Sequence and genomic organization of GBV-C: a novel member of the flaviviridae associated with human non-A-E hepatitis

Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family

Proposals are described for the assignment of recently reported viruses, infecting rodents, bats and other mammalian species, to new species within the Hepacivirus and Pegivirus genera (family Flaviviridae). Assignments into 14 Hepacivirus species (Hepacivirus A–N) and 11 Pegivirus species (Pegivirus A–K) are based on phylogenetic relationships and sequence distances between conserved regions extracted from complete coding sequences for members of each proposed taxon. We propose that the species Hepatitis C virus is renamed Hepacivirus C in order to acknowledge its unique historical position and so as to minimize confusion. Despite the newly documented genetic diversity of hepaciviruses and pegiviruses, members of these genera remain phylogenetically distinct, and differ in hepatotropism and the possession of a basic core protein; pegiviruses in general lack these features. However, other characteristics that were originally used to support their division into separate genera are no longer definitive; there is overlap between the two genera in the type of internal ribosomal entry site and the presence of miR-122 sites in the 5′ UTR, the predicted number of N-linked glycosylation sites in the envelope E1 and E2 proteins, the presence of poly U tracts in the 3′ UTR and the propensity of viruses to establish a persistent infection. While all classified hepaciviruses and pegiviruses have mammalian hosts, the recent description of a hepaci-/pegi-like virus from a shark and the likely existence of further homologues in other non-mammalian species indicate that further species or genera remain to be defined in the future.

GB Virus C/Hepatitis G Virus Envelope Glycoprotein E2: Computational Molecular Features and Immunoinformatics Study

INTRODUCTION

GB virus C (GBV-C) or hepatitis G virus (HGV) is an enveloped, RNA positive-stranded flavivirus-like particle. E2 envelope protein of GBV-C plays an important role in virus entry into the cytosol, genotyping and as a marker for diagnosing GBV-C infections. Also, there is discussion on relations between E2 protein and gp41 protein of HIV. The purposes of our study are to multi aspect molecular evaluation of GB virus C E2 protein from its characteristics, mutations, structures and antigenicity which would help to new directions for future researches.

EVIDENCE ACQUISITION

Briefly, steps followed here were; retrieving reference sequences of E2 protein, entropy plot evaluation for finding the mutational /conservative regions, analyzing potential Glycosylation, Phosphorylation and Palmitoylation sites, prediction of primary, secondary and tertiary structures, then amino acid distributions and transmembrane topology, prediction of T and B cell epitopes, and finally visualization of epitopes and variations regions in 3D structure.

RESULTS

Based on the entropy plot, 3 hypervariable regions (HVR) observed along E2 protein located in residues 133-135, 256-260 and 279-281. Analyzing primary structure of protein sequence revealed basic nature, instability, and low hydrophilicity of this protein. Transmembrane topology prediction showed that residues 257-270 presented outside, while residues 234- 256 and 271-293 were transmembrane regions. Just one N-glycosylation site, 5 potential phosphorylated peptides and two palmitoylation were found. Secondary structure revealed that this protein has 6 α-helix, 12 β-strand 17 Coil structures. Prediction of T-cell epitopes based on HLA-A*02:01 showed that epitope NH3-LLLDFVFVL-COOH is the best antigen icepitope. Comparative analysis for consensus B-cell epitopes regarding transmembrane topology, based on physico-chemical and machine learning approaches revealed that residue 231- 296 (NH2- EARLVPLILLLLWWWVNQLAVLGLPAVEAAVAGEVFAGPALSWCLGLPVVSMILGLANLVLYFRWL-COOH) is most effective and probable B cell epitope for E2 protein.

CONCLUSIONS

The comprehensive analysis of a protein with important roles has never been easy, and in case of E2 envelope glycoprotein of HGV, there is no much data on its molecular and immunological features, clinical significance and its pathogenic potential in hepatitis or any other GBV-C related diseases. So, results of the present study may explain some structural, physiological and immunological functions of this protein in GBV-C, as well as designing new diagnostic kits and besides, help to better understandingE2 protein characteristic and other members of Flavivirus family, especially HCV.

Hepatitis G virus genomic RNA is pathogenic to Macaca mulatta

AIM: To explore the pathogenicity and infectivity of hepatitis G virus (HGV) by observing replication and expression of the virus, as well as the serological and histological changes of Macaca mulatta infected with HGV genomic RNA or HGV RNA-positive serum.

METHODS: Full-length HGV cDNA clone (HGVqz) was constructed and proved to be infectious, from which HGV genomic RNA was transcribed in vitro. Macaca mulatta BY1 was intra-hepatically inoculated with HGV genomic RNA, HGV RNA-positive serum from BY1 was intravenously inoculated into Macaca mulatta BM1, and then BB1 was infected with serum from BM1. Serum and liver tissue were taken regularly, and checked with RT-PCR, in situ hybridization and other immunological, serological, histological assays.

RESULTS: Serum HGV RNA was detectable in all the 3 Macaca mulattas, serological and histological examinations showed the experimental animals had slightly elevated alanine transaminase (ALT) and developed HGV viremia during the infectious period. The histology, immunohis-tochemistry, and in situ hybridization in liver tissues of the inoculated animals demonstrated a very mild hepatitis with HGV antigen expression in cytoplasm of hepatocytes. RT-PCR and quantitative PCR results showed that HGV could replicate in liver.

CONCLUSION: The genomic RNA from full-length HGV cDNA is infectious to the Macaca mulatta and can cause mild hepatitis. HGV RNA-positive serum, from HGV RNA inoculated Macaca mulatta, is infectious to other Macaca mulattas. Macaca mulatta is susceptible to the inoculated HGV, and therefore can be used as an experimental animal model for the studies of HGV infection and pathogenesis.

Prevalence of hepatitis G virus infection and homology of different viral strains in Southern China

AIM: To investigate the prevalence of hepatitis G virus (HGV) infection and to analyse the homology of different HGV strains in Southern China.

METHODS: A total of 1993 sera from different groups in Guangdong, Hong Kong, and Yunnan were detected by reverse transcription polymerase chain reaction (RT-PCR). The nucleotide sequences of 5’untranslated region (5’UTR) derived from 20 strains and NS5 region from 3 strains were determined.

RESULTS: The positive rate of HGV RNA was 0.89% in community population, 2.57% in blood donors, 17.86% in intravenous drug abusers, 14.13% in patients with hemodialysis, 13.66% in those with hepatocellular carcinoma, 25.30% in non A-E hepatitis, 7.22% in hepatitis B, 12.73% in hepatitis C, 41.67% in patients received bone marrow transplantation, respectively. The homology was 90.40%-100% in 5’UTR among different strains, while that of NS5 region was 93.3%-94% in nucleotide sequence, and 97%-99.2% in amino acid sequence.

CONCLUSION: These results showed that there was a high incidence of HGV infection in patients from Southern China, being treated for bone marrow transplantation, hepatocellular carcinoma and those on haemodialysis. Furthermore, there was also a high frequency of co-infection of HGV with HBV, HCV, non A-E viral hepatitis and that among intravenous drug abusers. The study also showed that sequence variation in different strains was associated with geographical factors but there was no significant difference in 5’UTR in circulating viruses between different patient groups. Finally, by sequential analysis of viral species present in individual patients over a three months period there was no evidence of sequence variation in the 5' UTR.

Investigation of HGV and TTV infection in sera and saliva from non-hepatitis patients with oral diseases

AIM: To determine the frequencies of HGV and TTV infections in serum and saliva samples of non-hepatitis patients with oral diseases in Hangzhou area, and to understand the correlation between detected results of HGV RNA and/or TTV DNA in sera and in saliva from the same patients.

METHODS: RT-nested PCR for HGV RNA detection and semi-nested PCR for TTV DNA detection were performed in the serum and saliva samples from 226 non-hepatitis patients with oral diseases, and nucleotide sequence analysis.

RESULTS: Twenty-seven (11.9%) and 21 (9.3%) of the 226 serum samples were only positive for HGV RNA and TTV DNA, respectively. 10 (4.4%) and 9 (3.9%) of the 226 saliva samples were only positive for HGV RNA and TTV DNA, respectively. And 7 (3.1%) of the serum samples and 2 (0.9%) of the saliva samples showed the positive amplification results for both HGV RNA and TTV DNA. 12 saliva samples from the 34 patients (35.3%) with HGV or HGV/TTV viremia and 11 saliva samples from the 28 patients (39.3%) with TTV or HGV/TTV viremia were HGV RNA detectable, respectively, including two patients positive for both HGV RNA and TTV DNA in serum and saliva samples. No saliva samples from the 226 patients were found to be HGV RNA or TTV DNA detectable while their serum samples were negative for HGV or TTV. Homologies of the nucleotide sequences of HGV and TTV amplification products from the serum and saliva samples of the two patients compared with the reported sequences were 88.65%-91.49% and 65.32%-66.67%, respectively. In comparison with the nucleotide sequences of amplification products between serum and from saliva sample from any one of the two patients, the homologies were 98.58% and 99.29% for HGV, and were 98.65% and 98.20% for TTV, respectively.

CONCLUSION: Relatively high carrying rates of HGV and/or TTV in the sera of non-hepatitis patients with oral diseases in Hangzhou area are demonstrated. Parts of the carriers are HGV and/or TTV positive in their saliva. The results of this study indicate that dentists may be one of the populations with high risk for HGV and/or TTV infection, and by way of saliva HGV and TTV may be transmitted among individuals.

Prokaryotical expression of structural and non-structural proteins of hepatitis G virus

AIM: To study the epitope distribution of hepatitis G virus (HGV) and to seek for the potential recombinant antigens for the development of HGV diagnositic reagents.

METHODS: Fourteen clones encompassing HGV gene fragments from core to NS3 and NS5 were constructed using prokaryotic expression vector pRSE T and (or) pGEX, and expressed in E. coli. Western blotting and ELISA were used to detect the immunoreactivity of these recombinant proteins.

RESULTS: One clone with HGV fragment from core to E1 (G1), one from E2 (G31), three from NS3 (G6, G61, G7), one from NS5B (G821) and one chimeric fragment from NS3 and NS5B (G61-821) could be expressed well and showed obvious immunoreactivity by Western blotting. One clone with HGV framment from NS5B (G82) was also well expressed, but could not show immunoreactivity by Western blotting. No obvious expression was found in the other six clones. All the expressed recombinant proteins were in inclusion body form, except the protein G61 which could be expressed in soluble form. Further purified recombinant proteins G1, G31, G61, G821 and G61-821 were detected in indirected ELISA as coating antigen respectively. Only recombinant G1 could still show immunoreactivity, and the other four recombinant proteins failed to react to the HGV antibody positive sera. Western blotting results indicated that the immunoactivity of these four recombinant proteins were lost during purification.

CONCLUSION: Core to E1, E2, NS3 and NS5 fragment of HGV contain antigenic epitopes, which could be produced in prokaryotically expressed recombinant proteins. A high-yield recombinant protein (G1) located in HGV core to E1 could remain its epitope after purification, which showed the potential that G1 could be used as a coating antigen to develop an ELISA kit for HGV specific antibody diagnosis.

High frequencies of HGV and TTV infections in blood donors in Hangzhou

AIM: To determine the frequencies of HGV and TTV infections in blood donors in Hangzhou.

METHODS: RT-nested PCR for HGV RNA detection and semi-nested PCR for TTV DNA detection in the sera from 203 blood donors, and nucleotide sequence analysis were performed.

RESULTS: Thirty-two (15.8%) and 30 (14.8%) of the 203 serum samples were positive for HGV RNA and TTV DNA, respectively. And 5 (2.5%) of the 203 serum samples were detectable for both HGV RNA and TTV DNA. Homology of the nucleotide sequences of HGV RT-nested PCR products and TTV semi-nested PCR products from 3 serum samples compared with the reported HGV and TTV sequences was 89.36%, 87.94%, 88.65% and 63.51%, 65.77% and 67.12%, respectively.

CONCLUSION: The infection rates of HGV and/or TTV in blood donors are relatively high, and to establish HGV and TTV examinations to screen blood donors is needed for transfusion security. The genomic heterogeneity of TTV or HGV is present in the isolates from different areas.

A high frequency of GBV-C/HGV coinfection in hepatitis C patients in Germany

AIM: To detect infection rate of GBV-C/HGV in hepatitis C patients, to determine the methods of higher sensitivity and the primers of higher efficiency for GBV-C/HGV RNA detection and to study the dominant subtype and mutation of GBV-C/HGV.

METHODS: Quantitative RT-PCR for detection pf HCV RNA concentration in serum samples, RT-nested PCR with two sets of primers for detection of GBV-CRNA, RT-PCR ELISA with two sets of primers for detection of HGV RNA, nucleotide sequence and putative amino acid sequence analysis.

RESULTS: The positive rates of GBV-C RNA at the 5’-NCR and NS3 region in 211 serums amples from the patients with HCV infection were 31.8% and 22.8% respectively. The positive rates of HGV RNA at the 5’-NCR and NS5 region in the same samples were 47.9% and 31.8% respectively. The total positive rate of GBV-C/HGV RNA was as high as 55.5%. HCV copy numbers in the patients without GBV-C/HGV coinfection were statistically higher than that in the patients with GBV-C/HGV coinfection (P < 0.01). Frequent mutation of nucleotide residue was present in the amplification products. Frameshift mutation was found in two samples with GBV-C NS3 region nucleotide sequences. All nucleotide sequences from amplification products showed higher homology to HGV genome than to GBV-C genome even though part of the sequences were amplified with GBV-C primers.

CONCLUSION: A high frequency of GBV-C/HGV coinfection existed in the hepatitis C patients. RT-PCR ELISA was more sensitive than RT-nested PCR for detection of GBV-C/HGV RNA. The primers derived from the 5’-NCR was more efficient than those derived from the NS3 and NS5 regions. A reverse relationship was found to exist between HCV RNA concentration and GBV-C/HGV infection frequency. HGV was the dominant subtype of the virus in the local area. The major mutations of GBV-C/HGV genomes were random mutation of nucleotide residue.

Hepatitis G virus infection in patients with chronic non-A–E hepatitis

AIM: To elucidate the role of hepatitis G virus (HGV) infection in chronic non-A–E hepatitis and sequence the partial NS5 genome of HGV isolated from the serum of a Chinese patient with chronic non-A–E hepatitis

METHODS: Serum samples of patients with chronic non-A–E hepatitis were collected and total nucleic acids were extracted and subjected to reverse transcriptase-nested-polymerase chain reaction (RT-nested-PCR) using primers from the putative NS5 region of HGV genome. Then, 994bp cDNA was prepared from the positive serum, purified with electrophoresis of polyacrylamide gels, and directly sequenced using the dideoxy-mediated chain-termination method.

RESULTS: HGV-RNA was detected in 1 of the 35 patients with chronic non-A–E hepatitis. Compared with the 2 HGV isolates (PNF2161 and R10291) obtained from American patients, the HGV NS5 gene of this Beijing isolate (HG-G) showed homology of 88.0% and 89.2% respectively. On the other hand, in comparison with the West African isolate (GBV-C), the Beijing isolate showed homology of 93.5%. The patient showed persistent increase of alanine transaminase, but normal levels were achieved after interferon therapy with persistent positive HGV RNA.

CONCLUSION: HGV is one of the causes of chronic non-A–E hepatitis, but it may not be a very important cause. The nucleotide sequence of partial NS5 gene of HG-G was found to be highly homologous to the West Africa isolate.