Hepatitis C Virus Subtypes 1a Research Articles

Distribution of Hepatitis C Virus Genotypes among Azerbaijani Patients in Capital City of Iran-Tehran

BackgroundDetermination of the Hepatitis C virus (HCV) genotype distributed in a particular area has an important role on public health throughout the world.ObjectivesThe aim of this study was to determine the frequency of HCV genotypes in Azerbaijani patients.Patients and MethodsFrom 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.ResultsHCV 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%).ConclusionsThe 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%).

Occult Hepatitis C Virus Infection in Candidates for Liver Transplant With Cryptogenic Cirrhosis

BackgroundOccult hepatitis C virus (HCV) infection is a new entity described by the presence of HCV-RNA in liver biopsy and/or peripheral blood mononuclear cell (PBMC) specimens, and undetectable levels or absence of HCV-RNA and in the absence or presence of anti HCV antibodies in plasma by current laboratory methods.ObjectivesTo evaluate the detection of HCV-RNA in PBMC specimens of the liver transplant candidates with cryptogenic cirrhosis by reverse transcriptase-nested polymerase chain reaction (RT-nested PCR).Patients and MethodsFrom November 2007 to March 2013, 45 patients from Liver Transplant Center of Imam Khomeini Hospital, Tehran, were enrolled in this cross sectional study. PBMC specimens were separated from the peripheral blood sample. After extraction of RNA from plasma and PBMC specimens, HCV-RNA status was tested by RT-nested PCR. The 5′-untranslated region (5′-UTR) genotyping of HCV-RNA amplified from PBMC specimens was performed by a standard methodology with the INNO-LiPATM HCV II kit. The PCR products of 5′-UTR were sequenced after cloning into the pJET1.2 / blunt cloning vector.ResultsOf 45 patients, 4 (8.9% [95% CI: 4.4-15.6]) had detectable genomic HCV-RNA in their PBMC specimens. HCV genotypes were determined in the PBMCs of these subjects showed that 2 (50.0%) subjects with occult HCV infection had HCV subtype 3a, and 2 (50.0%) had HCV subtype 1b.ConclusionsThis study found that 8.9 % of the Iranian candidates for liver transplant with cryptogenic cirrhosis had occult HCV infection. Therefore, designing prospective studies focusing on the diagnosis of occult HCV infection in these subjects prior to liver transplantation could be valuable.

Hepatitis C genotype and associated risks factors of patients at University Kebangsaan Malaysia Medical Centre

Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective was to determine HCV genotype and their associations with certain risk factors at University Kebangsaan Malaysia Medical Centre (UKMMC). A total of 89 samples were collected from December 2009 to January 2011. Demographic data of patients were collected from medical record. Reverse Transcriptase Polymerase chain reaction (RT PCR) was performed and sixty-four samples yielded positive for HCV. Sequencing was performed and analyzed based on sequence information in GenBank. Statistical analysis were done using SPSS version 15. Results : HCV genotype 3 (73%) was the most frequent genotype, followed by genotype 1(27%). The distribution of HCV genotype/ subtype was as follows: 3a (64.8%), 1a (13.5%), 1 (10.8%), 3 (8.1%) and 1b (2.7%). HCV subtypes 3a, 1a, and 1b were identified in patients at UKMMC, Malaysia with subtype 3a being the most prevalent. No significant association was found between HCV genotypes and patients' demographic data.

Additional Glycosylation Within a Specific Hypervariable Region of Subtype 3a of Hepatitis C Virus Protects Against Virus Neutralization

The envelope glycoprotein E2 of hepatitis C virus (HCV) contains several hypervariable regions. Interestingly, 2 regions of intragenotypic hypervariability within E2 have been described as being specific to HCV subtype 3a. Based on their amino acid position in E2, they were named HVR495 and HVR575. Here, we further investigated these regions in order to better understand their role in HCV infection. Sequences of HCV envelope glycoproteins from Pakistani patients infected with subtype 3a were cloned and compared with other subtype 3a sequences. The entry functions and the sensitivity to antibody neutralization of selected HCV glycoprotein sequences were tested in the HCV pseudotyped particles (HCVpp) system. In addition, the cell-cultured HCV system (HCVcc) was also used to confirm some of the data obtained with the HCVpp system. We observed interesting new features within HVR495 and HVR575 for several subtype 3a isolates. Indeed, changes in glycosylation sites were observed with the appearance of a new glycosylation site within HVR495. Importantly, HCVpp and HCVcc that contained this new HVR495 glycosylation site were less sensitive to antibody neutralization. We identified a new glycosylation site within the HVR495 region of HCV subtype 3a that has a protective effect against antibody neutralization.

Triple Combination Therapy for Hepatitis C with Telaprevir Exhibits Greater Early Antiviral Activity than with Boceprevir

Achievement of early viral suppression is important in patients with chronic HCV infection treated with telaprevir (TLV) or boceprevir (BOC) to avoid selection of drug resistance and attain cure. No head-to-head studies comparing TLV and BOC have been performed so far. All consecutive individuals who initiated triple HCV therapy with TLV or BOC outside clinical trials at three European clinics were evaluated. Rapid virological response (RVR) was defined as unquantifiable HCV RNA (<25 IU/ml) at week 4 for TLV and at week 8 for BOC (4 weeks after lead-in). A total of 106 patients were evaluated, 33 treated with BOC and 73 with TLV. Median age, gender, body mass index, baseline HCV RNA, HCV subtype 1a (45% versus 42%) and IL28B-CC alleles (29% versus 23%) did not differ significantly in BOC and TLV groups, respectively. HIV coinfection was more prevalent in patients on TLV than BOC (24% versus 44%). Conversely, more patients on BOC than TLV had previously failed pegylated interferon plus ribavirin (82% versus 64%). RVR was achieved by 82% of patients on TLV versus 59% on BOC (P=0.001). Multivariate logistic regression analysis confirmed that TLV use was the strongest predictor of RVR (OR 3.54 [95% CI 1.23, 10.24]; P=0.02), others being HCV subtype 1b versus 1a (OR 3.26 [95% CI 1.17, 9.09]; P=0.02) and low baseline HCV RNA (OR 0.41 [95% CI 0.16, 1.03]; P=0.06). Prior interferon exposure, HIV coinfection or absence of advanced liver fibrosis did not influence the likelihood of RVR. Compared to BOC, triple therapy with TLV produces greater RVR rates. TLV might be a better option in more difficult-to-cure patients, such as those with high baseline HCV RNA and/or HCV 1a subtype. HIV coinfection does not influence early HCV RNA responses.

Genetic diversity of HCV among various high risk populations (IDAs, thalassemia, hemophilia, HD patients) in Iran

ObjectiveTo determine the patterns of distribution of HCV genotypes among high risk population in north of Iran. MethodsA cross-sectional study was conducted on 135 HCV RNA-positive high risk individuals including thalassemia, hemophilia, patients under hemodialysis and intravenous drug addicts. HCV genotypes were determined based on amplification with type-specific primers methods. ResultsAmong the 187 anti-HCV positive samples, only 135 (72.2%) gave HCV-RNA positvity. Over all, the most identified HCV type was genotype 3a (51.1%) followed by 1a (27.4%), 1b (8.2%). Sixteen (11.9%) out of 135 HCV RNA-positive participants have infected with more than one genotype or subtypes as follow; 1a/1b in 11 (8.2%), 2/3a in 3 (2.2%), and 1a/1b/3a in 2 (1.5%). Stratification of participants revealed that HCV subtype 3a was more prominent in thalassemia, hemophilia and HD patients but 1a and 1b were frequent in intravenous drug addicts. ConclusionsThis study is the first report on HCV genotypes among Iranian subjects with different exposure categories resided in Mazandaran, where genotype 3a was found to be the most frequent genotype in thalassemia, hemophilia, and hemodialysis patients but not in IDAs. Since the addiction age is decreasing in Iran and a lot of addicts are IDAs, it might change the subtype pattern of HCV in general population.

The Evolutionary Rates of HCV Estimated with Subtype 1a and 1b Sequences over the ORF Length and in Different Genomic Regions

BackgroundConsiderable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance.Methods/Results176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10−3 substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure.ConclusionAmong the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.

Chronic HCV - infection in the Kirov region: Dynamics of indices of disease in adults in 1995-2010

In the given article the analysis of an epidemiological situation concerning chronic forms of HCV infections in adults in the Kirov region in 1995-2010 is presented. In the region during analyzed period stable trend to the elevation of incidence of chronic hepatitis C and a slight decrease in the number of "carriers" of HCV on the background of steadily low indices of the occurrence of acute hepatitis C have been fixed. There are also presented the results of genotyping of HCV-virus in 730 patients with chronic hepatitis C treated at the Kirov Region infectious hospital and polyclinics in Kirov with the dominance of HCV subtypes 1b and 3a .

Molecular Epidemiology and Genetic History of Hepatitis C Virus Subtype 3a Infection in Thailand

Objective: Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. Methods: Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. Results: Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. Conclusion: The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.

Prevalence of occult hepatitis C virus infection in Iranian patients with lymphoproliferative disorders

Occult HCV infection is a form of chronic HCV infection characterized by absence of detectable anti-HCV antibodies or plasma HCV-RNA but presence of HCV-RNA in liver biopsy and/or peripheral blood mononuclear cells (PBMCs). The aim of this study was to determine the presence of HCV-RNA in PBMCs of patients with lymphoproliferative disorders. One hundred and four consecutive patients with lymphoproliferative disorders admitted to Firouzgar Hospital from January 2010 to March 2011 were recruited in this cross-sectional study. A 6-ml sample of whole blood was taken from the patients, the total RNA was extracted from the samples after the separation of plasma and PBMCs. The HCV-RNA of the samples was amplified by reverse transcriptase-nested polymerase chain reaction (RT-nested PCR). The HCV genotypes of the positive samples were tested using the INNO-LiPA™ HCV II kit, and the HCV genotypes were then confirmed by sequencing of the 5'-UTR fragments after the PCR products were cloned into a pJET1.2/blunt cloning vector. The mean age of the patients was 48.3 ± 1.76 years (range: 16-83). HCV-RNA was found in PBMCs from 2 (1.9%) of the 104 patients. Genotyping showed that the patients were infected with HCV subtype 1a. One patient suffered non-Hodgkin's lymphoma and the other suffered chronic lymphocytic leukemia. Patients with lymphoproliferative disorders with negative anti-HCV antibodies and negative plasma HCV-RNA may have occult HCV infection. Therefore, in the absence of a liver biopsy, the testing of PBMCs for the detection of genomic HCV-RNA may be beneficial.

Broadly neutralizing immune responses against hepatitis C virus induced by vectored measles viruses and a recombinant envelope protein booster.

Hepatitis C virus (HCV) infection remains a serious public health problem worldwide. Treatments are limited, and no preventive vaccine is available. Toward developing an HCV vaccine, we engineered two recombinant measles viruses (MVs) expressing structural proteins from the prototypic HCV subtype 1a strain H77. One virus directs the synthesis of the HCV capsid (C) protein and envelope glycoproteins (E1 and E2), which fold properly and form a heterodimer. The other virus expresses the E1 and E2 glycoproteins separately, with each one fused to the cytoplasmic tail of the MV fusion protein. Although these hybrid glycoproteins were transported to the plasma membrane, they were not incorporated into MV particles. Immunization of MV-susceptible, genetically modified mice with either vector induced neutralizing antibodies to MV and HCV. A boost with soluble E2 protein enhanced titers of neutralizing antibody against the homologous HCV envelope. In animals primed with MV expressing properly folded HCV C-E1-E2, boosting also induced cross-neutralizating antibodies against two heterologous HCV strains. These results show that recombinant MVs retain the ability to induce MV-specific humoral immunity while also eliciting HCV neutralizing antibodies, and that anti-HCV immunity can be boosted with a single dose of purified E2 protein. The use of MV vectors could have advantages for pediatric HCV vaccination.

Different impact of IL28B polymorphisms on response to peginterferon-α plus ribavirin in HIV-positive patients infected with HCV subtypes 1a or 1b

BackgroundHCV subtype 1a has emerged as a predictor of poor response to triple hepatitis C therapy including boceprevir or telaprevir, which largely has been attributed to a lower resistance barrier in HCV-1a compared to -1b. ObjectivesWe examined whether a lower efficacy of pegIFN/RBV on HCV-1a than HCV-1b could alternatively contribute to explain it. Study designAll chronic hepatitis C patients who had completed a course of pegIFN/RBV therapy at our institution were examined. For this study we selected individuals that were IFN-naïve and had been successfully subtyped as 1a or 1b. Moreover, only HIV-coinfected patients were included as they represented a more uniform population in terms of demographics and treatment exposure at our institution. The IL28B rs12979860 alleles were typed using the 5′ nuclease assay. ResultsA total of 96 individuals were examined, 58 of whom harbored HCV-1a and 38 HCV-1b. IL28B allele distribution was as follows: 33 CC and 63 CT/TT. SVR was achieved by 64% of CC vs 30% of CT/TT patients (p=0.001). On the other hand, SVR was 53% in HCV-1b vs 34% in HCV-1a (p=0.08). Interestingly, the effect of IL28B variants on SVR was mainly recognized in HCV-1a (63% in CC vs 20% in CT/TT; p=0.001), being marginal on HCV-1b (64% in CC vs 46% in CT/TT; p=0.27). ConclusionsThe rate of SVR to pegIFN/RBV therapy tends to be lower in HIV-infected patients with chronic hepatitis C due to HCV-1a than HCV-1b; being the impact of IL28B variants significantly stronger on HCV-1a than HCV-1b.

Complex patterns of HCV epidemic in Suzhou: Evidence for dual infection and HCV recombination in East China

BackgroundHCV transmission is closely associated with injection drug use (IDU), and co-circulation of multiple subtypes has been found among injection drug users (IDUs) in China. ObjectivesTo investigate HCV subtype characterizations among IDUs and general population (GP) in Suzhou, a city at the important “Hu-ning” transportation line. Study designDuring January 2010 to May 2011, 123 HCV positive plasma from IDUs and 131 stored HCV positive sera from general individuals were collected in Suzhou. HCV C/E2 and NS5B fragments were amplified using a new multiple RT-nested PCR strategy and subsequent sequenced. Genotypes were characterized by phylogenetic analyses. ResultsEight HCV subtypes (1a, 1b, 2a, 3a, 3b, 6a, 6n, and 6u) were detected among Suzhou IDUs, and six subtypes (1b, 2a, 3a, 3b, 6a and 6n) among GP. HCV subtype distribution is distinct between IDUs and GP. Interestingly, we detected discrepancy of genotyping results between C/E2 and NS5B regions in one general individual, indicating the presence of HCV intersubtype recombinant in China. The recombinant belongs to a 3a/1b recombinant. We also detected dual infections in one general individual and two IDUs. They include dual infections between 1b and 3a, 3a and 6a, and two distinct lineages of 3b. ConclusionsComplex patterns of HCV epidemic among IDUs, as well as GP, in Suzhou, might imply a spread of HCV from IDUs to GP. The finding of one HCV 3a/1b intersubtype recombinant might represent the first report of HCV recombination in China.

Epidemiology of Viral Hepatitis and Hepatocellular Carcinoma

Most cases of hepatocellular carcinoma (HCC) are associated with cirrhosis related to chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infection. Changes in the time trends of HCC and most variations in its age-, sex-, and race-specific rates among different regions are likely to be related to differences in hepatitis viruses that are most prevalent in a population, the timing of their spread, and the ages of the individuals the viruses infect. Environmental, host genetic, and viral factors can affect the risk of HCC in individuals with HBV or HCV infection. This review summarizes the risk factors for HCC among HBV- or HCV-infected individuals, based on findings from epidemiologic studies and meta-analyses, as well as determinants of patient outcome and the HCC disease burden, globally and in the United States.

Drug resistance: Prevalence and clinical implications during the treatment of chronic hepatitis C infection.

Drug resistance: Prevalence and clinical implications during the treatment of chronic hepatitis C infection.

Drug Resistance Testing in Hepatitis C Therapy

The first direct-acting antivirals (DAAs) have recently been approved for the treatment of chronic HCV infection. These molecules interact with different HCV proteins, including NS3/4A protease, NS5B polymerase and NS5A. Several compounds belonging to distinct drug families are in the advanced stages of clinical development. Whereas most DAAs have demonstrated a potent antiviral activity against HCV, emergence of drug resistance represents a huge challenge with almost all of these drugs. The use of combination therapy greatly increases the chances of achieving rapid and complete viral suppression, preventing selection of DAA resistance. Drug resistance mutations and pathways differ according to antiviral agents and HCV genotypes/subtypes. HCV subtype 1a displays a uniformly lower barrier to resistance than HCV subtype 1b when confronting most HCV protease inhibitors, NS5B non-nucleoside inhibitors and NS5A inhibitors. Broad cross-resistance exists between drugs belonging to the same family, except for NS5B non-nucleoside analogs that may exhibit at least four distinct drug resistance profiles. Second-generation inhibitors are in development that may overcome the reduced susceptibility caused by single mutations. The large genetic variability of HCV suggests that some drug resistance changes may exist as natural polymorphisms in certain HCV geno/subtypes at rates that may require the consideration drug resistance testing before recommending certain antivirals.

A clustering phenomenon among HCV‐1a strains among patients coinfected with HIV from Buenos Aires, Argentina

The human immunodeficiency virus (HIV) and hepatitis C virus (HCV) share the same transmission routes which lead to high coinfection rates. Among HIV-infected individuals such rates reached 21% in Argentina, being HCV-1a the most predominant subtype. In this work, 25 HCV subtype 1a (HCV-1a) strains from Argentinean patients coinfected with HIV were studied based on E2 and NS5A sequences. Phylogenetic analyses indicated that 12 strains were highly related to each other, constituting a highly supported (posterior probability = 0.95) monophyletic group that we called "M." The remaining HCV strains (group dispersed or "D") were interspersed along the phylogenetic trees. When comparing both groups of HCV-1a, 10 amino acid differences were located in functional domains of E2 and NS5A proteins that appeared to affect eventually the peptides binding to MHC-I molecules thus favoring immune escape and contributing to the divergence of HCV genotypes. Bayesian coalescent analyses for HCV-1a cluster M isolates indicated that the time to the most recent common ancestor (tMRCA) overlaps with the age estimated recently for the HIV-BF epidemic in Argentina. Furthermore, the genomic characterization based on pol gene analysis from HIV viremic patients showed that most HIV isolates from patients coinfected with HCV-1a cluster M were BF recombinants with identical recombination patterns. In conclusion, these results suggest the presence of an HCV-1a monophyletic cluster with a potential HIV co-transmission by phylogenetic analyses.

The role of ribavirin in direct acting antiviral drug regimens for chronic hepatitis C

Despite years of clinical use and extensive research efforts, the mechanism of action of ribavirin (RBV) is not well understood. Although it has only a mild, transient antiviral effect on HCV replication when administered as monotherapy, when combined with interferon, RBV improves sustained virological response (SVR) rates by approximately 25-30%. Proposed mechanisms of action for RBV against HCV include (1) a direct effect against the HCV RNA dependent RNA polymerase; (2) induction of misincorporation of nucleotides leading to lethal mutagenesis; (3) depletion of intracellular pools via inhibition of inosine monophosphate dehydrogenase; (4) alteration in the cytokine balance between a Th2 profile (anti-inflammatory) to a Th1 profile (pro-inflammatory); and (5) potentiating the effect of interferon via up-regulation of genes involved in interferon signalling. Given the lack of a clear understanding of RBV mechanism of action, it has been challenging to confidently position this drug with new direct antiviral agents (DAA). However, early clinical studies provide strong evidence for a benefit of RBV in combination with DAAs for both IFN containing and sparing regimens. The addition of RBV reduces viral breakthroughs and/or relapses, at least when drugs with low to moderate genetic barriers to resistance are paired together. This is particularly true in patients harbouring HCV subtype 1a. Ongoing studies are now addressing the utility of RBV in nucleoside containing DAA regimens, which offer both potent antiviral activity as well as a high genetic barrier to resistance. It is remarkable that the age-old question of the role of RBV in the future of HCV therapy remains as real today as it was two decades ago.

The mode and tempo of hepatitis C virus evolution within and among hosts

BackgroundHepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus' public health importance and a wealth of sequence data, basic aspects of HCV molecular evolution remain poorly understood. Here we investigate three sets of whole HCV genomes in order to directly compare the evolution of whole HCV genomes at different biological levels: within- and among-hosts. We use a powerful Bayesian inference framework that incorporates both among-lineage rate heterogeneity and phylogenetic uncertainty into estimates of evolutionary parameters.ResultsMost of the HCV genome evolves at ~0.001 substitutions/site/year, a rate typical of RNA viruses. The antigenically-important E1/E2 genome region evolves particularly quickly, with correspondingly high rates of positive selection, as inferred using two related measures. Crucially, in this region an exceptionally higher rate was observed for within-host evolution compared to among-host evolution. Conversely, higher rates of evolution were seen among-hosts for functionally relevant parts of the NS5A gene. There was also evidence for slightly higher evolutionary rate for HCV subtype 1a compared to subtype 1b.ConclusionsUsing new statistical methods and comparable whole genome datasets we have quantified, for the first time, the variation in HCV evolutionary dynamics at different scales of organisation. This confirms that differences in molecular evolution between biological scales are not restricted to HIV and may represent a common feature of chronic RNA viral infection. We conclude that the elevated rate observed in the E1/E2 region during within-host evolution more likely results from the reversion of host-specific adaptations (resulting in slower long-term among-host evolution) than from the preferential transmission of slowly-evolving lineages.

HCV Subtype Characterization among Injection Drug Users: Implication for a Crucial Role of Zhenjiang in HCV Transmission in China

BackgroundHCV transmission is closely associated with drug-trafficking routes in China. However, the transmission route of HCV in Eastern China remains unclear. Here, we investigate the role of Zhenjiang city of Jiangsu province, an important transportation hub linking Shanghai with other regions of China, in HCV transmission.Methodology/Principal FindingsA total of 141 whole blood samples were collected from injection drug users (IDUs) in Zhenjiang and then tested for HCV infection. Of them, 115 HCV positive plasmas were subjected to RNA extraction, RT-PCR amplification, and sequencing. The subtype characterization and the evolutionary origin of HCV strains circulating in Zhenjiang were determined using polygenetic or phylogeographic analyses. Seven HCV subtypes 1b, 2a, 3a, 3b, 6a, 6e and 6n were detected among Zhenjiang IDUs, showing a complex HCV epidemic. The most predominant subtypes were 3a (38%) and 1b (26.8%). Among these subtypes, subtypes 3b, 6n and 6e originated from Southwestern China (i.e., Yunnan and/or Guangxi), subtypes 2a and 6a from Southern China (i.e., Guangdong), subtype 1b from Central (i.e., Henan) and Northwestern (i.e., Xinjiang) China, and subtype 3a from Southwestern (i.e., Yunnan) and Northwestern (i.e., Xinjiang) China. From Zhenjiang, subtypes 1b and 2a were further spread to Eastern (i.e., Shanghai) and Northern (i.e., Beijing) China, respectively.Conclusions/SignificanceThe mixing of seven HCV subtypes in Zhenjiang from all quarters of China indicates that as an important middle station, Zhenjiang plays a crucial role in HCV transmission, just as it is important in population migration between other regions of China and Eastern China.