subtype 3a was the most prevalent (41.3%), followed by subtypes 1a (23.1%) and 1b (20.6%). A significant change in the distribution of prevalent genotypes occurred since 1965 (p=0.020). Genotype 3 infections declined from 48/116 (41.4%) in 1965-1985 to 22/84 (26.2%) in 1986-2006. The prevalence of genotype 4 was significantly higher in patients infected after 1985 compared to patients infected before this year (11/116 [9.5%] vs. 19/84 [22.6%], respectively; p=0.018).

CONCLUSIONS

Since 1965 the common HCV genotype 3 has become less common in Italy. Genotype 4, an imported genotype, has become more common.

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.

Hepatitis C in hemodialysis patients: current global magnitude, natural history, diagnostic difficulties, and preventive measures

Hepatitis C virus (HCV) infection is a significant cause of morbidity and mortality in hemodialysis (HD) patients. The reported prevalence of HCV among the HD population has varied greatly from 1.9 to 84.6% in different countries in recent years. The length of time on HD is generally believed to be associated with HCV acquisition in HD subjects. Nevertheless, several recent reports failed to recognize any significant role of blood transfusion. Although there are some considerations about the accuracy of serologic testing in detecting HCV in HD patients, the accumulated data in this review suggest the false-negativity rate to be not more than 1.66% (153/9,220). Therefore, substituting virologic for serologic testing in the routine diagnosis of HCV infection in HD patients seems unreasonable. Several phylogenetic analyzes of viral isolates suggested nosocomial patient-to-patient transmission of HCV among HD patients for which the main potential source is believed to be contaminated hands and articles. However, isolation of HCV-infected HD patients and use of dedicated machines are currently unjustified while strict adherence to universal precautions seems to be enough to control disease spread in HD units. The present article is an update on epidemiological and clinical features of HCV in HD population.

The changing epidemiology of hepatitis C virus infection in Europe

The epidemic of hepatitis C virus (HCV) infection in Europe is continuously evolving and epidemiological parameters (prevalence, incidence, disease transmission patterns and genotype distribution) have changed substantially during the last 15 years. Four main factors contribute to such changes: increased blood transfusion safety, improvement of healthcare conditions, continuous expansion of intravenous drug use and immigration to Europe from endemic areas. As a result, intravenous drug use has become the main risk factor for HCV transmission, prevalent infections have increased and genotype distribution has changed and diversified. Hence, prevalence data from studies conducted a decade ago may not be useful to estimate the current and future burden of HCV infection and additional epidemiological studies should be conducted, as well as new preventive strategies implemented to control the silent epidemic. This review summarizes recently published data on the epidemiology of HCV infection in Europe focusing on the factors currently shaping the epidemic.

Controversies in and challenges to our understanding of hepatitis C

Discovered in 1989, the hepatitis C virus (HCV) continues to cause significant morbidity and mortality world-wide despite a huge research commitment to defining and understanding the virus and the disease it causes. This paper discusses a number of areas where progress in the management of the HCV have not kept pace with the scientific understanding of the HCV. It is suggested that in the fields of HCV prevention and providing access to treatment, practice falls short of what could be achieved. The role of alcohol in the pathogenesis of HCV liver injury is discussed. Discrimination against those with HCV infection and particularly those in prison settings fails to match good clinical practice. The complicated processes of sharing information between specialty groups is also discussed in an attempt to optimise knowledge dissemination in this field.

Molecular epidemiology of hepatitis A in St. Petersburg, Russia, 1997-2003

The molecular epidemiology of hepatitis A virus (HAV) strains circulating in the St. Petersburg and Karelia regions was studied during 1997-2003. Hepatitis A virus RNA was isolated from both clinical samples (stools or sera) and environmental samples (sewage water). RT-PCR was carried out using different primer pairs from the VP1/2A and VP1 genomic regions, the variable parts of the HAV genome. PCR products were sequenced and 306 nucleotides from the VP1/2A and 332 nucleotides from the VP1 region were used for phylogenetic analysis. The results show that the IA subtype was the most common during the follow-up period: >90% of the isolated HAV strains belonged to that subtype. The HAV strains found in intravenous drug users belonged to subtypes IA and IIIA. Only one out of a total of 88 sequenced strains was of the IB subtype. The subtypes IB and IIIA were found only in 2001-2003, which suggests that new strains were introduced into the endemic situation. The results indicate the usefulness of molecular epidemiological methods in studying changes in the circulating HAV strains and in tracing transmission routes.

Genetic characterization of hepatitis C virus strains in Estonia: fluctuations in the predominating subtype with time

During the last decade, there has been a dramatic increase in intravenous drug use in young adults in Estonia with an increased incidence of both hepatitis B and C as a consequence. Since genetic data are limited regarding hepatitis C virus (HCV) strains in Estonia, the aim of the study was to characterize HCV strains in different risk groups to determine their relatedness to strains from other geographical regions. Three hundred fifty-three anti-HCV positive sera collected during 1994-2004 from hospitalized patients, blood donors and health care workers were used as source of HCV RNA. Two hundred nine (59%) of the sera were positive for HCV RNA by PCR directed to the 5'-UTR region. For 174 strains the HCV subtype was determined by analyses of the NS5B and/or the 5'UTR-core regions. 1b (71%) was the most common subtype followed by 3a (24%), 2c (2%), 1a (1%), and 2a (1%). The 1b and 3a strains were similar to strains from other regions of the former USSR. Within genotype 1b there were several HCV lineages. However, for 3a there seemed to be two separate introductions into Estonia. There was a relative shift from subtype 1b to 3a in 1999-2000 with a further replacement of 3a with 1b in intravenous drug users in 2001 and onwards (P < 0.05). However, both subtypes were found to co-circulate in the community independent of risk factors. One patient was infected with the 2k/1b recombinant presumed to originate from St. Petersburg being the first isolate of this recombinant recovered outside Russia.

Hepatitis C virus genotypes in Serbia and Montenegro: The prevalence and clinical significance

AIM: To investigate the prevalence of hepatitis C virus (HCV) genotypes in Serbia and Montenegro and their influence on some clinical characteristics in patients with chronic HCV infection.

METHODS: A total of 164 patients was investigated. Complete history, route of infection, assessment of alcohol consumption, an abdominal ultrasound, standard biochemical tests and liver biopsy were done. Gene sequencing of 5’ NTR type-specific PCR or commercial kits was performed for HCV genotyping and subtyping. The SPSS for Windows (version 10.0) was used for univariate regression analysis with further multivariate analysis.

RESULTS: The genotypes 1, 2, 3, 4, 1b3a and 1b4 were present in 57.9%, 3.7%, 23.2%, 6.7%, 6.7% and 1.8% of the patients, respectively. The genotype 1 (mainly the subtype 1b) was found to be independent of age in subjects older than 40 years, high viral load, more severe necro-inflammatory activity, advanced stage of fibrosis, and absence of intravenous drug abuse. The genotype 3a was associated with intravenous drug abuse and the age below 40. Multivariate analysis demonstrated age over 40 and intravenous drug abuse as the positive predictive factors for the genotypes 1b and 3a, respectively.

CONCLUSION: In Serbia and Montenegro, the genotypes 1b and 3a predominate in patients with chronic HCV infection. The subtype 1b is characteristic of older patients, while the genotype 3a is common in drug abusers. Association of the subtype 1b with advanced liver disease, higher viral load and histological activity suggests earlier infection with this genotype and eventually its increased pathogenicity.

Epidemic dynamics of two coexisting hepatitis C virus subtypes

Hepatitis C virus (HCV) infection affects about 3% of the human population. Phylogenetic analyses have grouped its variants into six major genotypes, which have a star-like distribution and several minor subtypes. The most abundant genotype in Europe is the so-called genotype 1, with two prevalent subtypes, 1a and 1b. In order to explain the higher prevalence of subtype 1b over 1a, a large-scale sequence analysis (100 virus clones) has been carried out over 25 patients of both subtypes in two regions of the HCV genome: one comprising hypervariable region 1 and another including the interferon sensitivity-determining region. Neither polymorphism analysis nor molecular variance analysis (attending to intra- and intersubtype differences, age, sex and previous history of antiviral treatment) was able to show any particular difference between subtypes that might account for their different prevalence. Only the demographic history of the populations carrying both subtypes and analysis of molecular variance (AMOVA) for risk practice suggested that the route of transmission may be the most important factor to explain the observed difference.

Molecular epidemiology of hepatitis C virus subtype 3a in injecting drug users

Hepatitis C virus subtype 3a (HCV-3a) originates from Asia and has spread widely among injecting drug users as well as other patient groups in industrialized countries. HCV subtype 3a infection remains highly prevalent and frequently transmitted in the population of intravenous drug users. The objective of this study was to understand better the mechanisms of the worldwide HCV-3a epidemics in drug users. Ninety-three sera from HCV-3a-infected IDUs from France, the United States, Brazil, Argentina, and Australia were studied. Phylogenetic analyses of the non-structural 5B region showed no specific clustering according to the continent of the patient's origin. Non-exclusive clusters of viral sequences from South America, Australia, and California were observed, but topologies were not supported by strong bootstrap values. The results suggest that HCV-3a has been transmitted from a common origin through a unique worldwide epidemic that rapidly spread among drug users. Regional transmission occurred in the recent past, leading to an embryonic genetic diversification of HCV-3a among local injecting drug user population.

Analysis of the 5' noncoding region versus the NS5b region in genotyping hepatitis C virus isolates from blood donors in France

The 5' noncoding region (5' NCR) of the hepatitis C virus (HCV) has become the standard for genotyping even though several reports show that its use can result in classification errors. The purpose of this study was to perform genotyping based on sequence analysis of the NS5b region in a set of 357 HCV strains isolated from blood donors in France in 2002 and 2003. Results were compared with those previously obtained using 5' NCR analysis, and HCV subtype distribution was reevaluated. Twenty-six of 120 strains (approximately 22%) initially identified as genotype 1b by 5' NCR region sequence analysis were reclassified as genotype 1a by NS5b region sequence analysis. Similarly, 14 of 23 strains (approximately 61%) initially identified as 2a/2c were reclassified as non-2a and non-2c subtypes, and 12 of 22 strains (approximately 45%) initially identified as 4c/4d subtypes were reclassified as non-4c and non-4d subtypes. Sequence analysis of the NS5b region also revealed 5 putative new subtype 2 variants and 2 putative new subtype 4 variants. Although these findings demonstrated full agreement between 5' NCR and NS5b sequence analysis with regard to type classification, genotyping based on phylogenetic analysis of the NS5b region is more accurate for subtype determination than genotyping based on analysis of the 5' NCR. Sequence analysis of the NS5b region is mandatory for epidemiologic studies.

Molecular tracing of the global hepatitis C virus epidemic predicts regional patterns of hepatocellular carcinoma mortality

BACKGROUND & AIMS

Molecular evolutionary analysis based on coalescent theory can provide important insights into epidemiologic processes worldwide. This approach was combined with analyses of the hepatitis C virus (HCV) epidemiologic-historical background and HCV-related hepatocellular carcinoma (HCC) in different countries.

METHODS

The HCV gene sequences of 131 genotype 1b (HCV-1b) strains from Japan, 38 HCV-1a strains from the United States, 33 HCV-1b strains from Spain, 27 HCV-3a strains from the former Soviet Union (FSU), 47 HCV-4a strains from Egypt, 25 HCV-5a strains from South Africa, and 24 HCV-6a strains from Hong Kong isolated in this study and previous studies were analyzed.

RESULTS

The coalescent analysis indicated that a transition from constant size to rapid exponential growth (spread time) occurred in Japan in the 1920s (HCV-1b), but not until the 1940s for the same genotype in Spain and other European countries. The spread time of HCV-1a in the United States was estimated to be in the 1960s; HCV-3a in the FSU, HCV-5a in South Africa, and HCV-6a in Hong Kong in the 1960s, mid-1950s, and late 1970s, respectively. Three different linear progression curves were determined by analysis of the relationship between HCV seroprevalence and HCC mortality in different geographic regions; a steep ascent indicated the greatest progression to HCC in Japan, a near horizontal line indicated the least progression in the United States and the FSU, and an intermediate slope was observed in Europe.

CONCLUSIONS

These findings strongly suggest that the initial spread time of HCV is associated with the progression dynamics of HCC in each area, irrespective of genotype.

Characterization of HCV strains in an oncohematological pediatric department reveals little horizontal transmission but multiple introductions by un-screened blood products in the past

Because several children were found infected with hepatitis C virus (HCV) at a pediatric oncohematological department in Vilnius, 474 children were tested for anti-HCV. Fifty-eight percent of 96 children treated with blood and plasma products manufactured before the introduction of anti-HCV screening of blood in Lithuania in 1994 were positive for anti-HCV versus 3.4% of those treated after 1994. The possible route of transmission for 45 of these was investigated by phylogenetic analyses within the NS5B region. Children treated before 1995 were infected with a multiplicity of strains of different subtypes, predominantly 1b found in 21 cases, 3a in 5 cases, 2 in 3 cases, 1a in 1 case, and not subtypeable genotype 1 strains in 2 cases. Children who had received blood products after 1994 were infected with only two subtypes, 1b in six and 3a in seven. Genetic analysis showed multiple introductions of HCV before 1995 and that horizontal spread between patients had occurred only to a minor extent at the department. However, two transmission chains involved children treated before 1995. Another chain involved five children treated after 1994. Since the most important risk factor for acquiring hepatitis C was blood products manufactured before the introduction of donor screening for anti-HCV, the spread between children would not have been revealed without molecular tools. These and the background strains provide the first reported sequence data on Lithuanian HCV strains. In general, these were shown to form autochthonous clades, except the 3a strains that were related to strains from the former USSR.

Genotype distribution and molecular epidemiology of hepatitis C virus in blood donors from southeast France

The genotype distribution of hepatitis C virus (HCV) in blood donors from southeast France was tracked for a period of 13 years (1991 to 2003). Virus genomes from 321 samples were analyzed by amplification and sequencing of the NS5b and E1 regions. The most frequent genotypes were 1b (30.2%), 1a (27.7%), and 3a (22.4%). Although it was less common, genotype 2 was characterized by the presence of strains belonging to 11 different subtypes, including 5 that had never been characterized. Genotypes 1a, 1b, 3a, and 4a presented typical "epidemic" profiles, with a large number of isolates per subtype and short mean genetic distances between isolates. Type 2 isolates displayed a typical "endemic" profile, with a large number of subtypes and very few isolates in each subtype. The epidemiology of HCV infection in southeast France changed radically during the study period in relation to modifications in the etiology of infection. We observed the emergence of new epidemic subtypes (subtypes 1a and 3) linked to intravenous drug use and a decrease in the types linked to blood transfusion and nosocomial infection (epidemic subtype 1b and endemic type 2). Comparison of strains from blood donors with strains from a cohort of inpatients in the same region during 2001 and 2002 demonstrated for the first time that the monitoring of blood donors is a generally valid indicator of HCV epidemiology in terms of genotype distribution.

Molecular epidemiology of HCV infection among acute and chronic liver disease patients in Kolkata, India

BACKGROUND

In recent years, hepatitis C virus (HCV) infection is gaining importance in Asian countries. Recent studies conducted in different parts of the world revealed that there is a genotypic correlation of disease severity and treatment outcome.

OBJECTIVES

A detailed study was carried out to delineate the genotypic distribution of HCV among acute and chronic liver disease patients in Kolkata, a city in eastern India.

STUDY DESIGN

Acute and chronic liver disease was diagnosed among patients attending hepatitis clinics in the city. Anti-HCV ELISA was performed on the blood samples of the cases and positive samples were tested for presence of HCV-RNA and genotyping of the samples were carried out by reverse transcription and polymerase chain reaction (RT-PCR) and sequencing.

RESULTS

Seroprevalence of HCV infection among acute (11.0%) and chronic (25.3%) hepatitis patients were high and among them 97 (75.8%) and 323 (86.1%) were HCV-RNA positive for acute and chronic hepatitis patients, respectively. Genotyping by PCR showed that the predominant genotype was 3b (42.3%) followed by 3a (28.9%) among acute hepatitis group whereas among chronic hepatitis group, the most prevalent genotypes were 3a (34.7%) and 3b (47.7%). Sequence analysis of the untypeable isolates revealed the presence of a rare subtype 6b.

CONCLUSIONS

The study revealed very high prevalence of HCV among acute and chronic hepatitis patients with predominance of genotype 3. Subtype 6b was commonly found in Thailand but not in India. The detection of this rare strain of Thai origin reveals the spread of HCV infection from Thailand to other parts of Asia. This observation necessitates further intensive surveillance of HCV infection in India to unravel the distribution of genotypes in the country and to correlate disease severity and treatment outcome to the genotype prevalence.

Molecular epidemiology of the hepatitis C virus in Western Siberia

Western Siberia is the region with little information on the prevalence of hepatitis C virus (HCV) infection, genotypic diversity of HCV isolates and risk factors. A molecular epidemiological survey was conducted to clarify these issues. Four groups of volunteers were included in a cross-sectional study (n = 500 in each group): health care workers; daycare patients from a hospital for drug users, daycare patients from an AIDS prevention and control center; and persons admitted to a local general practice clinic for any reason (outpatients). The anti-HCV IgG prevalence was 4.6% in health care workers, 48.0% in a narcological center, 35.8% in AIDS center, and 5.6% in outpatients. HCV RNA was found in 79.3%-86.3% of seropositives. A total of 388 HCV isolates were genotyped by direct sequencing and phylogenetic analysis of the 5'-UTR and NS5B regions of HCV genome. The genotypes distribution was: 1b--50.3%, 2a--4.4%, 2c--0.3%, 3a--44.8%. One isolate (0.3%) could not be typed unambiguously. This genotypic diversity is intermediate between that of European Russia and China. Genotype 1 prevailed in an older age group (75% among 51-60 years old), and genotype 3 was most prevalent in young people (51.4% in 16-20 years old). A statistically significant (P < 0.05) increase in risk was found in intravenous drug users (odds ratio (OR) = 77.5), unemployed persons (OR = 16.3), persons having >4 sexual partners during lifetime (OR = 4.3), and male homosexuals (OR = 6.6).

The hepatitis C virus genotype and subtype frequency in hepatitis C virus RNA-positive, hepatitis C virus antibody-negative blood donors identified in the nucleic acid test screening program in Poland

BACKGROUND

Since 2002, blood donors in Poland have been tested not only for hepatitis C virus antibodies (anti-HCV) but also for HCV RNA or HCV core antigen. This screening program identifies asymptomatic, recently infected individuals with no anti-HCV (in the "window period"). The aim of this study was to compare HCV genotype and subtype distribution in window-period (wp) donors, anti-HCV-positive donors, and chronic hepatitis C (CHC) patients.

STUDY DESIGN AND METHODS

A total of 2.37 million donors were investigated for HCV RNA, and 340,000 for HCV core antigen. HCV genotypes and subtypes were investigated in 50 HCV RNA-positive, anti-HCV-negative donors; in 70 anti-HCV-positive donors; and in 170 CHC patients. Re-questioning of wp donors for probable risk factors was introduced.

RESULTS

HCV RNA was detected in 50 donors of 2.71 million (1:54,200) anti-HCV-negative blood donations. Of these 50 donors, 36 percent exhibited Subtype 1b, whereas Subtypes 3a and 4c/d were identified in 40 and 14 percent, respectively. In anti-HCV-positive donors and CHC patients, the frequency of Subtype 1b was significantly higher (75.7 and 85.3%, respectively); in both groups the lower frequency of Subtypes 3a (14.3 and 10.6%, respectively) and 4c/d (4.3 and 1.2%, respectively) was found. The probable source of infection was identified in 9 wp donors.

CONCLUSIONS

The frequency of wp donors is 18.5 per 1 million. The unexpected high frequency of Genotype 4 and Subtype 3a and the low frequency of Subtype 1b was observed in wp donors compared to anti-HCV-positive individuals. Additional epidemiologic questioning introduced after HCV RNA detection may help to identify infection source.

Molecular epidemiology of hepatitis C virus in Iran as reflected by phylogenetic analysis of the NS5B region

Hepatitis C virus (HCV) subtypes were determined in 125 Iranian patients by phylogenetic analysis within the NS5B or 5'-UTR/core regions. Subtypes 1a and 3a were predominant accounting for 47 and 36%, whereas 1b and 4 accounted for 8 and 7%. This subtype distribution differs from that of Turkey and Pakistan, where subtypes 1b and 3a dominate and also from neighbouring Arabic countries where subtype 4 is the prevalent genotype. The Iranian 1a and 3a strains formed subclusters in the dendrogram indicating that these subtypes are indigenous to Iran. In contrast, the 1b strains intermixed with strains derived worldwide. Subtype 1a was frequent in South Iran (70%), while 3a was more prevalent in North-West Iran (83%), a region with a high proportion of Turkish inhabitants. Patients infected by blood products had more frequently subtype 1a (57%), while younger drug users had more frequently subtype 3a (54%). Genotype 4 was over-represented among haemodialysis patients in Tehran. One strain, most similar to genotype 5, was highly divergent in the NS5B region and further analysis is needed to assess the systematic status of this strain. In half of the patients with unknown source of infection only the 5'-UTR could be amplified, most of which were from North-West Iran and from patients younger than those with unknown source of infection with typable strains, mean age 29 versus 43 years. In conclusion, the NS5B sequence data revealed population based subtype patterns in Iran, the further study of which may help to understand the molecular epidemiology of HCV in a low-endemic area.

Genomic and phylogenetic analysis of hepatitis C virus isolates: a survey of 535 strains circulating in southern France

The present study examines the distribution of Hepatitis C virus (HCV) genotypes in Marseille, France in 2001-2002 and evaluates the efficiency of two in house direct sequence PCR protocols based on 5'NC analysis or NS5B analysis. By 5'NC sequencing, the distribution of 535 HCV strains derived from patients attending gastroenterology and AIDS referral centers, or dialysis units was as follows: 33% were infected by genotype 1a; 26% by 1b; 7% by 2; 22% by 3a; 10.7% by 4. In univariate analysis, HCV distribution was associated with age and source of infection, whereas in multivariate analysis only injecting drug use was an independent determinant for genotype distribution. Among the 535 specimens submitted to 5'NC direct sequencing, 18% could not be classified accurately into subtypes. A subset of 187 samples was amplified efficiently and sequenced by targeting the NS5B region of the viral genome. The two methods yielded concordant results in 70% of cases. Specimens unsubtypeable or misclassified most frequently by 5'NC analysis were type 1b and subtypes 2a/2c and 4a/4c. The data show that 5'NC direct sequence analysis is a sensitive method to identify genotypes in all cases, but that it can lead to subtyping misclassification (in particular, subtype 1b and 1a) or doubtful results (in particular subtypes 2a/2c and 4a/4c). Conversely, NS5B direct sequence assay, based on phylogenetic analysis, allowed better discrimination between subtypes. These two approaches are complementary and should be made available in clinical laboratories to ensure a reliable survey of HCV strains.

Hepatitis C virus molecular epidemiology in Uzbekistan

The aim of this study was to identify hepatitis C virus (HCV) genotypes and to estimate their prevalence in various risk groups and the regional distribution in Uzbekistan. Preliminary serological screening of 1,269 subjects revealed 6.5% anti-HCV-positive in a general population, 27.1% in patient groups, and 51.7% among intravenous drug users. HCV genotypes of 104 anti-HCV-positive subjects were determined using a PCR-genotyping system in core region, and the results were supported by nucleotide sequencing of the NS5B region. Genotype 1b identified in total 64.2%, was the most prevalent. The genotype 3a identified in 25.0% was the second one distributed. HCV genotypes 2a, 1a, 2b, and 3b were identified in 3.8%, 2.9%, 2.9%, and 1.0% of cases, respectively. The intravenous drug users were distinguished from other groups by having the highest prevalence of genotype 3a, i.e., 50.0%, higher than the 33.3% for genotype 1b in this group. Geographically, genotype 1b was common; genotype 3a was also found frequently in all three regions. Uncommon HCV genotypes (1a, 2a, 2b, and 3b) were found in comparatively greater variability in the western region. Molecular evolutionary analysis based on the NS5B region did not reveal specific clustering or indigenous strains among Uzbekistan HCV isolates. In summary, two main mechanisms of HCV infection distribution were observed in Uzbekistan: HCV 1b genotype infection is widespread through blood products, and HCV 3a genotype infection is spreading through the growing number of intravenous drug users.

Genetic diversity and models of viral evolution for the hepatitis C virus

In this review we discuss the application of theoretical frameworks to the interpretation of viral gene sequence data, with particular reference to the hepatitis C virus (HCV). The increasing availability of such data means that it is now possible (and necessary) to proceed from simple qualitative models of viral evolution, to more quantitative frameworks based on statistical inference, notably population genetics and molecular phylogenetics. We argue that these approaches are invaluable tools to the virologist and are essential for understanding the dynamics of viral infection and the outcome of therapeutic strategies. We use several recent HCV data-sets to illustrate the methods.

A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg

Hepatitis C virus (HCV) evolution is thought to proceed by mutations within the six genotypes. Here, we report on a viable spontaneous HCV recombinant and we show that recombination may play a role in the evolution of this virus. Previously, 149 HCV strains from St. Petersburg had been subtyped by limited sequencing within the NS5B region. In the present study, the core regions of 41 of these strains were sequenced to investigate the concordance of HCV genotyping for these two genomic regions. Two phylogenetically related HCV strains were found to belong to different subtypes, 2k and 1b, according to sequence analysis of the 5' untranslated region (5'UTR)-core and the NS5B regions, respectively. By sequencing of the E2-p7-NS2 region, the crossover point was mapped within the NS2 region, probably between positions 3175 and 3176 (according to the numbering system for strain pj6CF). Sequencing of the 5'UTR-core regions of four other HCV strains, phylogenetically related to the above-mentioned two strains (based on analysis within the NS5B region), revealed that these four strains were also recombinants. Since a nonrecombinant 2k strain was found in St. Petersburg, the recombination may have taken place there around a decade ago. Since the frequency of this recombinant is now high enough to allow the detection of the recombinant in a fraction of the city's population, it seems to be actively spreading there. The reported recombinant is tentatively designated RF1-2k/1b, in agreement with the nomenclature used for HIV recombinants. Recombination between HCV genotypes must now be considered in the classification, laboratory diagnosis, and treatment of HCV infection.