1
|
Alfson KJ, Beadles MW, Griffiths A. A new approach to determining whole viral genomic sequences including termini using a single deep sequencing run. J Virol Methods 2014; 208:1-5. [PMID: 25075935 DOI: 10.1016/j.jviromet.2014.07.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 12/20/2022]
Abstract
Next-generation sequencing is now commonly used for a variety of applications in virology including virus discovery, investigation of quasispecies, viral evolution, metagenomics, and analyses of antiviral resistance. However, there are limitations with the current sample preparation methods used for deep sequencing of viral genomes, especially during de novo sequencing. For example, current methods are unable to capture the terminal sequences of viral genomes in an efficient and effective manner; data representing the 3' and 5' ends are typically insufficient. Methods such as Rapid Amplification of cDNA Ends address this issue but these methods can be time consuming, may require some prior knowledge of the viral sequence, and require multiple independent procedures. The current study outlines a sample preparation technique that overcomes some of these shortcomings. The method relied on random fragmentation with divalent cations and subsequent adapter ligation directly to RNA, rather than cDNA, to maximize the quality and quantity of terminal reads. The technique was tested on RNA samples from two different RNA viruses, Ebola virus and hepatitis C virus. This method permits rapid preparation of samples for deep sequencing while eliminating the use of sequence specific primers and captures the entire genome sequence, including the 5' and 3' ends. This could improve the efficiency of virus discovery projects where the terminal ends are unknown.
Collapse
Affiliation(s)
- Kendra J Alfson
- Department of Virology and Immunology, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA; Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, Mail Code 7758, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Michael W Beadles
- Department of Virology and Immunology, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA; Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, Mail Code 7758, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| |
Collapse
|
2
|
Etiologic influence on chromosomal aberrations in European hepatocellular carcinoma identified by CGH. Pathol Res Pract 2013; 209:380-7. [PMID: 23706943 DOI: 10.1016/j.prp.2013.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/14/2013] [Accepted: 04/16/2013] [Indexed: 02/07/2023]
Abstract
Previous studies suggest different pathways in the molecular development of hepatocellular carcinoma (HCC). We investigated the pattern of chromosomal imbalances in HCC depending on the type of underlying liver disease as detected by comparative genomic hybridization in 67 cases of primary HCC occurring in non-cirrhotic livers (n=30), in liver cirrhosis (LC) related to alcohol intake (n=9), cryptogenic or metabolic changes (n=11), and chronic viral hepatitis B or C (n=17). HCC were treated by liver resection in 48 patients and transplantation in 19 patients. The 10-year disease-free and overall survival rates were 51% and 68%, respectively. The copy number changes occurring in more than 10% of cases were gains at 8q (55%), 1q (49%), 7q (15%), 7p (13%), 6p (12%), and 20q (12%), as well as losses at 8p (55%), 4q (33%), 6q (33%), 13q (25%), 14q (24%), 17p (22%), 16q (19%), 1p (18%), 18q (16%), 9p (13%), 10q (13%), 4p (12%), and 9q (12%). HCC arising in alcoholic LC showed a different pattern with significantly fewer net changes (p=0.008), particularly fewer chromosomal gains (p=0.008) and fewer breakpoints (p=0.003) compared to the other investigated HCC subgroups. Future clinical studies should evaluate the prognostic relevance of these findings.
Collapse
|
3
|
Shi JJ, Ji FH, He PL, Yang YX, Tang W, Zuo JP, Li YC. Synthesis and hepatitis C antiviral activity of 1-aminobenzyl-1H-indazole-3-carboxamide analogues. ChemMedChem 2013; 8:722-5. [PMID: 23512654 DOI: 10.1002/cmdc.201300083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Indexed: 11/09/2022]
Abstract
FIGHTING HCV: Two potent antiviral analogues were developed from a previously identified lead as novel agents against hepatitis C virus. Their potency and selectivity (5 n: IC50 =0.013 μM and EC50 =0.018 μM; 5 t: IC50 =0.007 μM and EC50 =0.024 μM) make them good candidates for further development as antiviral agents.
Collapse
Affiliation(s)
- Jing-Jing Shi
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Road Zu Chong Zhi, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China
| | | | | | | | | | | | | |
Collapse
|
4
|
Wang JH, Zheng X, Ke X, Dorak MT, Shen J, Boodram B, O'Gorman M, Beaman K, Cotler SJ, Hershow R, Rong L. Ethnic and geographical differences in HLA associations with the outcome of hepatitis C virus infection. Virol J 2009; 6:46. [PMID: 19409091 PMCID: PMC2679741 DOI: 10.1186/1743-422x-6-46] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 05/01/2009] [Indexed: 01/12/2023] Open
Abstract
Backgrounds The association of human leukocyte antigen (HLA) genes with the outcome of hepatitis C virus (HCV) infection may be modified by ethnic and geographical differences. Results HLA-A, -C, -DRB1 and -DQB1 genotyping were performed in a Midwestern American cohort of 105 HCV infected subjects among which 49 cleared HCV infection and 56 had persistent viral infection. A new protective association of HLA-Cw*05 to HCV infection of all ethnic populations was identified (OR = 0.12, 95% CI = 0.01–0.97, P = 0.03). It was surprising that HLA-A*02 (P for interaction = 0.02) and HLA-DRB1*12 (P for interaction = 0.05) showed statistical interaction with race indicating opposite associations in Caucasians (OR = 2.74 for A*02 and 2.15 for DRB1*12) and non-Caucasians (OR = 0.41 for A*02 and 0.15 for DRB1*12). In addition, HLA-DRB1*01 (OR = 0.26), DQB1*05 (OR = 0.23) and the haplotype DRB1*01-DQB1*05 (OR = 0.19) showed strong associations with viral clearance in Caucasians. The protective associations of A*03 (OR = 0.20) and DQB1*03 (OR = 0.20) were exclusive to non-Caucasians. In contrast, DQB1*02 (OR = 2.56, 95% CI = 1.15–7.71, P = 0.02) and the haplotype DRB1*07-DQB1*02 (OR = 5.25, 95% CI = 1.04–26.6, P = 0.03) were risk markers in Caucasians. Conclusion The associations of HLA-A*02 and HLA-DRB1*12 with HCV infection are opposite with different races. HLA-A*03, Cw*05, DRB1*01, DQB1*03 and DQB1*05 are associated with viral clearance while HLA-DRB1*07 and DQB1*02 are risk markers for viral persistence of HCV infection in Midwestern Americans. These results reveal ethnically and geographically different distribution of HLA-genes which are associated with the outcome of HCV infection.
Collapse
Affiliation(s)
- Jane H Wang
- Division of Hepatology, Department of Medicine, University of Illinois at Chicago, IL, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Wang XP, Goodwin L, Kahn P, Gawel C, Cunha CB, Laser B, Sahn B, Kaplan MH. Influence of increased CD4 cell counts on the genetic variability of hepatitis C virus in patients co-infected with human immunodeficiency virus I. J Biomol Tech 2006; 17:228-39. [PMID: 16870714 PMCID: PMC2291784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In order to study the effect of increased CD4 cell counts on the biology of hepatitis C virus (HCV), we analyzed the genetic variability of HCV generated over 8 y in eight human immunodeficiency virus-1 (HIV-1) and HCV co-infected patients. This was a retrospective study in which HIV patients were selected who had profound immune impairment evident over four years and were co-infected with HCV genotype 1 and who then went on highly active antiretroviral therapy (HAART). These patients achieved different degrees of immune reconstitution, measured as increased CD4 cell counts during a 4- to 8-y period, following initiation of HAART. HCV genetic variability was determined by measuring the genetic diversity (Hamming distance, HD), and complexity (number of viral variants) in plasma samples collected at yearly intervals just before and after the initiation of HAART. The parameters were assessed by molecular cloning and sequencing of a 575-bp fragment including the HCV envelope 1 and envelope 2 genes (E1/E2), containing the hypervariable region 1 (HVR1). significantly increased HVR1 genetic diversity was observed in analyzed samples where the patients' CD4 cell counts were > or =100 compared with CD4 cell counts <100. A significant increase in genetic diversity in HVR1 was detected in co-infected patients whose CD4 cell counts increased from <100 to >400 over a period of more than 4 y of HAART therapy. This was in contrast to a minimal increase in HCV genetic diversity of HVR1 occurring in patients whose CD4 cell counts failed to rise much over 200 over 7 y of follow up. Insertion and deletion of HCV genomic fragments in the E1/E2 region was documented in one patient who developed fulminant hepatitis C.
Collapse
Affiliation(s)
- Xue-Ping Wang
- Center of AIDS Research and Treatment, Division of Infectious Disease, Department of Medicine, North Shore University Hospital, Manhasset, NY, USA
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Yang M, Zhu F, Sønderstrup G, Eckels DD. Recognition of endogenously synthesized HLA-DR4 restricted HCV epitopes presented by autologous EBV transformed B-lymphoblastoid cell line. Vaccine 2005; 23:951-62. [PMID: 15603898 DOI: 10.1016/j.vaccine.2004.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Revised: 06/03/2004] [Accepted: 06/03/2004] [Indexed: 01/12/2023]
Abstract
Hepatitis C virus (HCV) causes non-A, non-B hepatitis and infects an estimated 170 million people worldwide. The treatment for HCV infection is often unsuccessful with high costs and many side-effects. There is a great need for alternative therapies including preventive and therapeutic vaccination for HCV infection. The experiments in this study were carried out to elucidate whether endogenously expressed antigen can be presented to helper T-cells restricted by class II molecules and to determine whether responses to plasmid-derived antigen resemble those that we have reported for recombinant antigens or synthetic peptides. To address these issues, a multi-epitope minigene was expressed in 293T-cells and Epstein-Barr virus (EBV)-transformed B-lymphoblastoid cells (BLCL). The transfected BLCLs were employed as APCs to stimulate epitope-specific T-cell hybridomas (THC). The results demonstrated that the endogenously expressed minigene antigens could be processed and presented to T-cell hybridomas by HLA matched BLCL. Five out of seven incorporated epitopes were recognized. Blockade of HLA DR could abolish the release of IL-2, which demonstrated that the endogenously expressed minigene antigens were presented by MHC class II molecules. The presentation of endogenously expressed antigens was much more efficient than that of exogenous antigens, at least in the present study. The findings obtained here have important significance for the development of an HCV DNA vaccine.
Collapse
Affiliation(s)
- Meiying Yang
- Department of Pediatrics (Endocrinology), Medical College of Wisconsin, 8710 Watertown Plank Road, P. O. Box 26509, Milwaukee, WI 53226-0509, USA
| | | | | | | |
Collapse
|
7
|
Waris G, Livolsi A, Imbert V, Peyron JF, Siddiqui A. Hepatitis C virus NS5A and subgenomic replicon activate NF-kappaB via tyrosine phosphorylation of IkappaBalpha and its degradation by calpain protease. J Biol Chem 2003; 278:40778-87. [PMID: 12909638 DOI: 10.1074/jbc.m303248200] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus nonstructural protein 5A (NS5A) has been implicated in the HCV antiviral resistance, replication, and transactivation of cellular gene expression. We have recently shown that HCV NS5A activates NF-kappaB via oxidative stress (22). In this study, we investigate the molecular mechanism(s) of NF-kappaB activation in response to oxidative stress induced by NS5A protein. In contrast to the classic Ser32,36 phosphorylation of IkappaBalpha, we report here that tyrosine phosphorylation of IkappaBalpha at Tyr42 and Tyr305 residues is induced by the HCV NS5A and the subgenomic replicons in the NF-kappaB activation process. Use of IkappaBalpha-Tyr42,305 double mutant provided the evidence for their key role in the activation of NF-kappaB. Activation of NF-kappaB was blocked by a series of tyrosine kinase inhibitors but not by IkappaB kinase inhibitor BAY 11-7085. More specifically, a ZAP-70 knock-out cell line expressing NS5A and other nonstructural proteins respectively prevented the NF-kappaB activation, indicating the involvement of ZAP-70 as a probable tyrosine kinase in the activation process. Evidence is also presented for the possible role of calpain proteases in the NS5A-induced IkappaBalpha degradation. These studies collectively define an alternate pathway of NF-kappaB activation by NS5A alone or in the context of the HCV subgenomic replicon. Constitutive activation of NF-kappaB by HCV has implications in the chronic liver disease including hepatocellular carcinoma associated with HCV infection.
Collapse
Affiliation(s)
- Gulam Waris
- Department of Microbiology and Program in Molecular Biology, B-172, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
| | | | | | | | | |
Collapse
|
8
|
Elahi E, Pourmand N, Chaung R, Rofoogaran A, Boisver J, Samimi-Rad K, Davis RW, Ronaghi M. Determination of hepatitis C virus genotype by Pyrosequencing. J Virol Methods 2003; 109:171-6. [PMID: 12711060 DOI: 10.1016/s0166-0934(03)00068-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A simple sequencing-based assay is described for genotyping of hepatitis C virus (HCV). RT-PCR was employed to amplify a 237-nucleotide-long fragment from the 5' untranslated region (UTR) of the genome using one biotinylated and one normal primer. Subsequent to capture of the PCR products on streptavidin-coated beads, single-stranded DNA separation, and hybridization of sequencing primer, Pyrosequencing was performed. The genotype of 98 samples out of which 77 samples were from American veterans and 21 samples were from Iran was determined. The samples from the American veterans contained six different subtypes, while five subtypes were found in Iranian samples. For rapid population-specific HCV subtyping, a multiplex assay was developed. This study demonstrates the suitability of this technology for low-cost, high throughput and accurate microbial genotyping.
Collapse
Affiliation(s)
- Elahe Elahi
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
Of all the hepatitis viruses, only the hepatitis B virus (HBV) and hepatitis C virus (HCV) cause chronic hepatitis, which can progress to cirrhosis and hepatocellular carcinoma. In this review, we discuss how these two biologically diverse viruses use common pathways to induce oxidative stress and activation of key transcription factors, known to be involved in inflammatory processes in cells. Activation of NF-kB and STAT-3 most likely contribute to the progression of viral infections to chronic hepatitis and liver oncogenesis associated with HBV and HCV infections. In this review, we focus on the mechanisms of action of HBx and HCV NS5A proteins in inducing intracellular events associated with the viral infections.
Collapse
Affiliation(s)
- G Waris
- Department of Microbiology, University of Colorado Health Sciences Center, 4200 E, 9th Ave, Denver, Colorado 80262, USA
| | | |
Collapse
|
10
|
Waris G, Tardif KD, Siddiqui A. Endoplasmic reticulum (ER) stress: hepatitis C virus induces an ER-nucleus signal transduction pathway and activates NF-kappaB and STAT-3. Biochem Pharmacol 2002; 64:1425-30. [PMID: 12417255 DOI: 10.1016/s0006-2952(02)01300-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Human hepatitis C virus (HCV) is the leading cause of chronic hepatitis, which often results in liver cirrhosis and hepatocellular carcinoma. The HCV RNA genome codes for at least ten proteins. The HCV non-structural protein 5A (NS5A) has generated considerable interest due to its effect on interferon sensitivity via binding and inactivating the cellular protein kinase, PKR. It has been shown that NS5A engages in the endoplasmic reticulum (ER)-nucleus signal transduction pathway. The expression of NS5A in the ER induces an ER stress ultimately leading to the activation of STAT-3 and NF-kappaB. This pathway is sensitive to inhibitors of Ca(2+) uptake in the mitochondria (ruthenium red), Ca(2+) chelators (TMB-8, EGTA-AM), and antioxidants (PDTC, NAC, Mn-SOD). The inhibitory effect of protein tyrosine kinase (PTK) inhibitors indicates the involvement of PTK in NF-kappaB activation by NS5A. This implicates an alternate pathway of NF-kappaB activation by NS5A. The actions of NS5A have also been studied in the context of an HCV subgenomic replicon inducing a similar intracellular event. Thus, activation of NF-kappaB leads to the induction of cellular genes, which are largely antiapoptotic in function. These studies suggest a potential function of NS5A in inducing chronic liver disease and hepatocellular carcinoma associated with HCV infection.
Collapse
Affiliation(s)
- Gulam Waris
- Department of Microbiology, Program in Molecular Biology, University of Colorado Health Sciences Center, 4200 East 9th Avenue, Denver, CO 80262, USA
| | | | | |
Collapse
|
11
|
Affiliation(s)
- W. Keith Paver
- PHLS North West, Public Health Laboratory, Withington Hospital, Manchester, UK; and
| | | |
Collapse
|
12
|
Tornillo L, Carafa V, Richter J, Sauter G, Moch H, Minola E, Gambacorta M, Bianchi L, Vecchione R, Terracciano LM. Marked genetic similarities between hepatitis B virus-positive and hepatitis C virus-positive hepatocellular carcinomas. J Pathol 2000; 192:307-12. [PMID: 11054713 DOI: 10.1002/1096-9896(2000)9999:9999<::aid-path706>3.0.co;2-o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common neoplasms worldwide. Well-established risk factors include infections with two very different viruses: the DNA virus causing hepatitis B (HBV) and the RNA virus inducing hepatitis C (HCV). In order to determine whether genetic differences exist between HBV- and HCV-induced HCC, 41 HCC samples of known vival status were examined by comparative genomic hybridization (CGH). The analysis revealed frequent deletions of 1p (24%), 4q (39%), 6q (41%), 8p (44%), 9p (24%), 11q (24%), 12q (22%), and 13q (39%), as well as common gains of 1q (46%), 6p+ (20%), 8q+ (41%), 11q (27%), and 17q+ (37%). There was no significant difference in the number and type of chromosomal imbalances between 25 HCV- and 16 HBV-infected tumours. This is consistent with models suggesting that HBV and HCV cause cancer through non-specific inflammatory and regenerative processes, rather than through virus-specific interactions with defined target genes. Chromosomal imbalances were also unrelated to the grade and stage of HCC. This may suggest that most gross genomic alterations occur early during HCC development and that further progression of these tumours may be associated with other types of genetic changes, not detectable by CGH. In summary, these data show that characteristic gross genomic changes occur in HCC, but these alterations at present do not appear to have diagnostic or prognostic applications.
Collapse
Affiliation(s)
- L Tornillo
- Institute of Pathology, University of Basel, Basel, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Sobolev BN, Poroikov VV, Olenina LV, Kolesanova EF, Archakov AI. Comparative analysis of amino acid sequences from envelope proteins isolated from different hepatitis C virus variants: possible role of conservative and variable regions. J Viral Hepat 2000; 7:368-74. [PMID: 10971825 DOI: 10.1046/j.1365-2893.2000.00242.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Sequences of the E1 and E2 envelope proteins of hepatitis C virus (HCV) (827 non-identical items) were collected from available sources and aligned. Analysis of the alignment identified regions with different sequence variability. It was found that 33% and 50% of positions within E1 and E2, respectively, were highly conservative. Such conservation can be considered as the minimum for maintaining stability of the three-dimensional structure and function of these proteins. Conserved cysteines in E1 and E2 (eight and 18 residues, respectively) were presumed to form intramolecular disulphide bonds. Both envelope proteins were predicted to contain 14 conservative glycosylation sites. Two additional glycosylation sites were predicted in 58% of E1 and 30% of E2 sequences within the corresponding regions. We describe the positions of six conservative regions in E1 and E2, which have several charged and aromatic residues known to participate frequently in protein-protein recognition. Peculiarities in the amino acid content of conservative fragments and putative differences in glycosylation were considered with regard to antigenic specificity and possible binding to surface structures of target cells. We also analysed the hypervariable region 1 (HVR1), located in the E2 protein. Aligned positions of HVR1 were described in relation to the maintenance of conformational stability and recognition of cell receptors.
Collapse
Affiliation(s)
- B N Sobolev
- Institute of Biomedical Chemistry, Russian Academy of Medical Science, Moscow, Russia
| | | | | | | | | |
Collapse
|
14
|
Zhang SZ, Liang JJ, Qi ZT, Hu YP. Cloning of the non-structural gene 3 of hepatitis C virus and its inducible expression in cultured cells. World J Gastroenterol 1999; 5:125-127. [PMID: 11819409 PMCID: PMC4688522 DOI: 10.3748/wjg.v5.i2.125] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To study the inducible expression of hepatitis C virus ns3 gene (HCV-ns3) in eukaryotic cells.
METHODS The ns3 gene was obtained from plasmid pBns3 by polymerase chain reaction and inserted into the cloning vector pGEM-T. Then, the ns3 was subcloned into the vector pMSG to generate dexamethasone (DM)inducible expression plasmid pMSG-ns3. CHO cells were transfected by pMSG-ns3 using calcium phosphate precipitation method and cultivated for 12 h-24 h. The transfected cells were induced with DM and the transient expression of NS3 protein was analyzed by ELISA and Western-blot methods.
RESULTS After treated with 3 × 10-8 mol/L DM, the expression of NS3 was observed in the transfected CHO cells. A slightly higher level of NS3 was shown along with the time of DM treatment.
CONCLUSION The inducible expressing vector pMSG-ns3 might be helpful for further studies of the characteristics of the ns3 gene in vivo.
Collapse
|
15
|
Wang H, Eckels DD. Mutations in Immunodominant T Cell Epitopes Derived from the Nonstructural 3 Protein of Hepatitis C Virus Have the Potential for Generating Escape Variants That May Have Important Consequences for T Cell Recognition. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.162.7.4177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
One of the most disturbing features of hepatitis C virus (HCV) is its long-term persistence in the host. One hypothesis to explain this phenomenon is that HCV escapes immune recognition through its intrinsic hypermutability. To determine whether immunodominant T cell epitopes derived from HCV nonstructural 3 (NS3) protein might be subject to sequence variations leading to escape mutants, we examined sequence variations of one IL-2-producing epitope, NS3358–375, and one IL-10-producing epitope, NS3505–521. By PCR amplification, cloning, and sequencing, we observed significant sequence variations in the two epitopes, although the selection intensity for each epitope was different. For NS3358–375, more variants were observed, and for NS3505–521, fewer mutations were observed. Moreover, functional studies revealed that three NS3358–375 and one NS3505–521 variants failed to stimulate T cell proliferation, and two other NS3358–375 and NS3505–521 variants weakly stimulated T cell responses. Our results are consistent with immune selection of viral variants at the epitope level, which may enable HCV to evade host defenses over time.
Collapse
Affiliation(s)
- Huiru Wang
- The Blood Research Institute, The Blood Center, Milwaukee, WI 53201
| | - David D. Eckels
- The Blood Research Institute, The Blood Center, Milwaukee, WI 53201
| |
Collapse
|
16
|
Tsopanomichalou M, Ergazaki M, Spandidos DA. Evaluation of Western Blot in Routine Diagnosis of Hepatitis C Virus. Int J Biol Markers 1997; 12:35-41. [PMID: 9176716 DOI: 10.1177/172460089701200107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hepatitis C virus (HCV) is among the major causes of parenterally transmitted hepatitis. Detection of infected persons would greatly diminish transmission rates and is therefore a significant parameter for prevention. Current assays are not able to resolve all cases and sometimes the results are controversial. The present study outlines problems that arise during routine testing. Two ELISA tests and three confirmatory tests were used and Polymerase Chain Reaction (PCR) data were available for some of the samples. The results of this study show that only 77.4% of samples positive for both ELISAs were confirmed as being positive. Controversial ELISA results remained controversial, depending on the confirmatory test used. PCR results, though not complete, point to the major problem of Western blot (WB) negative sera that prove positive for the viral genome and have to be excluded from screening for blood and organ donation. Since PCR cannot be used as a routine screening procedure, improvement of the routine assays is needed to minimize ambiguous results.
Collapse
Affiliation(s)
- M Tsopanomichalou
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, Greece
| | | | | |
Collapse
|
17
|
Affiliation(s)
- D D Eckels
- Blood Research Institute, Blood Center of Southeastern Wisconsin, Milwaukee, USA
| | | | | |
Collapse
|
18
|
Gastaldi M, Massacrier A, Planells R, Robaglia-Schlupp A, Portal-Bartolomei I, Bourlière M, Quilici F, Fiteni J, Mazzella E, Cau P. Detection by in situ hybridization of hepatitis C virus positive and negative RNA strands using digoxigenin-labeled cRNA probes in human liver cells. J Hepatol 1995; 23:509-18. [PMID: 8583137 DOI: 10.1016/0168-8278(95)80055-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In situ hybridization was performed using cRNA probes on human liver biopsies to localize both positive and negative RNA strands of hepatitis C virus. From the 5' non-coding region of the viral genome, 210 bp, were amplified by reverse transcriptase-polymerase chain reaction and cloned in a plasmid. Probes were produced by in vitro transcription, and labeled using digoxigenin-11-UTP. Positive HCV-RNA strands were detected in all 20 of the patients analyzed, whereas negative strands were detected in only nine patients, as confirmed using computerized image analysis. Both probes labeled the cytoplasm of hepatocytes with a perinuclear intensification. Few of the mononuclear cells infiltrating the portal connective space contained positive HCV-RNA strands only. Stacks of dilated endoplasmic reticulum cisternae were observed by electron microscopy and their relationship with the infection was discussed. This study confirmed that non-radioactive in situ hybridization represents a useful tool to analyze the localization and replication of hepatitis C virus in liver tissue.
Collapse
Affiliation(s)
- M Gastaldi
- Laboratoire de Biologie Cellulaire (Equipe DRED 868), Faculté de Médecine, Marseille, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Rey D, Hassairi N, Partisani M, Jacquemin C, Kempf G, De Mautort E, North M, Lang J. Séroprévalence du virus de l'hépatite C par tests ELISA et RIBA de 2e génération chez des patients infectés par le virus de l'immunodéficience humaine. Med Mal Infect 1995. [DOI: 10.1016/s0399-077x(05)80402-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
20
|
Abstract
Even though IV IgG concentrates are considered to be among the safest products derived from human plasma, some preparations have been associated with the sporadic transmission of NANB hepatitis and, specifically of hepatitis C. The risk of transmission may have decreased markedly for several IgG preparations since the availability of an immunological test to detect the antibodies against HCV in the starting plasma, but it has not been fully eradicated. Thus, in addition to established viral inactivation treatments, such as acid pH incubation, new methods have been (or are being) implemented to further reduce the risk of HCV infection through IV IgG concentrates. Among these methods are the solvent-detergent treatment already shown to be highly effective for the inactivation of HCV and other enveloped viruses in clotting factor concentrates, and nanofiltration for the specific removal of viruses on the basis of their size. Also, chromatographic methods have helped to improve the overall safety of the product not only by removing viruses but also by improving purity and thus favoring a better in vivo tolerance. This paper reviews the reported cases of HCV transmission and the viral validation data for various IV IgG processing steps and current specific viral inactivation methods. An overview of the present safety status of IV IgG concentrates is presented as well as the recent introduction of new promising techniques for the overall improvement of the safety of this plasma derivative.
Collapse
Affiliation(s)
- M Burnouf-Radosevich
- Unité de Recherche et Développement, Laboratoire Français du Fractionnement et des Biotechnologies, Lille
| |
Collapse
|
21
|
Wang C, Siddiqui A. Structure and function of the hepatitis C virus internal ribosome entry site. Curr Top Microbiol Immunol 1995; 203:99-115. [PMID: 7555093 DOI: 10.1007/978-3-642-79663-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- C Wang
- Department of Microbiology, University of Colorado Health Sciences Center, Denver 80262, USA
| | | |
Collapse
|
22
|
Nübling CM, von Wangenheim G, Staszewski S, Löwer J. Hepatitis C virus antibody prevalence among human immunodeficiency virus-1-infected individuals: analysis with different test systems. J Med Virol 1994; 44:49-53. [PMID: 7798885 DOI: 10.1002/jmv.1890440110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sera of 383 human immunodeficiency virus (HIV)-1-infected individuals from Frankfurt (Main)/Germany were assayed by two hepatitis C virus (HCV) screening tests (Abbott second generation, Ortho second generation). This population showed a prevalence for reactivity with both tests of 20.8% (80/383). Examination of all reactive sera (91/383) by a supplemental assay (Chiron RIBA 2) gave for 46 sera a positive, for 33 sera an indeterminate, and for 12 sera a negative result. Further analysis focussed on these RIBA 2-indeterminate and -negative samples. Analysis of the sera using an in-house Western blot with three different Escherichia coli-expressed HCV proteins revealed that none of the RIBA 2-negative, but 24 of the 33 RIBA 2-indeterminate sera, including 3 of 4 c33c (NS3)-reactive samples, were reactive with a recombinant core protein. Twenty-one of 22 c22-3 (core) indeterminates stained the core antigen in the in-house Western blot and 3 of them in addition a NS5 moiety. HCV-polymerase chain reaction (PCR) was positive for 14 of the 24 RIBA 2-indeterminate sera, but for none of the RIBA 2-negative or Western blot nonreactive samples. Discrepant results between the two screening tests could not be explained by differences in the antigen compositions (i.e., a NS3-NS4 moiety of 111 amino acids present in the Ortho enzyme-linked immunosorbent assay (ELISA), not present in the Abbott or RIBA 2 assays).
Collapse
|
23
|
Affiliation(s)
- G V Gregorio
- Department of Child Health, King's College Hospital, London
| | | | | |
Collapse
|
24
|
Khudyakov YE, Fields HA, Favorov MO, Khudyakova NS, Bonafonte MT, Holloway B. Synthetic gene for the hepatitis C virus nucleocapsid protein. Nucleic Acids Res 1993; 21:2747-54. [PMID: 7687345 PMCID: PMC309613 DOI: 10.1093/nar/21.11.2747] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A synthetic gene encoding the hepatitis C virus (HCV) nucleocapsid protein was constructed and expressed in E. coli. To synthesize this gene, we developed a new method that results in the enzymatic synthesis of long polydeoxyribonucleotides from oligodeoxyribonucleotides. The method, designated as the 'Exchangeable Template Reaction' (ETR), uses oligonucleotides as templates for DNA polymerase. A special mechanism was designed to exchange the templates during the polymerase reaction. The mechanism relies on the formation of a single-stranded 3'-protrusion at the 'growing point' of the elongating DNA such that it can be subsequently annealed, in a sequence-specific manner, with the next synthetic oligonucleotide. When annealed to the 3'-protrusion, the added oligonucleotide becomes a template for DNA polymerase, and the protruding 3'-end of the double-stranded DNA is used as the primer. The HCV nucleocapsid gene was assembled with DNA ligase from three fragments synthesized by ETR. The data verify that this method is efficient. The main advantage of ETR is the ability to combine more than two oligonucleotides in one tube together with polymerase and an enzymatic activity that produces a 3'-protrusion (e.g., BstXI) rather than the sequential addition of each component. The data demonstrate that as many as five oligonucleotides can be used simultaneously, resulting in a synthesized DNA fragment of designed sequence. The synthetic gene expressed in E. coli produced a 27 kDa protein that specifically interacted with antibodies from sera obtained from HCV-infected individuals.
Collapse
Affiliation(s)
- Y E Khudyakov
- Hepatitis Branch, Centers for Disease Control, Atlanta, GA 30333
| | | | | | | | | | | |
Collapse
|
25
|
Wang C, Sarnow P, Siddiqui A. Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism. J Virol 1993; 67:3338-44. [PMID: 8388503 PMCID: PMC237677 DOI: 10.1128/jvi.67.6.3338-3344.1993] [Citation(s) in RCA: 359] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The human hepatitis C virus (HCV) contains a long 5' noncoding region (5' NCR). Computer-assisted and biochemical analyses suggest that there is a complex secondary structure in this region that is comparable to the secondary structures that are found in picornaviruses (E.A. Brown, H. Zhang, L.-H. Ping, and S.M. Lemon, Nucleic Acids Res. 20:5041-5045, 1992). Previous in vitro studies suggest that the HCV 5' NCR plays an important role during translation (K. Tsukiyama-Kohara, N. Iizuka, M. Kohara, and A. Nomoto, J. Virol. 66:1476-1483, 1992). Dicistronic and monocistronic expression vectors, in vitro translation, RNA transfections, and deletion mutagenesis studies were utilized to demonstrate unambiguously that the HCV 5' NCR is involved in translational control. Our data strongly support the conclusion that an internal ribosome entry site exists within the 5' noncoding sequences proximal to the initiator AUG. Furthermore, our results suggest that the HCV genome is translated in a cap-independent manner and that the sequences immediately upstream of the initiator AUG are essential for internal ribosome entry site function during translation.
Collapse
Affiliation(s)
- C Wang
- Department of Microbiology and Immunology, University of Colorado Medical School, Denver 80262
| | | | | |
Collapse
|
26
|
Abstract
BACKGROUND Type II cryoglobulinemia is a vasculitis characterized by cryoglobulins consisting of complexes of polyclonal IgG and monoclonal IgM rheumatoid factors. The cause of these immune complexes is unknown, though both the hepatitis B (HBV) and C (HCV) viruses have been suspected. METHODS We studied 19 patients with Type II cryoglobulinemia for markers of HCV and HBV infection. Quantitative HCV antibody and RNA studies were performed on whole serum, cryoprecipitates, and supernatants. RESULTS Eight patients (42 percent) had HCV antibodies, and 16 (84 percent) had HCV RNA: Of the 19 patients, 5 (26 percent) had HBV markers, but only 1 had evidence of active HBV infection. Control serum samples from nine patients with Type I cryoglobulinemia were negative for HCV antibody and HCV RNA: There was a close, although not exclusive, association of one type of rheumatoid factor (WA) with HCV RNA: HCV antibody and HCV RNA were concentrated approximately 10-fold and 1000-fold, respectively, in the Type II cryoglobulins examined. CONCLUSIONS Type II cryoglobulinemia is strongly associated with concomitant HCV infection and a high rate of false negative serologic tests. HCV virions and HCV antigen-antibody complexes are concentrated in the cryoprecipitates, most commonly in association with the WA type of rheumatoid factor, suggesting a role for HCV in the pathogenesis of mixed cryoglobulinemia.
Collapse
Affiliation(s)
- V Agnello
- Department of Medicine, Massachusetts General Hospital, Boston
| | | | | |
Collapse
|