1
|
Mathew S, Fatima K, Fatmi MQ, Archunan G, Ilyas M, Begum N, Azhar E, Damanhouri G, Qadri I. Computational Docking Study of p7 Ion Channel from HCV Genotype 3 and Genotype 4 and Its Interaction with Natural Compounds. PLoS One 2015; 10:e0126510. [PMID: 26030803 PMCID: PMC4451521 DOI: 10.1371/journal.pone.0126510] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 04/02/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The current standard care therapy for hepatitis C virus (HCV) infection consists of two regimes, namely interferon-based and interferon-free treatments. The treatment through the combination of ribavirin and pegylated interferon is expensive, only mildly effective, and is associated with severe side effects. In 2011, two direct-acting antiviral (DAA) drugs, boceprevir and telaprevir, were licensed that have shown enhanced sustained virologic response (SVR) in phase III clinical trial, however, these interferon-free treatments are more sensitive to HCV genotype 1 infection. The variable nature of HCV, and the limited number of inhibitors developed thus aim in expanding the repertoire of available drug targets, resulting in targeting the virus assembly therapeutically. AIM We conducted this study to predict the 3D structure of the p7 protein from the HCV genotypes 3 and 4. Approximately 63 amino acid residues encoded in HCV render this channel sensitive to inhibitors, making p7 a promising target for novel therapies. HCV p7 protein forms a small membrane known as viroporin, and is essential for effective self-assembly of large channels that conduct cation assembly and discharge infectious virion particles. METHOD In this study, we screened drugs and flavonoids known to disrupt translation and production of HCV proteins, targeted against the active site of p7 residues of HCV genotype 3 (GT3) (isolatek3a) and HCV genotype 4a (GT4) (isolateED43). Furthermore, we conducted a quantitative structure-activity relationship and docking interaction study. RESULTS The drug NB-DNJ formed the highest number of hydrogen bond interactions with both modeled p7 proteins with high interaction energy, followed by BIT225. A flavonoid screen demonstrated that Epigallocatechin gallate (EGCG), nobiletin, and quercetin, have more binding modes in GT3 than in GT4. Thus, the predicted p7 protein molecule of HCV from GT3 and GT4 provides a general avenue to target structure-based antiviral compounds. CONCLUSIONS We hypothesize that the inhibitors of viral p7 identified in this screen may be a new class of potent agents, but further confirmation in vitro and in vivo is essential. This structure-guided drug design for both GT3 and GT4 can lead to the identification of drug-like natural compounds, confirming p7 as a new target in the rapidly increasing era of HCV.
Collapse
Affiliation(s)
- Shilu Mathew
- Department of Biotechnology, Jamal Mohamed College, Tiruchirappalli, India
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, India
| | - Kaneez Fatima
- IQ Institute of Infection and Immunity, Lahore, Punjab, Pakistan
| | - M. Qaiser Fatmi
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad, Pakistan
| | | | - Muhammad Ilyas
- Department of Botany, Jamal Mohamed College, Tiruchirappalli, Tamil Nadu, India
| | - Nargis Begum
- Department of Biotechnology, Jamal Mohamed College, Tiruchirappalli, India
| | - Esam Azhar
- King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Ghazi Damanhouri
- King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Ishtiaq Qadri
- King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| |
Collapse
|
2
|
Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4. mBio 2015; 6:e02518. [PMID: 25714714 PMCID: PMC4358020 DOI: 10.1128/mbio.02518-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) infection is characterized by persistent replication of a complex mixture of viruses termed a “quasispecies.” Transmission is generally associated with a stringent population bottleneck characterized by infection by limited numbers of “transmitted/founder” (T/F) viruses. Characterization of T/F genomes of human immunodeficiency virus type 1 (HIV-1) has been integral to studies of transmission, immunopathogenesis, and vaccine development. Here, we describe the identification of complete T/F genomes of HCV by single-genome sequencing of plasma viral RNA from acutely infected subjects. A total of 2,739 single-genome-derived amplicons comprising 10,966,507 bp from 18 acute-phase and 11 chronically infected subjects were analyzed. Acute-phase sequences diversified essentially randomly, except for the poly(U/UC) tract, which was subject to polymerase slippage. Fourteen acute-phase subjects were productively infected by more than one genetically distinct virus, permitting assessment of recombination between replicating genomes. No evidence of recombination was found among 1,589 sequences analyzed. Envelope sequences of T/F genomes lacked transmission signatures that could distinguish them from chronic infection viruses. Among chronically infected subjects, higher nucleotide substitution rates were observed in the poly(U/UC) tract than in envelope hypervariable region 1. Fourteen full-length molecular clones with variable poly(U/UC) sequences corresponding to seven genotype 1a, 1b, 3a, and 4a T/F viruses were generated. Like most unadapted HCV clones, T/F genomes did not replicate efficiently in Huh 7.5 cells, indicating that additional cellular factors or viral adaptations are necessary for in vitro replication. Full-length T/F HCV genomes and their progeny provide unique insights into virus transmission, virus evolution, and virus-host interactions associated with immunopathogenesis. Hepatitis C virus (HCV) infects 2% to 3% of the world’s population and exhibits extraordinary genetic diversity. This diversity is mirrored by HIV-1, where characterization of transmitted/founder (T/F) genomes has been instrumental in studies of virus transmission, immunopathogenesis, and vaccine development. Here, we show that despite major differences in genome organization, replication strategy, and natural history, HCV (like HIV-1) diversifies essentially randomly early in infection, and as a consequence, sequences of actual T/F viruses can be identified. This allowed us to capture by molecular cloning the full-length HCV genomes that are responsible for infecting the first hepatocytes and eliciting the initial immune responses, weeks before these events could be directly analyzed in human subjects. These findings represent an enabling experimental strategy, not only for HCV and HIV-1 research, but also for other RNA viruses of medical importance, including West Nile, chikungunya, dengue, Venezuelan encephalitis, and Ebola viruses.
Collapse
|
3
|
Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 2014; 59:318-27. [PMID: 24115039 PMCID: PMC4063340 DOI: 10.1002/hep.26744] [Citation(s) in RCA: 924] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/29/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED The 2005 consensus proposal for the classification of hepatitis C virus (HCV) presented an agreed and uniform nomenclature for HCV variants and the criteria for their assignment into genotypes and subtypes. Since its publication, the available dataset of HCV sequences has vastly expanded through advancement in nucleotide sequencing technologies and an increasing focus on the role of HCV genetic variation in disease and treatment outcomes. The current study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near-)complete genome sequences of HCV available on public databases in May 2013. Analysis resolved several nomenclature conflicts between genotype designations and using consensus criteria created a classification of HCV into seven confirmed genotypes and 67 subtypes. There are 21 additional complete coding region sequences of unassigned subtype. The study additionally describes the development of a Web resource hosted by the International Committee for Taxonomy of Viruses (ICTV) that maintains and regularly updates tables of reference isolates, accession numbers, and annotated alignments (http://talk.ictvonline.org/links/hcv/hcv-classification.htm). The Flaviviridae Study Group urges those who need to check or propose new genotypes or subtypes of HCV to contact the Study Group in advance of publication to avoid nomenclature conflicts appearing in the literature. While the criteria for assigning genotypes and subtypes remain unchanged from previous consensus proposals, changes are proposed in the assignment of provisional subtypes, subtype numbering beyond "w," and the nomenclature of intergenotypic recombinant. CONCLUSION This study represents an important reference point for the consensus classification of HCV variants that will be of value to researchers working in clinical and basic science fields.
Collapse
Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenDenmark
| | - Carla Kuiken
- Theoretical Biology and Biophysics group, Los Alamos National LaboratoryLos Alamos, NM, USA
| | | | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller UniversityNew York, NY, USA
| | - Jack T Stapleton
- Medical Service, Iowa City Veterans Affairs Medical Center, Departments of Internal Medicine and Microbiology, University of IowaIowa City, IA, USA
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
| |
Collapse
|
4
|
Saeed M, Gondeau C, Hmwe S, Yokokawa H, Date T, Suzuki T, Kato T, Maurel P, Wakita T. Replication of hepatitis C virus genotype 3a in cultured cells. Gastroenterology 2013; 144:56-58.e7. [PMID: 22999961 DOI: 10.1053/j.gastro.2012.09.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 08/17/2012] [Accepted: 09/10/2012] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) genotype 3a is widespread worldwide, but no replication system exists for its study. We describe a subgenomic replicon system for HCV genotype 3a. We determined the consensus sequence of an HCV genome isolated from a patient, and constructed a subgenomic replicon using this clone. The replicon was transfected into HuH-7 cells and RNA replication was confirmed. We identified cell culture-adaptive mutations that increased colony formation multiple-fold. We have therefore established a genotype 3a replicon system that can be used to study this HCV genotype.
Collapse
Affiliation(s)
- Mohsan Saeed
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Ali I, Khan S, Attaullah S, Khan SN, Khan J, Siraj S, Iqbal A, Swati ZA, Idrees M. Response to combination therapy of HCV 3a infected Pakistani patients and the role of NS5A protein. Virol J 2011; 8:258. [PMID: 21609495 PMCID: PMC3118205 DOI: 10.1186/1743-422x-8-258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/25/2011] [Indexed: 12/16/2022] Open
Abstract
Background Hepatitis C virus (HCV) genotype 3a is known to show comparatively better response to combination therapy than genotype 1 and 4. Mutations within NS5A gene of HCV have earlier been implicated with response to interferon (IFN) therapies in chronic HCV patients among various populations. As response to therapy are available in different populations because of the ethnic and viral factors and there was no study available on the phenomenon of resistivity to IFN. Results Chronic HCV 3a infected Pakistani patients were kept on IFN-α and ribavirin therapy for six months. NS5A gene of HCV was amplified and sequenced in the case of all the patients prior to therapy and the sequences were analysed for mutations. Out of the total 27 patients, 20 (74.07%) were observed with sustained virological response (SVR), 4 (14.81%) patients were non responder (NR) while 3 (11.11%) patients exhibited in end of treatment response (ETR). Three (3/20) (15%) SVR patients and two (2/3) ETR patients had mutations (ranging from I-V amino acids) within the NS5A ISDR regions. While the rest of the SVR patients (85%) and the NR had no mutations at ISDR region when compared with HCV K3a ISDR. Conclusions Mutations within the NS5A gene of HCV 3a genotype may not influence the outcome of combination therapy in Pakistani populations.
Collapse
Affiliation(s)
- Ijaz Ali
- Institute of Biotechnology and Genetic Engineering, KP University ofAgriculture, Peshawar, Pakistan
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Gottwein JM, Scheel TKH, Callendret B, Li YP, Eccleston HB, Engle RE, Govindarajan S, Satterfield W, Purcell RH, Walker CM, Bukh J. Novel infectious cDNA clones of hepatitis C virus genotype 3a (strain S52) and 4a (strain ED43): genetic analyses and in vivo pathogenesis studies. J Virol 2010; 84:5277-93. [PMID: 20200247 PMCID: PMC2863810 DOI: 10.1128/jvi.02667-09] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/19/2010] [Indexed: 12/19/2022] Open
Abstract
Previously, RNA transcripts of cDNA clones of hepatitis C virus (HCV) genotypes 1a (strains H77, HCV-1, and HC-TN), 1b (HC-J4, Con1, and HCV-N), and 2a (HC-J6 and JFH1) were found to be infectious in chimpanzees. However, only JFH1 was infectious in human hepatoma Huh7 cells. We performed genetic analysis of HCV genotype 3a (strain S52) and 4a (strain ED43) prototype strains and generated full-length consensus cDNA clones (pS52 and pED43). Transfection of Huh7.5 cells with RNA transcripts of these clones did not yield cells expressing HCV Core. However, intrahepatic transfection of chimpanzees resulted in robust infection with peak HCV RNA titers of approximately 5.5 log(10) international units (IU)/ml. Genomic consensus sequences recovered from serum at the times of peak viral titers were identical to the sequences of the parental plasmids. Both chimpanzees developed acute hepatitis with elevated liver enzymes and significant necroinflammatory liver changes coinciding with detection of gamma interferon-secreting, intrahepatic T cells. However, the onset and broadness of intrahepatic T-cell responses varied greatly in the two animals, with an early (week 4) multispecific response in the ED43-infected animal (3 weeks before the first evidence of viral control) and a late (week 11) response with limited breadth in the S52-infected animal (without evidence of viral control). Autologous serum neutralizing antibodies were not detected during the acute infection in either animal. Both animals became persistently infected. In conclusion, we generated fully functional infectious cDNA clones of HCV genotypes 3a and 4a. Proof of functionality of all genes might further the development of recombinant cell culture systems for these important genotypes.
Collapse
Affiliation(s)
- Judith M. Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Troels K. H. Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Benoit Callendret
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Yi-Ping Li
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Heather B. Eccleston
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Ronald E. Engle
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Sugantha Govindarajan
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - William Satterfield
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Robert H. Purcell
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Christopher M. Walker
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, The Center for Vaccines and Immunity, Nationwide Children's Hospital, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, Liver Research Laboratory, Rancho Los Amigos Medical Center, Downey, California, Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, M. D. Anderson Cancer Center, Bastrop, Texas
| |
Collapse
|
7
|
Mihm U, Ackermann O, Welsch C, Herrmann E, Hofmann WP, Grigorian N, Welker MW, Lengauer T, Zeuzem S, Sarrazin C. Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C. J Hepatol 2009; 50:49-58. [PMID: 19022516 DOI: 10.1016/j.jhep.2008.08.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 08/26/2008] [Accepted: 08/27/2008] [Indexed: 01/22/2023]
Abstract
BACKGROUND/AIMS Interferon-alpha induces 2'-5'-oligoadenylate synthetase which activates RNase L. Viral RNA is cleaved by RNase L at UU/UA dinucleotides. The clinical relevance of RNase L cleavage for response to an interferon-alpha-based therapy in chronic hepatitis C is unknown. METHODS RNase L cleavage sites within pre-treatment sequences coding for structural and non-structural hepatitis C virus proteins were compared between non-responders and responders to an interferon-alpha-based therapy. Furthermore, RNase L cleavage sites were analyzed in full length and partial genome isolates of hepatitis C virus genotype 1b infected non-responders before and during treatment and in different hepatitis C virus genotypes (1b, 2a/b, 3a/b). RESULTS No differences in RNase L cleavage sites were observed between non-responders and responders within a given hepatitis C genotype. Non-responders with hepatitis C virus genotype 1b infection did not eliminate UA/UU dinucleotides during therapy. Hepatitis C virus genotype 1b isolates showed a lower number of UA/UU dinucleotides than hepatitis C virus genotypes 2/3 (p < 0.001). CONCLUSIONS Response or non-response to an interferon-alpha-based therapy within a given hepatitis C virus genotype is not explained by differences for RNase L cleavage sites. General differences of interferon sensitivity between hepatitis C virus genotypes correlate significantly with frequencies of RNase L cleavage sites.
Collapse
Affiliation(s)
- Ulrike Mihm
- Medizinische Klinik I, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Giangaspero M, Harasawa R, Zanetti A. Taxonomy of genus Hepacivirus. Application of palindromic nucleotide substitutions for the determination of genotypes of human hepatitis C virus species. J Virol Methods 2008; 153:280-99. [PMID: 18657575 DOI: 10.1016/j.jviromet.2008.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 06/23/2008] [Accepted: 06/25/2008] [Indexed: 12/20/2022]
Abstract
The palindromic nucleotide substitutions (PNS) in the 5'-untranslated region (UTR) of Pestivirus RNA have been described as a new, simple and practical method for genotyping. Given the genetic relatedness between Pestivirus and hepatitis C virus species, the application of the method was investigated preliminarily on 180 isolates, including reference strains. The keys for hepatitis C virus identification have been determined at the genus, species, genotype and subtype levels. Secondary structure nucleotide substitutions were characteristics to the genus included in a complex stem-loop structure composed of 112-115 nucleotides. Due to the worldwide importance of hepatitis C virus, and the difficulties encountered in the control of the disease, it is, therefore, important to understand the genetic aspects of the virus. The application of the PNS method might represent an additional useful tool for determining the genetic variations among hepatitis C virus strains. The identification of viral types or subtypes based on genetic changes should improve our understanding of hepatitis C virus and might provide markers for biological differences, such as virulence, and improve understanding of the evolution of the virus.
Collapse
Affiliation(s)
- M Giangaspero
- Veterinary Microbiology, School of Veterinary Medicine, Faculty of Agriculture, Iwate University, 18-8 Ueda 3 Chome, Morioka 020-8550, Iwate, Japan.
| | | | | |
Collapse
|
9
|
Investigation of putative multisubtype hepatitis C virus infections in vivo by heteroduplex mobility analysis of core/envelope subgenomes. J Virol 2008; 82:7524-32. [PMID: 18495766 DOI: 10.1128/jvi.02220-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The frequency that multiple different subtypes of hepatitis C virus (HCV) simultaneously infect a given individual is controversial. To address this question, heteroduplex mobility analysis (HMA) of portions of the HCV core and envelope 1 region was optimized for sensitive and specific detection of mixtures of HCV genomes of different genotype or subtype. Using the standard HCV genotyping approach of 5'-untranslated region (UTR) analysis, 28 of 374 (7.5%) chronic hepatitis C research subjects were classified as having either multiple-subtype HCV infections (n = 21) or switching HCV subtypes over time (n = 7), the latter pattern implying viral superinfection. Upon retesting of specimens by HMA, 25 of 28 multiple-subtype results could not be reproduced. All three patients with positive results were injection drug users with potential multiple HCV exposures. To address the hypothesis of tissue sequestration of multiple-subtype HCV infections, liver (n = 22), peripheral blood mononuclear cell (n = 13), perihepatic lymph node (n = 16), and serum (n = 19) specimens from 23 subjects with end-stage hepatitis C were collected and analyzed by the HMA technique. Whereas 5'-UTR results implicated mixed-subtype HCV infections in 2 subjects, HMA testing revealed no evidence of a second HCV subtype in any tissue compartment (0 of 70 compartments [0%]) or within any given subject (0 of 23 subjects [0%]). In summary, a large proportion of mixed-genotype and switching-genotype patterns generated by 5'-UTR analysis were not reproducible using the HMA approach, emphasizing the need for additional study.
Collapse
|
10
|
Goyal A, Hofmann WP, Hermann E, Traver S, Hissar SS, Arora N, Blum HE, Zeuzem S, Sarrazin C, Sarin SK. The hepatitis C virus NS5A protein and response to interferon alpha: mutational analyses in patients with chronic HCV genotype 3a infection from India. Med Microbiol Immunol 2006; 196:11-21. [PMID: 16955308 DOI: 10.1007/s00430-006-0024-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Indexed: 12/28/2022]
Abstract
The hepatitis C virus (HCV) non-structural (NS)5A protein is linked to interferon alpha resistance in vitro and higher numbers of NS5A amino acid (aa) variations in HCV 1a/b isolates are associated with virologic response to interferon alpha-based therapy in vivo. Here, we aimed to study NS5A aa variations in Indian patients undergoing interferon alpha/ribavirin treatment infected with HCV 3a. The NS5A region [aa 2194-2401, comprising interferon sensitivity determining region, protein kinase resource (PKR) binding domain, V3 region] was sequenced from pre-treatment sera of 24 patients with HCV 3a infection. Mean number and physicochemical properties of aa variations (conserved vs. non-conserved) were assessed. Additionally, published NS5A sequences [NS5A region (n = 61), PKR binding domain (n = 111)] of characterized HCV 3a isolates were analyzed. The mean number of NS5A aa variations was not correlated with treatment response in our cohort. When all available NS5A sequences were included, a higher number of non-conserved aa variations within PKR binding domain and an extended V3 region of NS5A was associated with virologic response (P = 0.004 and 0.05, respectively). Mutational analyses of a large number of NS5A sequences suggest, that a higher number of non-conserved aa variations within the PKR binding domain and the extended V3 region is correlated with virologic response in HCV 3a infected patients.
Collapse
Affiliation(s)
- Ankur Goyal
- Department of Gastroenterology, G.B. Pant Hospital, University of Delhi, New Delhi, India
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Simmonds P, Bukh J, Combet C, Deléage G, Enomoto N, Feinstone S, Halfon P, Inchauspé G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shin-I T, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 2005; 42:962-73. [PMID: 16149085 DOI: 10.1002/hep.20819] [Citation(s) in RCA: 1058] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
International standardization and coordination of the nomenclature of variants of hepatitis C virus (HCV) is increasingly needed as more is discovered about the scale of HCV-related liver disease and important biological and antigenic differences that exist between variants. A group of scientists expert in the field of HCV genetic variability, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re-examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised criteria for the assignment of new genotypes as they are discovered in the future. A comprehensive listing of all currently classified variants of HCV incorporates a number of agreed genotype and subtype name re-assignments to create consistency in nomenclature. The paper also contains consensus proposals for the classification of new variants into genotypes and subtypes, which recognizes and incorporates new knowledge of HCV genetic diversity and epidemiology. A proposal was made that HCV variants be classified into 6 genotypes (representing the 6 genetic groups defined by phylogenetic analysis). Subtype name assignment will be either confirmed or provisional, depending on the availability of complete or partial nucleotide sequence data, or remain unassigned where fewer than 3 examples of a new subtype have been described. In conclusion, these proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future.
Collapse
Affiliation(s)
- Peter Simmonds
- Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Bartenschlager R, Frese M, Pietschmann T. Novel insights into hepatitis C virus replication and persistence. Adv Virus Res 2005; 63:71-180. [PMID: 15530561 DOI: 10.1016/s0065-3527(04)63002-8] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hepatitis C virus (HCV) is a small enveloped RNA virus that belongs to the family Flaviviridae. A hallmark of HCV is its high propensity to establish a persistent infection that in many cases leads to chronic liver disease. Molecular studies of the virus became possible with the first successful cloning of its genome in 1989. Since then, the genomic organization has been delineated, and viral proteins have been studied in some detail. In 1999, an efficient cell culture system became available that recapitulates the intracellular part of the HCV life cycle, thereby allowing detailed molecular studies of various aspects of viral RNA replication and persistence. This chapter attempts to summarize the current state of knowledge in these most actively worked on fields of HCV research.
Collapse
Affiliation(s)
- Ralf Bartenschlager
- Department of Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
13
|
Kronenberger B, Sarrazin C, Hofmann WP, von Wagner M, Herrmann E, Welsch C, Elez R, Rüster B, Piiper A, Zeuzem S. Mutations in the putative HCV-E2 CD81 binding regions and correlation with cell surface CD81 expression. J Viral Hepat 2004; 11:310-8. [PMID: 15230853 DOI: 10.1111/j.1365-2893.2004.00508.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The hepatitis C virus (HCV) envelope (E)2 protein interacts with the cellular receptor CD81 leading to modulation of B and T cell function. Recently, a higher binding affinity of subtype 1a in comparison with 1b derived E2 proteins for CD81 in vitro was described. The importance of mutations within the putative CD81 binding regions of different HCV geno-/subtypes in correlation with CD81 expression is unknown. In the present study, CD81 expression on blood lymphocytes of patients with chronic hepatitis C infected with different HCV geno-/subtypes were analysed by fluorescence activated cell sorter analyses. In addition, the putative CD81 binding regions on the E2 gene comprising the hypervariable region (HVR)2 were analysed by direct sequencing. CD81 expression on CD8(+) T-lymphocytes from patients infected with subtype 1a (n = 6) was significantly higher in comparison with subtype 1b (n = 12) and 3 (n = 5) infected patients before and during antiviral therapy (P = 0.006; P = 0.021, respectively). Sequencing of the putative CD81 binding regions in the E2 protein comprising the HVR2 (codon 474-495 and 522-552 according to the HCV-1a prototype HCV-H) showed a highly conserved motif within HVR2 for subtype 1a isolates and an overall low number of mutations within the putative CD81 binding regions, whereas numerous mutations were detected for subtype 1b isolates (12.0 vs 23.6%). HCV-3 isolates showed an intermediate number of mutations within the putative binding sites (19.2%; P = 0.022). In conclusion, the highly conserved sequence within HVR2 and putative CD81 binding sites of subtype 1a isolates previously associated with a high CD81 binding affinity in vitro is correlated with high CD81 expression on CD8(+) T-lymphocytes in vivo.
Collapse
Affiliation(s)
- B Kronenberger
- Klinik für Innere Medizin II, Universitätsklinikum des Saarlandes, Homburg/Saar, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Ballesteros AL, Franco S, Fuster D, Planas R, Martínez MA, Acosta L, Sirera G, Salas A, Tor J, Rey-Joly C, Clotet B, Tural C. Early HCV dynamics on Peg-interferon and ribavirin in HIV/HCV co-infection: indications for the investigation of new treatment approaches. AIDS 2004; 18:59-66. [PMID: 15090830 DOI: 10.1097/00002030-200401020-00007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
OBJECTIVES To describe the 28-day hepatitis C virus (HCV) kinetics under Pegylated-interferon (Peg-IFN) + ribavirin (RBV) therapy in HIV/HCV co-infected patients. To evaluate the predictive value of early virological response (EVR) of achieving a sustained virological response (SVR). To investigate the baseline mutations in the interferon sensitivity determining region (ISDR)2209-2248 in the non-structural 5A protein of HCV according to genotype. METHODS Open, prospective trial including 28 co-infected patients with directly observed treatment with Peg-IFN + RBV. We assessed the predictive values of EVR (> or = 2 log10 of HCV decay or a negative qualitative test) at days 1, 7, 28 and in week 12 of the SVR. RESULTS The SVR in an intention-to-treat analysis was 28.6% (genotype 1, 1/13; genotype 3, 6/10; genotype 4, 1/5). Patients who reached SVR presented a significantly faster HCV plasma viral load reduction compared to non-responders from the first 24 h [-1.06 log10 (interquartile range, -1.7 to -0.4) versus -0.05 log10 (interquartile range, -0.4 to +0.14) respectively; P = 0.002]. The median HCV viral load at week 12 was significantly different from that at baseline in responder and transient responders but not in non-responder patients. The positive predictive value was 100% within the first month and the best negative predictive value was 92% and 88.8% at weeks 4 and 12 respectively. The only genotype 1 responder patient had eight mutations in ISDR2209-2248. CONCLUSIONS A very early HCV viral decay is observed in responder patients. An early virological response assessment at week 4 and 12 might be a useful tool in the clinical management of the co-infected population.
Collapse
Affiliation(s)
- Angel Luis Ballesteros
- HIV Clinical Unit, University Hospital Germans Trias i Pujol, Universitat Autónoma de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Yoshioka K, Kobayashi M, Orito E, Watanabe K, Yano M, Sameshima Y, Kusakabe A, Hirofuji H, Fuji A, Kuriki J, Arao M, Murase K, Mizokami M, Kakumu S. Biochemical response to interferon therapy correlates with interferon sensitivity-determining region in hepatitis C virus genotype 1b infection. J Viral Hepat 2001; 8:421-9. [PMID: 11703573 DOI: 10.1046/j.1365-2893.2001.00323.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Biochemical responders maintain normal alanine aminotransferase levels after interferon (IFN) therapy despite persistent presence of hepatitis C virus (HCV) RNA in their sera. There have been few reports on predictive factors for biochemical response. A region associated with sensitivity to IFN was identified in the nonstructural protein 5 A of genotype 1b [aa 2209-2248; IFN sensitivity-determining region (ISDR)]. The substitutions in ISDR correlate with sustained response to IFN. In this report, we assessed the association of ISDR with biochemical response. The sequences of ISDR were determined in 62 patients with HCV genotype 1b treated by IFN in two randomized controlled trials. 30 patients had wild ISDR (identical to HCV-J), 20 intermediate ISDR (1-3 amino acid substitutions compared with HCV-J), and 12 mutant ISDR (four or more amino acid substitutions). All 12 patients with mutant ISDR had a sustained response, while only one of those with wild or intermediate ISDR had a sustained response (P < 0.0001). In the 49 patients other than sustained responders, the patients with intermediate ISDR obtained biochemical response significantly more frequently (52.6%, 10/19) than those with wild-type ISDR (20.0%, 6/30) (P < 0.05). Multivariate analysis indicated the number of substitutions in ISDR as the most important predictor for biochemical response (discriminant coefficient=1.08, P < 0.05) and sustained response (discriminant coefficient=6.13, P < 0.0001). In phylogenetic analysis, clustering of sustained responders and biochemical responders was observed. These results demonstrate that the substitutions in ISDR are the most important predictor for biochemical response to IFN in patients infected with genotype 1b as well as for sustained response.
Collapse
Affiliation(s)
- K Yoshioka
- Third Department of Internal Medicine, Nagoya University School of Medicine, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Puig-Basagoiti F, Sáiz JC, Forns X, Ampurdanès S, Giménez-Barcons M, Franco S, Sánchez-Fueyo A, Costa J, Sánchez-Tapias JM, Rodés J. Influence of the genetic heterogeneity of the ISDR and PePHD regions of hepatitis C virus on the response to interferon therapy in chronic hepatitis C. J Med Virol 2001. [PMID: 11505441 DOI: 10.1002/jmv.1098] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Two genomic regions of hepatitis C virus (HCV), the interferon sensitivity-determining region (ISDR) of the non-structural 5A gene (NS5A) and the protein kinase-RNA activated (PKR)-eukariotic transcription factor (eIF2-alpha) phosphorylation homology domain (PePHD) of the structural E2 gene, interact in vitro with the interferon-inducible cellular PKR protein kinase. Mutations within these regions might, therefore, influence the response to interferon therapy. Viral load at baseline and sequence heterogeneity of HCV in NS5A and E2 regions was studied in 74 HCV-1b and in 12 HCV-3a infected patients with chronic hepatitis C who were treated with interferon. As previously reported by us, in a smaller series of patients in which the ISDR region was analyzed [Saiz et al. (1998) Journal Infectious Diseases 177:839-847], in the present study a low viral load and a high number of amino acid mutations within the ISDR, but not within the PePHD region, were significantly associated with long-term response to interferon among HCV-1b infected patients. No relationship between these viral features and response to therapy was disclosed in patients infected with HCV-3a.
Collapse
Affiliation(s)
- F Puig-Basagoiti
- Liver Unit, Institut de Malalties Digestives, IDIBAPS, Department de Medicina, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Sarrazin C, Bruckner M, Herrmann E, Rüster B, Bruch K, Roth WK, Zeuzem S. Quasispecies heterogeneity of the carboxy-terminal part of the E2 gene including the PePHD and sensitivity of hepatitis C virus 1b isolates to antiviral therapy. Virology 2001; 289:150-63. [PMID: 11601926 DOI: 10.1006/viro.2001.1092] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Two regions within the HCV genome, hypervariable region 1 (HVR1) within the envelope (E)2 region and the PKR-binding domain (PKRbD) comprising the interferon sensitivity determining region (ISDR) within the nonstructural (NS)5A protein, have been reported to correlate with the outcome of antiviral treatment. Recently, a PKR/eIF2alpha phosphorylation homology domain (PePHD) within the E2 protein of HCV-1 isolates was described to inhibit PKR in vitro. PePHD deleted HCV-1 mutants remain capable of binding PKR to some extent while inhibition of PKR was found to be abolished by carboxy-terminal truncated E2 protein. The importance of mutations and quasispecies heterogeneity within the carboxy-terminal part of the E2 protein comprising the PePHD of HCV-1b is unknown. Therefore, the carboxy-terminal part of the HCV E2 gene (codons 618-746) including the PePHD was analyzed by sequencing of PCR products and individual clones of 41 HCV-1b-infected patients with sustained (SR, n = 12), end-of-treatment (ETR, n = 10), or no virological (NR, n = 19) response to antiviral therapy. Two highly conserved regions (codons 658-673 comprising the PePHD and codons 675-704) and one variable region (codons 705-720) were detected within the carboxy-terminal part of E2. No significant correlation of specific mutations or number of mutations with treatment response was observed for the PePHD and the carboxy-terminal part of the E2 protein. Phylogenetic and conformational analyses showed no specific clusters related to treatment outcome. Calculation of genetic complexity and diversity based on nucleotide sequence analyses of 20 individual clones per patient showed no differences between matched SR, ETR, and NR patients. However, calculation of genetic complexity and diversity on the basis of amino acid sequences showed significantly lower normalized Shannon entropy as well as mean Hamming distances for SR patients than in ETR and NR patients (P = 0.029 and P = 0.027, respectively). This indicates that patients achieving a sustained virological response to interferon-alpha-based antiviral therapy may elicit more effective immunological pressure, resulting in continuous clearing of individual variants of HCV quasispecies.
Collapse
Affiliation(s)
- C Sarrazin
- Medizinische Klinik II, J.W. Goethe-Universität, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | | | | | | | | | | | | |
Collapse
|
18
|
Kato N. Genome of human hepatitis C virus (HCV): gene organization, sequence diversity, and variation. MICROBIAL & COMPARATIVE GENOMICS 2001; 5:129-51. [PMID: 11252351 DOI: 10.1089/omi.1.2000.5.129] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hepatitis C virus (HCV) is the major etiologic agent of non-A, non-B hepatitis. HCV infection frequently causes chronic hepatitis, which progresses to liver cirrhosis and hepatocellular carcinoma. Since the discovery of HCV in 1989, a large number of genetic analyses of HCV have been reported, and the viral genome structure has been elucidated. An enveloped virus, HCV belongs to the family Flaviviridae, whose genome consists of a positive-stranded RNA molecule of about 9.6 kilobases and encodes a large polyprotein precursor (about 3000 amino acids). This precursor protein is cleaved by the host and viral proteinase to generate at least 10 proteins: the core, envelope 1 (E1), E2, p7, nonstructural (NS) 2, NS3, NS4A, NS4B, NS5A, and NS5B. These HCV proteins not only function in viral replication but also affect a variety of cellular functions. HCV has been found to have remarkable genetic heterogeneity. To date, more than 30 HCV genotypes have been identified worldwide. Furthermore, HCV may show quasispecies distribution in an infected individual. These findings may have important implications in diagnosis, pathogenesis, treatment, and vaccine development. The hypervariable region 1 found within the envelope E2 protein was shown to be a major site for the genetic evolution of HCV after the onset of hepatitis, and might be involved in escape from the host immunesurveillance system.
Collapse
Affiliation(s)
- N Kato
- Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Japan.
| |
Collapse
|
19
|
Sarrazin C, Kornetzky I, Rüster B, Lee JH, Kronenberger B, Bruch K, Roth WK, Zeuzem S. Mutations within the E2 and NS5A protein in patients infected with hepatitis C virus type 3a and correlation with treatment response. Hepatology 2000; 31:1360-70. [PMID: 10827164 DOI: 10.1053/jhep.2000.7987] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Defined regions of hepatitis C virus (HCV) envelope 2 (E2), PePHD, and nonstructural 5A (NS5A) protein (PKR-binding domain) have been shown to interact with interferon alfa (IFN-alpha)-inducible double-stranded RNA-activated protein kinase (PKR) in vitro, suggesting a possible mechanism of HCV to evade antiviral effects of IFN-alpha. The clinical correlation between amino acid mutations within the E2 PePHD or the NS5A PKR-binding domain and response to antiviral treatment in HCV-3a-infected patients is unknown. Thirty-three patients infected with HCV-3a isolates were treated with IFN-alpha with or without ribavirin. The carboxyterminal half of E2 and of the NS5A gene were sequenced. Sixteen patients achieved a sustained virological response (SR), 6 patients an end-of-treatment response with relapse thereafter (ETR), and 11 patients were nonresponders (NR). Within the PePHD of the E2 protein 0.5 (range, 0-2) mutations were observed in SR patients, whereas the number of mutations in ETR or NR patients was 0.2 (0-1). Quasispecies analyses showed almost no heterogeneity. The mean number of mutations within the PKR-binding domain of the NS5A protein was 1.6 (range, 0-4) in SR patients, 1 (0-2) in ETR patients, and 1.6 (0-3) in NR patients. Patients with higher numbers of mutations within the E2 or NS5A region showed a trend towards lower pretreatment viremia. Phylogenetic and conformational analyses of E2 or NS5A sequences allowed no differentiation between sensitive and resistant isolates. However, mutations within the E2 PePHD in SR patients were frequent, and hydrophobic mutations within the hydrophilic area of PePHD at codon 668 and 669 were exclusively observed in sustained virological responders.
Collapse
Affiliation(s)
- C Sarrazin
- Medizinische Klinik II, J. W. Goethe-University, Frankfurt am Main, Germany
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Hagedorn CH, van Beers EH, De Staercke C. Hepatitis C virus RNA-dependent RNA polymerase (NS5B polymerase). Curr Top Microbiol Immunol 1999; 242:225-60. [PMID: 10592663 DOI: 10.1007/978-3-642-59605-6_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- C H Hagedorn
- Division of Digestive Diseases and Genetics-Winship Cancer Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | |
Collapse
|
21
|
Schröter M, Feucht HH, Schäfer P, Zöllner B, Laufs R. Serological determination of hepatitis C virus subtypes 1a, 1b, 2a, 2b, 3a, and 4a by a recombinant immunoblot assay. J Clin Microbiol 1999; 37:2576-80. [PMID: 10405404 PMCID: PMC85286 DOI: 10.1128/jcm.37.8.2576-2580.1999] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/1998] [Accepted: 05/04/1999] [Indexed: 11/20/2022] Open
Abstract
Serological determination of hepatitis C virus (HCV) subtypes has been hampered by the lack of suitable assays. Therefore, a recombinant immunoblot assay has been established for serological differentiation of HCV subtypes 1a, 1b, 2a, 2b, 3a, and 4a. It consists of recombinant HCV proteins from the NS-4 region propagated in Escherichia coli. To confirm the serotyping assay results, the results were compared with those obtained by nucleotide sequencing of the NS-5 region. Sera from 157 patients with chronic HCV infection were examined by this assay, and specific antibodies could be detected in 86% (n = 135) of them. The HCV genotype was determined correctly in all but one sample, and the subtypes determined by the serotyping assay corresponded to the HCV subtypes detected by nucleotide sequencing for 95% (n = 128) of the samples. These data indicate that HCV subtypes can be distinguished serologically. The assay that is described provides an easier means of identification of infection with different HCV subtypes for wider clinical and epidemiological applications.
Collapse
Affiliation(s)
- M Schröter
- Institut für Medizinische Mikrobiologie und Immunologie, Universitäts-Krankenhaus Eppendorf, 20246 Hamburg, Germany.
| | | | | | | | | |
Collapse
|
22
|
Abstract
To permit accurate identification of the 5' end of the HCV genome, we used RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) where an RNA molecule of known sequence (transcribed in vitro from a cDNA template) was ligated to RNA purified from a hepatitis C virus (HCV)-infected liver sample. After ligation, the product was amplified by nested polymerase chain reaction (PCR) and amplicons that were equal to or greater in size than those predicted from the recognized 5' terminus of the HCV genome were cloned into pBluescriptKS. Twelve clones were sequenced, including three that were identical and contained an additional eight nucleotides, namely CCCCCCCA. Thus, the HCV 5' untranslated region (UTR) is now recognized as comprising 349 nucleotides, although it is possible to speculate that these additional nucleotides are part of a second, as yet undetected, stem-loop at the extreme 5' terminus of the genome.
Collapse
Affiliation(s)
- R Trowbridge
- Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Australia
| | | |
Collapse
|
23
|
Wong DKH, Dudley DD, Afdhal NH, Dienstag J, Rice CM, Wang L, Houghton M, Walker BD, Koziel MJ. Liver-Derived CTL in Hepatitis C Virus Infection: Breadth and Specificity of Responses in a Cohort of Persons with Chronic Infection. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.160.3.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Hepatitis C virus (HCV)-specific CTL have been found within the inflammatory infiltrate of the liver of chronically infected individuals, but the breadth and specificity of the CTL response in relation to viral load are less well characterized. In this study, we analyzed the intrahepatic CTL response in liver biopsy specimens from 44 chronically infected subjects. Liver-infiltrating lymphocytes were expanded polyclonally in bulk cultures, and multiple clones were derived by limiting dilution. HCV-specific CTL responses directed at genotype 1a structural proteins were assessed in all subjects, and 22 subjects were tested more comprehensively using vectors expressing all structural and nonstructural HCV Ags. CTL responses were further characterized to determine the HLA restriction and optimal epitopes recognized. In those persons screened for recognition of all HCV Ags, HLA class I-restricted CTL were detected in 45%. Nineteen different CTL epitopes were identified, which were distributed throughout the genome; only one epitope was targeted by more than one person. In those persons with CTL responses, the breadth of response ranged from one to five epitopes. There was no correlation between the presence of a detectable CTL response and viral load. These results indicate considerable heterogeneity in detectable HCV-specific CTL responses in chronically infected persons. The mechanisms by which HCV persists during chronic infection remain to be clarified.
Collapse
Affiliation(s)
| | | | - Nezam H. Afdhal
- §Division of Gastroenterology, Boston City Hospital, Boston, MA 02118
| | - Jules Dienstag
- †Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114
| | | | | | | | | | - Margaret J. Koziel
- *Infectious Diseases Unit and
- ‡Infectious Disease Lab, Beth Israel Deaconess Medical Center West, Harvard Institutes of Medicine, Boston, MA 02215
| |
Collapse
|
24
|
Abstract
The carboxyl-terminal three-fourths of the hepatitis C virus (HCV) NS3 protein has been shown to possess an RNA helicase activity, typical of members of the DEAD box family of RNA helicases. In addition, the NS3 protein contains four amino acid motifs conserved in DEAD box proteins. In order to inspect the roles of individual amino acid residues in the four conserved motifs (AXXXXGKS, DECH, TAT, and QRRGRTGR) of the NS3 protein, mutational analysis was used in this study. Thirteen mutant proteins were constructed, and their biochemical activities were examined. Lys1235 in the AXXXXGKS motif was important for basal nucleoside triphosphatase (NTPase) activity in the absence of polynucleotide cofactor. A serine in the X position of the DEXH motif disrupted the NTPase and RNA helicase activities. Alanine substitution at His1318 of the DEXH motif made the protein possess high NTPase activity. In addition, we now report inhibition of NTPase activity of NS3 by polynucleotide cofactor. Gln1486 was indispensable for the enzyme activity, and this residue represents a distinguishing feature between DEAD box and DEXH proteins. There are four Arg residues in the QRRGRTGR motif of the HCV NS3 protein, and the second, Arg1488, was important for RNA binding and enzyme activity, even though it is less well conserved than other Arg residues. Arg1490 and Arg1493 were essential for the enzymatic activity. As the various enzymatic activities were altered by mutation, the enzyme characteristics were also changed.
Collapse
Affiliation(s)
- D W Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Taejon
| | | | | | | | | |
Collapse
|
25
|
Yamakawa A, Kameoka Y, Hashimoto K, Yoshitake Y, Nishikawa K, Tanihara K, Date T. cDNA cloning and chromosomal mapping of genes encoding novel protein kinases termed PKU-alpha and PKU-beta, which have nuclear localization signal. Gene X 1997; 202:193-201. [PMID: 9427565 DOI: 10.1016/s0378-1119(97)00495-2] [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: 02/05/2023] Open
Abstract
We have cloned cDNAs for novel serine/threonine protein kinases (PK), termed PKU-alpha and PKU-beta, by screening a bacteriophage expression library for kinase activity. Sequence analysis of PKU-alpha and PKU-beta genes revealed that their open reading frames (ORF) were 2151 and 2361 nucleotides (nt) encoding polypeptides of 717 and 787 amino acid (aa) residues, respectively. The deduced aa sequences of PKU-alpha and PKU-beta contained typical serine/threonine PK domains at the C-terminal region and were 86% identical to each other, indicating that they belong to the same PK family. Northern analysis reveals that they are expressed in nearly all human tissues and in cultured cells. The genes for PKU-alpha and PKU-beta were mapped to chromosome 17q23 and 8p12-p22, respectively, by fluorescence in situ hybridization. The proteins encoded by both cDNAs contain a putative nuclear localization signal (NLS) in their N-terminal region. These signals are likely to function in nuclear localization. Glutathione S-transferase (GST)-fusions to regions of PKU-alpha and beta containing the NLS were efficiently localized to the nucleus. In addition, PKU-beta transiently expressed in COS-1 cells was predominantly nuclear. PKU-alpha and PKU-beta differ: a consensus sequence for a nt binding motif is present near the NLS of PKU-beta. These results suggest that PKU-alpha and beta may phosphorylate serine and/or threonine residues on similar proteins, but their activities are regulated through distinct interactions with a nuclear component.
Collapse
Affiliation(s)
- A Yamakawa
- Department of Biochemistry, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | | | | | | | | | | | | |
Collapse
|
26
|
Brojer E, Gloskowska-Moraczewska Z, Kacperska E, Medyńska J, Cianciara J, Juszczyk J, Loch T, Flieger J, Seyfried H. Hepatitis C virus genotypes in blood donors and patients with chronic hepatitis C. Vox Sang 1996; 71:51-4. [PMID: 8837358 DOI: 10.1046/j.1423-0410.1996.7110051.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- E Brojer
- Institute of Hematology and Blood Transfusion, Warsaw, Poland
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
It has been shown that hepatitis C virus (HCV) populations in infected individuals are composed of quasispecies with diverse mutations. The analysis of these variants may reveal mechanisms of the persistence of HCV infection, carcinogenesis and resistance to antiviral therapy. Recently, genetic features of interferon-resistant HCV have been elucidated through the analysis of interferon-resistant quasispecies, making it possible to predict interferon efficacy by detecting interferon-resistant strains.
Collapse
Affiliation(s)
- N Enomoto
- Second Department of Internal medicine, Faculty of Medicine, Tokyo Medical and Dental University, Japan
| | | |
Collapse
|
28
|
Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, Izumi N, Marumo F, Sato C. Comparison of full-length sequences of interferon-sensitive and resistant hepatitis C virus 1b. Sensitivity to interferon is conferred by amino acid substitutions in the NS5A region. J Clin Invest 1995; 96:224-30. [PMID: 7542279 PMCID: PMC185192 DOI: 10.1172/jci118025] [Citation(s) in RCA: 447] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have previously demonstrated that sensitivity to interferon is different among hepatitis C virus (HCV) quasispecies simultaneously detected in same individuals and that interferon-resistant HCV quasispecies are selected during the treatment. To determine the genetic basis of their resistance to interferon, HCV genotype-1b was obtained from serum of three patients before and during interferon therapy, and their full-length nucleotide and deduced amino acid sequences were determined. Comparison of the pairs of interferon-resistant and interferon-sensitive HCV isolates in respective individuals demonstrated clusters of amino acid differences in the COOH-terminal half of the NS5A region (codon 2154-2383), which contained a common unique amino acid difference at codon 2218. Additional sequence data of the COOH-terminal half of the NS5A region obtained from six interferon-resistant and nine interferon-sensitive HCV confirmed the exclusive existence of missense mutations in a 40 amino acid stretch of the NS5A region around codon 2218 (from codon 2209 to 2248) in interferon-sensitive HCV. On the other hand, this region of interferon-resistant HCV was identical to that of prototype HCV genotype-1b (HCV-J, HCV-JTa, or HC-J4). We designated this region as the interferon sensitivity determining region. Thus, HCV genotype-1b with the prototype interferon sensitivity determining region appears to be interferon-resistant strains. The specific nature of these mutations might make it possible to predict prognostic effects of interferon treatment.
Collapse
Affiliation(s)
- N Enomoto
- Second Department of Internal Medicine, Faculty of Medicine, Tokyo Medical and Dental University, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|