The entire nucleotide sequence of two hepatitis G virus isolates belonging to a novel genotype: isolation in Myanmar and Vietnam

Effect of human pegivirus route of transmission on the genetic distribution of the virus: an institution based cross-sectional study

Introduction

Human pegivirus (HPgV), formally called GB virus C (GBV-C), is a member of the pegivirus genus in Flaviviridae family. High prevalence of HPgV infection is seen among sex workers, blood transfusion recipients and intravenous drug users (IDUs). So far, there are seven genotypes and many subtypes identified in different countries. The predominant genotype in Asia including China is genotype 3, although genotype 7 has been reported recently in China. The aim of this study was to evaluate the effect of the transmission routes of HPgV infection on the genotype distribution of the virus, to determine the prevalence rate, and identify the dominant genotype among men who have sex with men (MSM) and IDUs co-infected with human immunodeficiency virus type one (HIV-1) in Guangzhou, China.

Methods

A total of 131 MSM and 70 IDUs co-infected with HIV-1 were randomly selected in Guangdong Dermatology Hospital. HPgV RNA was detected by nested reverse transcriptase polymerase chain reaction (RT-PCR) using primers. The PCR products were sequenced and phylogenetically analyzed by using MEGA6.06 version software to determine the genotypes. Chi-square and Fisher exact test were implemented for comparing the proportion between different variables.

Results

The prevalence of HPgV infection was 32.9% among IDUs and 18.3% in MSM with a statistically significant difference between the two groups (p = 0.02). In IDU group, 82.6% infected with genotype 3 and the rest (17.4%) were categorized to genotype 7. Similarly, in MSM group, 83.3% belonged to genotype 3, and the remaining 16.7% were classified as sub-genotype 2a and 2b.

Conclusion

In Guangzhou, China, the prevalence rate of HPgV infection in IDUs was higher than MSM. The dominant genotype in the two groups was genotype 3. Our results indicated that routes of transmission did not affect the genotype distribution but did affect the prevalence rate of HPgV infection.

Prevalence of GB virus type C viraemia in MSM with or without HIV-1 infection in Beijing, China

GB virus C (GBV-C) is frequently identified in patients co-infected with human immunodeficiency virus type 1 (HIV-1) due to the similar transmission routes. However, it remains unclear how these two viruses interact with each other and how one virus affects the replication of the other in the human body. In this study, we performed a case-control study to determine whether GBV-C viraemia could prevent the acquisition of HIV-1 infection, and a cohort study to determine the prevalence, genotypic characteristics and incidence of GBV-C infection in men who have sex with men (MSM) populations in Beijing, China. The prevalence of GBV-C infection in HIV-1-negative subjects was similar to that in HIV-1-positive subjects. Before HIV-1 acquisition, the prevalence of GBV-C was 17·7%, which increased to 27·2% at the acute stage and to 34% at the chronic stage. Genotype 3 was the major genotype of GBV-C in both groups. A significantly positive correlation was observed between the CD4+ T-cell counts and GBV-C viral loads at the acute stage of HIV infection. At the chronic stage (12 months later), this correlation was no longer significant, although it was still positive. Overall, this study demonstrated that pre-existing GBV-C viraemia could not prevent the acquisition of HIV-1 infection and transmission of HIV-1 significantly increased the prevalence of GBV-C viraemia.

Evidence for extensive genotypic diversity and recombination of GB virus C (GBV-C) in Germany

Multiple genotypes of GB virus C (GBV-C)-a non-pathogenic flavivirus-have been identified to date, although they are not uniformly distributed worldwide. It has also been suggested that GBV-C genotype may play a role in modulating HIV disease; however, the prevalence and genotype distribution of GBV-C has not been adequately studied in most countries. Among 408 HIV positive subjects in Germany, 97 (23.8%) had detectable GBV-C RNA. Based on sequencing of the 5' untranslated region (5'-UTR), the GBV-C genotypes were 1 (n=8; 8.2%), 2 (n=81; 83.5%), and 3 (n=2; 2.1%), as well as a unique genotype not previously reported (n=6; 6.2%). Among 17 samples also sequenced in the envelope 2 (E2) region, 14 had concordant genotype results when comparing the 5'-UTR and E2, while evidence of intergenotypic recombination was observed among E2 sequences from 3 individuals. These results suggest that genotypic diversity and viral recombination contribute to the overall genetic variability of GBV-C.

Full Genomic Analysis of Hepatitis Delta Virus Prevalent on Miyako Island, Japan

The aims of this study were to determine the full-length genome sequences of hepatitis delta virus (HDV) in HDV RNA-positive subjects, and to elucidate the molecular specificity of the HDVs that are clustered on a distant island in Japan. This study included 3 subjects with chronic hepatitis who were positive for hepatitis B surface (HBs) antigen and HDV RNA, and who were admitted to the Okinawa Prefectural Miyako Hospital in 1998. The full-length genome sequence of HDV was determined by nested polymerase chain reaction (PCR) using four kinds of primer sets. The genomic length of HDV was 1,675, 1,679 and 1,681 base pairs, respectively. There was 90-92% nucleotide homology between each pair of isolates. In comparison with HDV isolates in geographically neighboring regions, the nucleotide homology of the 3 HDV isolates were 73-75% with the China isolate of genotype I; 77-78% with the Taiwan isolate of genotype I; 83-84% with a Japan isolate of genotype IIa; 85-87% with the Taiwan isolate of genotype IIa, and 87-88% with the Taiwan isolates of genotype IIb. Therefore, the Miyako Island isolates had high homology with the Taiwan isolate of genotype IIa and IIb. Phylogenetic analysis of the full-length genome sequences of HDV revealed that the two Miyako Island isolates were classified into a genotype IIb'. The other one was classified as genotype IIb. In conclusion, the HDV of Miyako Island isolates can be classified as a novel subgroup of genotype IIb, designated type IIb', and genotype IIb.

SEN virus infection influences the pathological findings in liver but does not affect the incidence of hepatocellular carcinoma in patients with chronic hepatitis C and liver cirrhosis

BACKGROUND/AIMS

This investigation compared the histological findings in the livers of chronic hepatitis C patients who were or were not co-infected with SEN virus (SEN-V) to determine the histological and clinical characteristics of SEN-V infection in Japan.

METHODS

Three hundred and ninety-two patients with hepatitis C virus-associated chronic hepatitis (CH) or liver cirrhosis (LC) were included in the study. Serum samples were tested for the presence of SEN-V DNA by nested polymerase chain reaction. The liver biopsy specimen of each patient was examined and scores were assigned to indicate the severity of each of the following features: inflammatory cell infiltration in the periportal, parenchymal, and portal areas; F stage; portal sclerotic change; perivenular fibrosis; pericellular fibrosis; damage to the bile ducts; steatosis and irregular regeneration of hepatocytes (IR).

RESULTS

Of the 473 patients, 194 (41.0%) were positive for SEN-V DNA. The rate of progression of F stage correlated with SEN-V DNA positivity. The blood biochemical parameters did not differ significantly between the SEN-V DNA-positive and -negative patients. The histological features of the livers of SEN-V DNA-positive patients included more severe parenchymal inflammatory cell infiltration and more IR. In particular, among those at the F2, F3 and F4 stages, the degree of IR of the SEN-V DNA-positive patients was significantly greater than that of the SEN-V DNA-negative patients. The cumulative probability of hepatocellular carcinoma (HCC) incidence and survival rate did not differ between the SEN-V DNA-positive and-negative patients.

CONCLUSIONS

SEN-V co-infection may influence the histopathological features of the livers of patients with type C CH and LC but does not affect the outcome of patients with type C chronic liver disease.

GB virus C/hepatitis G virus infection in dialysis patients and kidney transplant recipients in Central Brazil

In order to investigate the prevalence of GB virus C (GBV-C)/hepatitis G virus (HGV) infection in dialysis patients and kidney transplant recipients in Central Brazil and also to analyze the virus genotypes distribution, a total of 123 patients including 98 on hemodialysis, 13 on continuous ambulatory peritoneal dialysis treatment, and 12 who received kidney transplantation were interviewed in one unit of dialysis treatment in Goiania city. Blood samples were collected and serum samples tested for GBV-C/HGV RNA by polymerase chain reaction. Genotypes were determined by restriction fragment length polymorphism (RFLP) analysis. Eighteen samples were GBV-C/HGV RNA-positive, resulting in an overall prevalence of 14.6% (95% CI: 9.2-21.7). A high positivity for GBV-C/HGV RNA was observed in patients who had received kidney transplant (16.7%), followed by those on hemodialysis (15.3%), and peritoneal dialysis (7.7%). RFLP analysis revealed the presence of genotypes 1, 2, and 3 of GBV-C/HGV; more precisely, 9 (50%) samples were found belonging to the 2b subtype, 4 (22%) to the 2a subtype, 3 (17%) to genotype 1, and 2 (11%) to genotype 3. The present data indicate an intermediate prevalence of GBV-C/HGV infection among dialysis patients and kidney transplant recipients in Central Brazil. Genotype 2 (subtype 2b) seems to be the most prevalent GBV-C/HGV genotype in our region.

Genotyping of GB virus C by restriction pattern analysis of the 5' untranslated region

GB virus C (GBV-C) is a virus that has been proposed as a member of the Flaviviridae family, distantly related to hepatitis C virus (HCV). The virus is able to infect humans parenterally and perinatally, although its true pathogenicity remains unknown. The 5' terminal region of GBV-C is the most highly conserved region of the virus genome. Comparison of 5' untranslated region (5' UTR) sequences from GBV-C infected individuals shows that variation is limited to particular sites that are often covariant and associated with different virus genotypes. Extensive sequence analysis of the GBV-C genome provides evidence for the existence of at least five major genotypes, some of which can be further divided into subtypes. For genotyping by restriction fragment length polymorphism (RFLP), it is essential to identify genomic positions that not only reflect genotype differences, but that also harbor restriction sites that allow recognition of these differences. Restriction site analysis of type-specific sequence motifs predicted that endonucleases BsmFI, HaeII, HinfI, and ScrFI could be used for the identification all known genotypes (types 1-5) with 99.6% accuracy. The method was applied to serum samples from 46 chronic GBV-C carriers of heterogeneous geographical and ethnic origin, comparing observed cleavage patterns of GBV-C variants amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) of the 5' UTR with the RFLP predicted from sequences deposited in GenBank database. cDNA sequencing and subsequent alignment of the 46 GBV-C isolates confirmed RFLP profiles predicted theoretically. The observed geographical distribution of genotypes is also in agreement with previous reports. This method may be useful for rapid and reliable characterization of GBV-C isolates when either epidemiological or transmission studies are carried out.

A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases

A systematic bioinformatic approach to identifying the evolutionarily conserved regions of proteins has verified the universality of a newly described conserved motif in RNA-dependent RNA polymerases (motif F). In combination with structural comparisons, this approach has defined two regions that may be involved in unwinding double-stranded RNA (dsRNA) for transcription. One of these is the N-terminal portion of motif F and the second is a large insertion in motif F present in the RNA-dependent RNA polymerases of some dsRNA viruses.

Prevalence and genotypes of GB virus C/hepatitis G virus among blood donors in Central Brazil

A survey was conducted in a blood donor population of Central Brazil aiming to investigate the prevalence of GB virus C (GBV-C)/hepatitis G virus (HGV) infection and also to analyze the virus genotypes distribution. A total of 241 voluntary blood donors were interviewed at the State Blood Bank in Goiânia, State of Goiás, Brazil. Blood samples were collected and serum samples tested for GBV-C/HGV RNA by polymerase chain reaction. Genotypes were determined by restriction fragment length polymorphism (RFLP) analysis. Seventeen samples were GBV-C/HGV RNA-positive, resulting in a prevalence of 7.1% (95% CI: 4.2-11.1). A significant trend of GBV-C/HGV RNA positivity in relation to age was observed, with the highest prevalence in donors between 29-39 years old. Ten infected individuals were characterized by reporting parenteral (30%), sexual (18%), both (6%) and intrafamiliar (6%) transmission. However, 7 (40%) GBV-C/HGV RNA-positive donors did not mention any potential transmission route. RFLP analysis revealed the presence of genotypes 1 and 2 of GBV-C/HGV; more precisely, 10 (58.9%) samples were found belonging to the 2b subtype, 4 (23.5%) to the 2a subtype, and 3 (17.6%) to genotype 1. The present data indicate an intermediate endemicity of GBV-C/HGV infection among this blood donor population, and a predominant circulation of genotype 2 (subtype 2b) in Central Brazil.

Direct evidence for GB virus C/hepatitis G virus (GBV-C/HGV) superinfection: elimination of resident viral strain by donor strain in a patient undergoing liver transplantation

The viral genome of GB virus C/hepatitis G virus (GBV-C/HGV), a single-strand RNA virus, is subject to considerable variability and at least four genotypes have been suggested based on phylogenetic analysis. While co-infection of GBV-C/HGV with other infectious agents such as hepatitis C virus (HCV) has been frequently observed, there is no report whether or not co-infection and/or superinfection occurs among different GBV-C/HGV strains. By studying a GBV-C/HGV positive recipient/donor pair in the context of undergoing liver transplantation, we have sequenced multiple clones derived from serum samples serially collected over four years. Detailed phylogenetic analyses have been performed with these sequences. The donor was infected with GBV-C/HGV genotype 1 and this strain completely replaced recipient GBV-C/HGV strain (genotype 2) after liver transplantation. The recipient's original viral strain became undetectable during follow-up. Sequence analysis failed to identify genetic recombination between the two genotypes, at least in whole structural domain. This study, therefore, provides direct evidence for GBV-C/HGV superinfection of one strain by another with one of them predominating probably due to replication competition.

Molecular characteristic-based epidemiology of hepatitis B, C, and E viruses and GB virus C/hepatitis G virus in Myanmar

We carried out a molecular characteristic-based epidemiological survey of various hepatitis viruses, including hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and GB virus C (GBV-C)/hepatitis G virus (HGV), in Myanmar. The study population of 403 subjects consisted of 213 healthy individuals residing in the city of Yangon, Myanmar, and the surrounding suburbs and 190 liver disease patients (155 virus-related liver disease patients and 35 nonviral disease patients). The infection rates of the viruses among the 213 healthy subjects were as follows: 8% for HBV (16 patients), 2% for HCV (4 patients), and 8% for GBV-C/HGV (17 patients). In contrast, for 155 patients with acute hepatitis, chronic hepatitis, liver cirrhosis, or hepatocellular carcinoma, the infection rates were 30% for HBV (46 patients), 27% for HCV (41 patients), and 11% for GBV-C/HGV (17 patients). In the nonviral liver disease group of 35 patients with alcoholic liver disease, fatty liver, liver abscess, and biliary disease, the infection rates were 6% for HBV (2 patients), 20% for HCV (7 patients), and 26% for GBV-C/HGV (9 patients). The most common viral genotypes were type C of HBV (77%), type 3b of HCV (67%), and type 2 of GBV-C/HGV (67%). Moreover, testing for HEV among 371 subjects resulted in the detection of anti-HEV immunoglobulin G (IgG) in 117 patients (32%). The age prevalence of anti-HEV IgG was 3% for patients younger than 20 years and 30% or more for patients 20 years of age or older. Furthermore, a high prevalence of anti-HEV IgG (24%) was also found in swine living together with humans in Yangon. These results suggest that these hepatitis virus infections are widespread in Myanmar and have led to a high incidence of acute and chronic liver disease patients in the region.

Homologous recombination in GB virus C/hepatitis G virus

Analysis of 33 GB virus C/hepatitis G virus (GBV-C/HGV) full or nearly full genome sequences revealed several putative inter- and intrasubtype recombinants. The breakpoints of the recombinant regions were mapped using a maximum-likelihood method, and the statistical significance for each region was tested using Monte Carlo simulation. The results were highly significant and provided evidence for the existence of complex mosaic genomes showing as many as nine recombination events, with breakpoints in the 5' UTR and in all of the coding regions except the short NS4b gene. Recombination was confirmed by separate phylogenetic analysis of the various recombinant regions and by Sawyer's runs test. Taken together, these findings demonstrate for the first time that recombination is common in natural populations of GBV-C and that it takes place both within and between subtypes. The wide-ranging implications of such nonclonal history for reconstructing the spread and timescale of GBV-C evolution are discussed.

Rapid and specific genotyping system for hepatitis B virus corresponding to six major genotypes by PCR using type-specific primers

A simple and precise genotyping system based on PCR using type-specific primers was developed for the determination of genotypes A through F of hepatitis B virus (HBV). This assay system is considered to be a useful tool for the molecular diagnosis of HBV infection and for large-scale surveys.

Genotyping system of GBV-C/HGV type 1 to type 4 by the polymerase chain reaction using type-specific primers and geographical distribution of viral genotypes

Based on variation in nucleotide sequence of 5'-untranslated region, GB virus type C (GBV-C) and hepatitis G virus (HGV) can be classified into three major genotypes. In addition to this classification, a novel genotype of GBV-C/HGV was identified and designated type 4. However, genotyping of GBV-C/HGV has been hampered by the lack of suitable assays. In this study, a simple and precise genotyping system based on PCR using the type-specific primers was developed for the determination of genotypes 1, 2, 3, and 4 of GBV-C/HGV. A total of 235 serum samples obtained from 11 different countries were tested by our PCR genotyping system of GBV-C/HGV. The results revealed that type 1 was prevalent mainly in Ghana, type 2 was prevalent in the USA, Spain, Egypt, Nepal and Myanmar, type 3 was prevalent in Japan and Bolivia, and type 4 was prevalent in Vietnam and Myanmar among the countries investigated in the present study. To confirm the specificity of the results of genotyping by PCR, phylogenetic analysis in the 5'-untranslated region of GBV-C/HGV was undertaken in 99 serum samples. By this analysis, the specificity of the genotyping system by PCR was confirmed. This assay system may be useful for rapid typing of GBV-C/HGV RNA when either epidemiological or transmission studies of this agent are carried out.