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Newman RM, Kuntzen T, Weiner B, Berical A, Charlebois P, Kuiken C, Murphy DG, Simmonds P, Bennett P, Lennon NJ, Birren BW, Zody MC, Allen TM, Henn MR. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J Infect Dis 2013; 208:17-31. [PMID: 23136221 PMCID: PMC3666132 DOI: 10.1093/infdis/jis679] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 08/08/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Infection with hepatitis C virus (HCV) is a burgeoning worldwide public health problem, with 170 million infected individuals and an estimated 20 million deaths in the coming decades. While 6 main genotypes generally distinguish the global geographic diversity of HCV, a multitude of closely related subtypes within these genotypes are poorly defined and may influence clinical outcome and treatment options. Unfortunately, the paucity of genetic data from many of these subtypes makes time-consuming primer walking the limiting step for sequencing understudied subtypes. METHODS Here we combined long-range polymerase chain reaction amplification with pyrosequencing for a rapid approach to generate the complete viral coding region of 31 samples representing poorly defined HCV subtypes. RESULTS Phylogenetic classification based on full genome sequences validated previously identified HCV subtypes, identified a recombinant sequence, and identified a new distinct subtype of genotype 4. Unlike conventional sequencing methods, use of deep sequencing also facilitated characterization of minor drug resistance variants within these uncommon or, in some cases, previously uncharacterized HCV subtypes. CONCLUSIONS These data aid in the classification of uncommon HCV subtypes while also providing a high-resolution view of viral diversity within infected patients, which may be relevant to the development of therapeutic regimens to minimize drug resistance.
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Affiliation(s)
- Ruchi M Newman
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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Heim MH. 25 years of interferon-based treatment of chronic hepatitis C: an epoch coming to an end. Nat Rev Immunol 2013; 13:535-42. [PMID: 23743475 DOI: 10.1038/nri3463] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chronic hepatitis caused by infection with hepatitis C virus C (HCV) (therefore known as chronic hepatitis C (CHC)) is a leading cause of liver disease worldwide. For the past 25 years, recombinant interferon-α (IFNα) has been the main component of treatments for HCV infection. Treatment efficacy has shown a stepwise improvement following the pegylation of IFNα and its use in combination with other antiviral drugs. However, viral escape mechanisms, refractory IFNα signalling in the liver and substantial drug toxicity still limit the efficacy of this treatment. A new generation of HCV-specific antiviral drugs will probably improve response rates and might replace IFNs in CHC treatment in the next few years. This Timeline article summarizes the history of CHC treatment using recombinant IFNα with an emphasis on the mechanisms of action and the causes of non-response.
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Affiliation(s)
- Markus H Heim
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.
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53
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Tripathi LP, Kambara H, Chen YA, Nishimura Y, Moriishi K, Okamoto T, Morita E, Abe T, Mori Y, Matsuura Y, Mizuguchi K. Understanding the Biological Context of NS5A–Host Interactions in HCV Infection: A Network-Based Approach. J Proteome Res 2013; 12:2537-51. [DOI: 10.1021/pr3011217] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lokesh P. Tripathi
- National Institute of Biomedical Innovation, 7-6-8 Saito Asagi, Ibaraki,
Osaka, 567-0085, Japan
| | - Hiroto Kambara
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Yi-An Chen
- National Institute of Biomedical Innovation, 7-6-8 Saito Asagi, Ibaraki,
Osaka, 567-0085, Japan
| | - Yorihiro Nishimura
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Kohji Moriishi
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Toru Okamoto
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Eiji Morita
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Takayuki Abe
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Yoshio Mori
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology,
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Kenji Mizuguchi
- National Institute of Biomedical Innovation, 7-6-8 Saito Asagi, Ibaraki,
Osaka, 567-0085, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita, Osaka, 565-0871,
Japan
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54
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Li C, Njouom R, Pépin J, Nakano T, Bennett P, Pybus OG, Lu L. Characterization of full-length hepatitis C virus sequences for subtypes 1e, 1h and 1l, and a novel variant revealed Cameroon as an area in origin for genotype 1. J Gen Virol 2013; 94:1780-1790. [PMID: 23677792 DOI: 10.1099/vir.0.048835-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this study, we characterized the full-length genome sequences of seven hepatitis C virus (HCV) isolates belonging to genotype 1. These represent the first complete genomes for HCV subtypes 1e, 1h, 1l, plus one novel variant that qualifies for a new but unassigned subtype. The genomes were characterized using 19-22 overlapping fragments. Each was 9400-9439 nt long and contained a single ORF encoding 3019-3020 amino acids. All viruses were isolated in the sera of seven patients residing in, or originating from, Cameroon. Predicted amino acid sequences were inspected and unique patterns of variation were noted. Phylogenetic analysis using full-length sequences provided evidence for nine genotype 1 subtypes, four of which are described for the first time here. Subsequent phylogenetic analysis of 141 partial NS5B sequences further differentiated 13 subtypes (1a-1m) and six additional unclassified lineages within genotype 1. As a result of this study, there are now seven HCV genotype 1 subtypes (1a-1c, 1e, 1g, 1h, 1l) and two unclassified genotype 1 lineages with full-length genomes characterized. Further analysis of 228 genotype 1 sequences from the HCV database with known countries is consistent with an African origin for genotype 1, and with the hypothesis of subsequent dissemination of some subtypes to Asia, Europe and the Americas.
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Affiliation(s)
- Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Richard Njouom
- Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur, Yaoundé, Cameroon
| | - Jacques Pépin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada
| | - Tatsunori Nakano
- Department of Internal Medicine, Fujita Health University Nanakuri Sanatorium Otoricho 424-1, Tsu, Mie 514-1295, Japan
| | - Phil Bennett
- Micropathology Ltd, University of Warwick Science Park, Coventry CV4 7EZ, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road OX1 3PS, UK
| | - Ling Lu
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
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55
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Bittar C, Shrivastava S, Bhanja Chowdhury J, Rahal P, Ray RB. Hepatitis C virus NS2 protein inhibits DNA damage pathway by sequestering p53 to the cytoplasm. PLoS One 2013; 8:e62581. [PMID: 23638118 PMCID: PMC3640050 DOI: 10.1371/journal.pone.0062581] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/22/2013] [Indexed: 12/13/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection is an important cause of morbidity and mortality globally, and often leads to end-stage liver disease. The DNA damage checkpoint pathway induces cell cycle arrest for repairing DNA in response to DNA damage. HCV infection has been involved in this pathway. In this study, we assess the effects of HCV NS2 on DNA damage checkpoint pathway. We have observed that HCV NS2 induces ataxia-telangiectasia mutated checkpoint pathway by inducing Chk2, however, fails to activate the subsequent downstream pathway. Further study suggested that p53 is retained in the cytoplasm of HCV NS2 expressing cells, and p21 expression is not enhanced. We further observed that HCV NS2 expressing cells induce cyclin E expression and promote cell growth. Together these results suggested that HCV NS2 inhibits DNA damage response by altering the localization of p53, and may play a role in the pathogenesis of HCV infection.
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Affiliation(s)
- Cintia Bittar
- Department of Pathology, Saint Louis University, St. Louis, Missouri, United States of America
- Deaprtment of Biology, UNESP – São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Shubham Shrivastava
- Department of Pathology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Joydip Bhanja Chowdhury
- Department of Pathology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Paula Rahal
- Deaprtment of Biology, UNESP – São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Ratna B. Ray
- Department of Pathology, Saint Louis University, St. Louis, Missouri, United States of America
- * E-mail:
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Modulation of hepatitis C virus genome encapsidation by nonstructural protein 4B. J Virol 2013; 87:7409-22. [PMID: 23616661 DOI: 10.1128/jvi.03523-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hepatitis C Virus (HCV) NS4B protein has many roles in HCV genome replication. Recently, our laboratory (Q. Han, J. Aligo, D. Manna, K. Belton, S. V. Chintapalli, Y. Hong, R. L. Patterson, D. B. van Rossum, and K. V. Konan, J. Virol. 85:6464-6479, 2011) and others (D. M. Jones, A. H. Patel, P. Targett-Adams, and J. McLauchlan, J. Virol. 83:2163-2177, 2009; D. Paul, I. Romero-Brey, J. Gouttenoire, S. Stoitsova, J. Krijnse-Locker, D. Moradpour, and R. Bartenschlager, J. Virol. 85:6963-6976, 2011) have also reported NS4B's function in postreplication steps. Indeed, replacement of the NS4B C-terminal domain (CTD) in the HCV JFH1 (genotype 2a [G2a]) genome with sequences from Con1 (G1b) or H77 (G1a) had a negligible impact on JFH1 genome replication but attenuated virus production. Since NS4B interacts weakly with the HCV genome, we postulated that NS4B regulates the function of host or virus proteins directly involved in HCV production. In this study, we demonstrate that the integrity of the JFH1 NS4B CTD is crucial for efficient JFH1 genome encapsidation. Further, two adaptive mutations (NS4B N216S and NS5A C465S) were identified, and introduction of these mutations into the chimera rescued virus production to various levels, suggesting a genetic interaction between the NS4B and NS5A proteins. Interestingly, cells infected with chimeric viruses displayed a markedly decreased NS5A hyperphosphorylation state (NS5A p58) relative to JFH1, and the adaptive mutations differentially rescued NS5A p58 formation. However, immunofluorescence staining indicated that the decrease in NS5A p58 did not alter NS5A colocalization with the core around lipid droplets (LDs), the site of JFH1 assembly, suggesting that NS5A fails to facilitate the transfer of HCV RNA to the capsid protein on LDs. Alternatively, NS4B's function in HCV genome encapsidation may entail more than its regulation of the NS5A phosphorylation state.
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Induction of broadly neutralising HCV antibodies in mice by integration-deficient lentiviral vector-based pseudotyped particles. PLoS One 2013; 8:e62684. [PMID: 23626846 PMCID: PMC3633868 DOI: 10.1371/journal.pone.0062684] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/24/2013] [Indexed: 12/26/2022] Open
Abstract
Introduction Integration-deficient lentiviral vectors (IDLVs) are a promising platform for immunisation to elicit both humoral immunity and cellular mediated immunity (CMI). Here, we compared the specific immunity in mice immunised via different regimens (homologous and cocktail) with IDLV-based HCV pseudoparticles (HCVpps) carrying pseudotyped glycoproteins E1E2 and bearing the HCV NS3 gene. Humoral and cell-mediated immune responses were also evaluated after IDLV-HCVpp immunisation combined with heterologous rAd5-CE1E2 priming protocols. Sera from the mice effectively elicited anti-E1, -E2, and -NS3 antibody responses, and neutralised various HCVpp subtypes (1a, 1b, 2a, 3a and 5a). No significant CMI was detected in the groups immunised with IDLV-based HCVpps. In contrast, the combination of rAd5-CE1E2 priming and IDLV-based HCVpp boosting induced significant CMI against multiple antigens (E1, E2, and NS3). Conclusion IDLV-based HCVpps are a promising vaccination platform and the combination of rAd5-CE1E2 and IDLV-based HCVpp prime-boost strategy should be further explored for the development of a cross-protective HCV vaccine.
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58
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Delaney WE. Molecular virology of chronic hepatitis B and C: parallels, contrasts and impact on drug development and treatment outcome. Antiviral Res 2013; 99:34-48. [PMID: 23602852 DOI: 10.1016/j.antiviral.2013.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/29/2013] [Accepted: 04/09/2013] [Indexed: 12/17/2022]
Abstract
Chronic infections with hepatitis B virus (HBV) and hepatitis C virus (HCV) are highly prevalent worldwide, causing significant liver disease and thus representing high unmet medical needs. Accordingly, substantial pharmaceutical and clinical research efforts have been made to develop and improve treatments for these viruses. While HBV and HCV are both hepatotropic viruses that can cause similar disease in chronically infected patients, they belong to different viral families. There are substantial differences in the molecular virology of HBV and HCV that have profound implications for therapeutic strategy. In particular, HBV has a long-lived nuclear form of its genome (covalently closed circular DNA) that is able to persist in the face of potent inhibition of viral replication. In contrast, HCV does not have a long-lived genome form and depends on active replication to maintain infection; HCV is therefore much more susceptible to eradication by potent antiviral agents. Additional differences between HBV and HCV with therapeutic implications include the size, structure and heterogeneity of their respective viral genomes. These factors influence the number of targets available for therapeutic intervention, response to therapy among viral genotypes and the emergence of viral resistance. Substantial progress has been made in treating each infection, but unique challenges remain. In this review, key differences in the molecular virology of hepatitis B and C will be presented, highlighting their impact on antiviral therapy (particularly with respect to direct-acting antivirals) and the challenges they present to the cure of each disease.
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Abstract
Hepatitis C virus (HCV) and human pegivirus (HPgV or GB virus C) are globally distributed and infect 2 to 5% of the human population. The lack of tractable-animal models for these viruses, in particular for HCV, has hampered the study of infection, transmission, virulence, immunity, and pathogenesis. To address this challenge, we searched for homologous viruses in small mammals, including wild rodents. Here we report the discovery of several new hepaciviruses (HCV-like viruses) and pegiviruses (GB virus-like viruses) that infect wild rodents. Complete genome sequences were acquired for a rodent hepacivirus (RHV) found in Peromyscus maniculatus and a rodent pegivirus (RPgV) found in Neotoma albigula. Unique genomic features and phylogenetic analyses confirmed that these RHV and RPgV variants represent several novel virus species in the Hepacivirus and Pegivirus genera within the family Flaviviridae. The genetic diversity of the rodent hepaciviruses exceeded that observed for hepaciviruses infecting either humans or non-primates, leading to new insights into the origin, evolution, and host range of hepaciviruses. The presence of genes, encoded proteins, and translation elements homologous to those found in human hepaciviruses and pegiviruses suggests the potential for the development of new animal systems with which to model HCV pathogenesis, vaccine design, and treatment. The genetic and biological characterization of animal homologs of human viruses provides insights into the origins of human infections and enhances our ability to study their pathogenesis and explore preventive and therapeutic interventions. Horses are the only reported host of nonprimate homologs of hepatitis C virus (HCV). Here, we report the discovery of HCV-like viruses in wild rodents. The majority of HCV-like viruses were found in deer mice (Peromyscus maniculatus), a small rodent used in laboratories to study viruses, including hantaviruses. We also identified pegiviruses in rodents that are distinct from the pegiviruses found in primates, bats, and horses. These novel viruses may enable the development of small-animal models for HCV, the most common infectious cause of liver failure and hepatocellular carcinoma after hepatitis B virus, and help to explore the health relevance of the highly prevalent human pegiviruses.
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Koutsoudakis G, Forns X, Pérez-Del-Pulgar S. [The molecular biology of hepatitis C virus]. GASTROENTEROLOGIA Y HEPATOLOGIA 2013; 36:280-93. [PMID: 23490024 DOI: 10.1016/j.gastrohep.2012.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 12/12/2022]
Abstract
Since the discovery of the hepatitis C virus (HCV), a plethora of experimental models have evolved, allowing the virus's life cycle and the pathogenesis of associated liver diseases to be investigated. These models range from inoculation of cultured cells with serum from patients with hepatitis C to the use of surrogate models for the study of specific stages of the HCV life cycle: retroviral pseudoparticles for the study of HCV entry, replicons for the study of HCV replication, and the HCV cell culture model, which reproduces the entire life cycle (replication and production of infectious particles). The use of these tools has been and remains crucial to identify potential therapeutic targets in the different stages of the virus's life cycle and to screen new antiviral drugs. A clear example is the recent approval of two viral protease inhibitors (boceprevir and telaprevir) in combination with pegylated interferon and ribavirin for the treatment of chronic hepatitis C. This review analyzes the advances made in the molecular biology of HCV and highlights possible candidates as therapeutic targets for the treatment of HCV infection.
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Affiliation(s)
- George Koutsoudakis
- Servicio de Hepatología, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, España
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Abstract
Hepatitis C virus (HCV) infections become chronic in the majority of infected individuals, and chronic hepatitis C (CHC) can lead to cirrhosis and hepatocellular carcinoma. The innate immune system is central to host-virus interactions during the entire natural course of the disease. The HCV NS3/4A protease efficiently cleaves and inactivates two important signaling molecules in the sensory pathways that react to HCV pathogen-associated molecular patterns (PAMPs) to induce interferons (IFNs), i.e., mitochondrial antiviral signaling protein (MAVS) and Toll-IL-1 receptor domain-containing adaptor inducing IFN-β (TRIF). Despite this viral escape mechanism, the innate immune system strongly reacts to HCV within the first days after infection. The sensory pathways, the type(s) of IFNs involved and the cellular source of IFNs are largely unknown. After 4-8weeks, HCV specific T cells are recruited to the liver. IFN-γ-stimulated genes get strongly expressed in the liver. In about 30% of patients, the virus is eliminated during the acute phase of the infection by T cell-mediated antiviral mechanisms. In the remaining 70% of patients, HCV persists for decades. During this phase, T cell-derived IFN-γ cannot be detected any more in liver biopsies. Instead, in about half of the patients, hundreds of type I or III IFN-stimulated genes become again strongly expressed. However, this innate immune reaction is ineffective against HCV. Moreover, patients with constitutive IFN-stimulated gene (ISG) expression have a poor response to treatment with pegylated IFN-α (PegIFN-α) and ribavirin. The viral escape mechanisms that protect HCV from IFN-mediated innate immune reactions are not entirely understood, but might involve blockade of ISG protein translation at the ribosome, localization of viral replication to cells with refractory IFN signal transduction pathways or to cell compartments that are not accessible to antiviral IFN-stimulated effector systems. Recently, genetic variations near the IL28B (IFN-λ3) were found to be strongly associated with spontaneous clearance of HCV and response to treatment with PegIFN-α and ribavirin. The finding supports a central role of the innate immune response in host-viral interactions. The signaling pathways that link genetic variants of IL28B with immune answers to HCV remain to be elucidated. The present review article attempts to summarize current knowledge of some central aspects of the interactions of HCV with the innate immune system.
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Affiliation(s)
- Markus H Heim
- Division of Gastroenterology and Hepatology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
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Abstract
The classification of hepatitis E virus (HEV) variants is currently in transition without agreed definitions for genotypes and subtypes or for deeper taxonomic groupings into species and genera that could incorporate more recently characterized viruses assigned to the Hepeviridae family that infect birds, bats, rodents, and fish. These conflicts arise because of differences in the viruses and genomic regions compared and in the methodology used. We have reexamined published sequences and found that synonymous substitutions were saturated in comparisons between and within virus genotypes. Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes (types 1 to 4 and two additional genotypes from wild boar). Variants isolated from rabbits, closely related to genotype 3, occupy an intermediate position. No consistent criteria could be defined for the assignment of virus subtypes. Analysis of amino acid sequences from these viruses with the more divergent variants from chickens, bats, and rodents in three conserved subgenomic regions (residues 1 to 452 or 974 to 1534 of ORF1 or residues 105 to 458 of ORF2) provided consistent support for a division into 4 groups, corresponding to HEV variants infecting humans and pigs, those infecting rats and ferrets, those from bats, and those from chickens. This approach may form the basis for a future genetic classification of HEV into four species, with the more divergent HEV-like virus from fish (cutthroat trout virus) representing a second genus.
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Cabezas-Fernandez MT, Cabeza-Barrera MI. Introduction of an automated system for the diagnosis and quantification of hepatitis B and hepatitis C viruses. Open Virol J 2012; 6:122-34. [PMID: 23284598 PMCID: PMC3531716 DOI: 10.2174/1874357901206010122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infections pose major public health problems because of their prevalence worldwide. Consequently, screening for these infections is an important part of routine laboratory activity. Serological and molecular markers are key elements in diagnosis, prognosis and treatment monitoring for HBV and HCV infections. Today, automated chemiluminescence immunoassay (CLIA) analyzers are widely used for virological diagnosis, particularly in high-volume clinical laboratories. Molecular biology techniques are routinely used to detect and quantify viral genomes as well as to analyze their sequence; in order to determine their genotype and detect resistance to antiviral drugs. Real-time PCR, which provides high sensitivity and a broad dynamic range, has gradually replaced other signal and target amplification technologies for the quantification and detection of nucleic acid. The next-generation DNA sequencing techniques are still restricted to research laboratories.The serological and molecular marker methods available for HBV and HCV are discussed in this article, along with their utility and limitations for use in Chronic Hepatitis B (CHB) diagnosis and monitoring.
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Castilho MCB, Martins AN, Horbach IS, Perez RDM, Figueiredo FAF, Pinto PDTA, Nabuco LC, Lima DBD, Tanuri A, Porto LC, Ferreira Júnior ODC. Association of hepatitis C virus NS5B variants with resistance to new antiviral drugs among untreated patients. Mem Inst Oswaldo Cruz 2012; 106:968-75. [PMID: 22241118 DOI: 10.1590/s0074-02762011000800011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 09/08/2011] [Indexed: 01/06/2023] Open
Abstract
Mutations located in the 109-amino acid fragment of NS5B are typically associated with resistance to interferon (IFN) and ribavirin (RIB) and to new antiviral drugs. The prevalence of these mutations was examined in 69 drug-naïve individuals with hepatitis C virus (HCV) infections in Rio de Janeiro, Brazil. Mutations related to non-response to IFN/RIB were observed in all subtypes studied (1a, 1b, 2b, 3a and 4). The most common mutation was Q309R, present in all subtypes, except subtype 2b with frequency above 20%. D244N was detected only in subtype 3a and A333E was detected only in subtype 2b. We did not detect the S282T, S326G or T329I mutations in any of the samples analysed. Of note, the C316N mutation, previously related to a new non-nucleoside compound (HCV796 and AG-021541), was observed in only eight of 33 (24%) samples from subtype 1b. Site 316 was under positive selection in this HCV variant. Our data highlight the presence of previously described resistance mutations in HCV genotypes from drug-naïve patients.
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Affiliation(s)
- Magda Cristina Bernardino Castilho
- Laboratório de Histocompatibilidade e Criopreservação, Policlínica Piquet Carneiro, Departamento de Histologia e Embriologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil.
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Preclinical Profile and Characterization of the Hepatitis C Virus NS3 Protease Inhibitor Asunaprevir (BMS-650032). Antimicrob Agents Chemother 2012; 56:5387-96. [PMID: 22869577 DOI: 10.1128/aac.01186-12] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Asunaprevir (ASV; BMS-650032) is a hepatitis C virus (HCV) NS3 protease inhibitor that has demonstrated efficacy in patients chronically infected with HCV genotype 1 when combined with alfa interferon and/or the NS5A replication complex inhibitor daclatasvir. ASV competitively binds to the NS3/4A protease complex, with K(i) values of 0.4 and 0.24 nM against recombinant enzymes representing genotypes 1a (H77) and 1b (J4L6S), respectively. Selectivity was demonstrated by the absence of any significant activity against the closely related GB virus-B NS3 protease and a panel of human serine or cysteine proteases. In cell culture, ASV inhibited replication of HCV replicons representing genotypes 1 and 4, with 50% effective concentrations (EC(50)s) ranging from 1 to 4 nM, and had weaker activity against genotypes 2 and 3 (EC(50), 67 to 1,162 nM). Selectivity was again demonstrated by the absence of activity (EC(50), >12 μM) against a panel of other RNA viruses. ASV exhibited additive or synergistic activity in combination studies with alfa interferon, ribavirin, and/or inhibitors specifically targeting NS5A or NS5B. Plasma and tissue exposures in vivo in several animal species indicated that ASV displayed a hepatotropic disposition (liver-to-plasma ratios ranging from 40- to 359-fold across species). Twenty-four hours postdose, liver exposures across all species tested were ≥110-fold above the inhibitor EC(50)s observed with HCV genotype-1 replicons. Based on these virologic and exposure properties, ASV holds promise for future utility in a combination with other anti-HCV agents in the treatment of HCV-infected patients.
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Broecker F, Moelling K. Short hairpin-looped oligodeoxynucleotides reduce hepatitis C virus replication. Virol J 2012; 9:134. [PMID: 22823899 PMCID: PMC3508801 DOI: 10.1186/1743-422x-9-134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 07/23/2012] [Indexed: 11/10/2022] Open
Abstract
Background Persistent infection with hepatitis C virus (HCV) is a leading cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Standard therapy consists of a combination of interferon-alpha and ribavirin, but many patients respond poorly, especially those infected with HCV genotypes 1 and 4. Furthermore, standard therapy is associated with severe side-effects. Thus, alternative therapeutic approaches against HCV are needed. Findings Here, we studied the effect of a new class of antiviral agents against HCV, short, partially double-stranded oligodeoxynucleotides (ODNs), on viral replication. We targeted the 5’ nontranslated region (5’ NTR) of the HCV genome that has previously been shown as effective target for small interfering RNAs (siRNAs) in vitro. One of the investigated ODNs, ODN 320, significantly and efficiently reduced replication of HCV replicons in a sequence-, time- and dose-dependent manner. ODN 320 targets a genomic region highly conserved among different HCV genotypes and might thus be able to inhibit a broad range of genotypes and subtypes. Conclusions ODNs provide an additional approach for inhibition of HCV, might be superior to siRNAs in terms of stability and cellular delivery, and suitable against HCV resistant to standard therapy. This study underlines the potential of partially double-stranded ODNs as antiviral agents.
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Hepatitis C virus infection modulates expression of interferon stimulatory gene IFITM1 by upregulating miR-130A. J Virol 2012; 86:10221-5. [PMID: 22787204 DOI: 10.1128/jvi.00882-12] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have examined the underlying mechanism of hepatitis C virus (HCV)-mediated IFITM1 regulation. IFITM1 is a potential target of miR-130a. Our results demonstrated that miR-130a expression was significantly higher in HCV-infected hepatocytes and liver biopsy specimens than in controls. Introduction of anti-miR-130a in hepatocytes increased IFITM1 expression. Hepatocytes stably expressing IFITM1 reduced HCV replication. Together, these results suggested that HCV infection of hepatocytes upregulates miR-130a and that use of anti-miR-130a may have potential for restriction of HCV replication.
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68
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Bolcic F, Laufer N, Trinchero J, Jones LR, Quarleri J. A clustering phenomenon among HCV-1a strains among patients coinfected with HIV from Buenos Aires, Argentina. J Med Virol 2012; 84:570-81. [PMID: 22337295 DOI: 10.1002/jmv.23243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The human immunodeficiency virus (HIV) and hepatitis C virus (HCV) share the same transmission routes which lead to high coinfection rates. Among HIV-infected individuals such rates reached 21% in Argentina, being HCV-1a the most predominant subtype. In this work, 25 HCV subtype 1a (HCV-1a) strains from Argentinean patients coinfected with HIV were studied based on E2 and NS5A sequences. Phylogenetic analyses indicated that 12 strains were highly related to each other, constituting a highly supported (posterior probability = 0.95) monophyletic group that we called "M." The remaining HCV strains (group dispersed or "D") were interspersed along the phylogenetic trees. When comparing both groups of HCV-1a, 10 amino acid differences were located in functional domains of E2 and NS5A proteins that appeared to affect eventually the peptides binding to MHC-I molecules thus favoring immune escape and contributing to the divergence of HCV genotypes. Bayesian coalescent analyses for HCV-1a cluster M isolates indicated that the time to the most recent common ancestor (tMRCA) overlaps with the age estimated recently for the HIV-BF epidemic in Argentina. Furthermore, the genomic characterization based on pol gene analysis from HIV viremic patients showed that most HIV isolates from patients coinfected with HCV-1a cluster M were BF recombinants with identical recombination patterns. In conclusion, these results suggest the presence of an HCV-1a monophyletic cluster with a potential HIV co-transmission by phylogenetic analyses.
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Affiliation(s)
- Federico Bolcic
- Microbiology Department, National Reference Center for AIDS Research, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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69
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Structural basis of hepatitis C virus neutralization by broadly neutralizing antibody HCV1. Proc Natl Acad Sci U S A 2012; 109:9499-504. [PMID: 22623528 DOI: 10.1073/pnas.1202924109] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) infects more than 2% of the global population and is a leading cause of liver cirrhosis, hepatocellular carcinoma, and end-stage liver diseases. Circulating HCV is genetically diverse, and therefore a broadly effective vaccine must target conserved T- and B-cell epitopes of the virus. Human mAb HCV1 has broad neutralizing activity against HCV isolates from at least four major genotypes and protects in the chimpanzee model from primary HCV challenge. The antibody targets a conserved antigenic site (residues 412-423) on the virus E2 envelope glycoprotein. Two crystal structures of HCV1 Fab in complex with an epitope peptide at 1.8-Å resolution reveal that the epitope is a β-hairpin displaying a hydrophilic face and a hydrophobic face on opposing sides of the hairpin. The antibody predominantly interacts with E2 residues Leu(413) and Trp(420) on the hydrophobic face of the epitope, thus providing an explanation for how HCV isolates bearing mutations at Asn(415) on the same binding face escape neutralization by this antibody. The results provide structural information for a neutralizing epitope on the HCV E2 glycoprotein and should help guide rational design of HCV immunogens to elicit similar broadly neutralizing antibodies through vaccination.
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70
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Giang E, Dorner M, Prentoe JC, Dreux M, Evans MJ, Bukh J, Rice CM, Ploss A, Burton DR, Law M. Human broadly neutralizing antibodies to the envelope glycoprotein complex of hepatitis C virus. Proc Natl Acad Sci U S A 2012; 109:6205-10. [PMID: 22492964 PMCID: PMC3341081 DOI: 10.1073/pnas.1114927109] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) infects ∼2% of the world's population. It is estimated that there are more than 500,000 new infections annually in Egypt, the country with the highest HCV prevalence. An effective vaccine would help control this expanding global health burden. HCV is highly variable, and an effective vaccine should target conserved T- and B-cell epitopes of the virus. Conserved B-cell epitopes overlapping the CD81 receptor-binding site (CD81bs) on the E2 viral envelope glycoprotein have been reported previously and provide promising vaccine targets. In this study, we isolated 73 human mAbs recognizing five distinct antigenic regions on the virus envelope glycoprotein complex E1E2 from an HCV-immune phage-display antibody library by using an exhaustive-panning strategy. Many of these mAbs were broadly neutralizing. In particular, the mAb AR4A, recognizing a discontinuous epitope outside the CD81bs on the E1E2 complex, has an exceptionally broad neutralizing activity toward diverse HCV genotypes and protects against heterologous HCV challenge in a small animal model. The mAb panel will be useful for the design and development of vaccine candidates to elicit broadly neutralizing antibodies to HCV.
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Affiliation(s)
- Erick Giang
- Department of Immunology and Microbial Science and
| | - Marcus Dorner
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065
| | - Jannick C. Prentoe
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, DK-2650 Hvidovre, Denmark
- Department of International Health, Immunology, and Microbiology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Matthew J. Evans
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029; and
| | - Jens Bukh
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, DK-2650 Hvidovre, Denmark
- Department of International Health, Immunology, and Microbiology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Charles M. Rice
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065
| | - Alexander Ploss
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065
| | - Dennis R. Burton
- Department of Immunology and Microbial Science and
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02129
| | - Mansun Law
- Department of Immunology and Microbial Science and
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Khattab MA, Eslam M. The impact of host factors on management of hepatitis C virus. HEPATITIS MONTHLY 2012; 12:235-41. [PMID: 22690229 PMCID: PMC3360931 DOI: 10.5812/hepatmon.709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 05/25/2011] [Accepted: 06/25/2011] [Indexed: 02/07/2023]
Affiliation(s)
- Mahmoud Aboelneen Khattab
- Department of Internal Medicine, Minia University, Minia, Egypt
- Corresponding author: Mahmoud Aboelneen Khattab, Division of Gastroenterology and Hepatology, Minia University, P.O. Box: 61111, Minia, Egypt. Tel.: +20-225197818,+20-862378181, Fax: +20-86242813, E-mail:
| | - Mohammed Eslam
- Department of Internal Medicine, Minia University, Minia, Egypt
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Abstract
Until recently, chronic hepatitis C caused by persistent infection with the hepatitis C virus (HCV) has been treated with a combination of pegylated interferon-alpha (PEG-IFNα) and ribavirin (RBV). This situation has changed with the development of two drugs targeting the NS3/4A protease, approved for combination therapy with PEG-IFNα/RBV for patients infected with genotype 1 viruses. Moreover, two additional viral proteins, the RNA-dependent RNA polymerase (residing in NS5B) and the NS5A protein have emerged as promising drug targets and a large number of antivirals targeting these proteins are at different stages of clinical development. Although this progress is very promising, it is not clear whether these new compounds will suffice to eradicate the virus in an infected individual, ideally by using a PEG-IFNα/RBV-free regimen, or whether additional compounds targeting other factors that promote HCV replication are required. In this respect, host cell factors have emerged as a promising alternative. They reduce the risk of development of antiviral resistance and they increase the chance for broad-spectrum activity, ideally covering all HCV genotypes. Work in the last few years has identified several host cell factors used by HCV for productive replication. These include, amongst others, cyclophilins, especially cyclophilinA (cypA), microRNA-122 (miR-122) or phosphatidylinositol-4-kinase III alpha. For instance, cypA inhibitors have shown to be effective in combination therapy with PEG-IFN/RBV in increasing the sustained viral response (SVR) rate significantly compared to PEG-IFN/RBV. This review briefly summarizes recent advances in the development of novel antivirals against HCV.
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Affiliation(s)
- Sandra Bühler
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
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74
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Ciccozzi M, Zehender G, Cento V, Lo Presti A, Teoharov P, Pavlov I, Bogdanova V, Perno CF, Ciotti M. Molecular analysis of hepatitis C virus infection in Bulgarian injecting drug users. J Med Virol 2012; 83:1565-70. [PMID: 21739447 DOI: 10.1002/jmv.22154] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intravenous drug users constitute a group at risk for hepatitis C virus (HCV) infection. Today, no data are available on the molecular epidemiology of HCV in Bulgaria despite the fact that in recent years the incidence of acute hepatitis C infection among Bulgarian intravenous drug users increased sixfold and about 2/3 of them developed a chronic infection. The aim of this study was to determine the circulation of hepatitis C genotypes among drug users and to study the evolution and transmission history of the virus by molecular clock and Bayesian methods, respectively. Sequencing of NS5B gene showed that the genotype 3a was the most prevalent type among intravenous drug users. In the Bayesian tree, the 3a subtypes grouped in one main clade with one small cluster well statistically supported. The root of the tree was dated back to the year 1836, and the main clade from Bulgaria was dated 1960. The effective number of infections remained constant until about years 1950s, growing exponentially from the 1960s to the 1990s, reaching a plateau in the years 2000. The not significant intermixing with isolates from other countries may suggest a segregated circulation of the epidemic between 1940s and 1980s. The plateau reached by the epidemic in the early 2000s may indicate the partial success of the new preventive policies adopted in Bulgaria.
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Affiliation(s)
- Massimo Ciccozzi
- Department of Infectious, Parasitic and Immunomediated Disease, Istituto Superiore di Sanita', Rome, Italy
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75
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Abdel-Moneim AS, Bamaga MS, Shehab GMG, Abu-Elsaad AASA, Farahat FM. HCV infection among Saudi population: high prevalence of genotype 4 and increased viral clearance rate. PLoS One 2012; 7:e29781. [PMID: 22253780 PMCID: PMC3258249 DOI: 10.1371/journal.pone.0029781] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 12/05/2011] [Indexed: 12/31/2022] Open
Abstract
HCV is a major etiological agent of liver disease with a high rate of chronic evolution. The virus possesses 6 genotypes with many subtypes. The rate of spontaneous clearance among HCV infected individuals denotes a genetic determinant factor. The current study was designed in order to estimate the rate of HCV infection and ratio of virus clearance among a group of infected patients in Saudi Arabia from 2008 to 2011. It was additionally designed to determine the genotypes of the HCV in persistently infected patients. HCV seroprevalence was conducted on a total of 15,323 individuals. Seropositive individuals were tested by Cobas AmpliPrep/Cobas TaqMan HCV assay to determine the ratio of persistently infected patients to those who showed spontaneous viral clearance. HCV genotyping on random samples from persistently infected patients were conducted based on the differences in the 5'untranslated region (5'UTR). Anti-HCV antibodies were detected in 7.3% of the totally examined sera. A high percentage of the HCV infected individuals experienced virus clearance (48.4%). HCV genotyping revealed the presence of genotypes 1 and 4, the latter represented 97.6% of the tested strains. Evidences of the widespread of the HCV genotype 4 and a high rate of HCV virus clearance were found in Saudi Arabia.
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76
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Yamasaki LH, Arcuri HA, Jardim ACG, Bittar C, de Carvalho-Mello IMV, Rahal P. New insights regarding HCV-NS5A structure/function and indication of genotypic differences. Virol J 2012; 9:14. [PMID: 22239820 PMCID: PMC3271958 DOI: 10.1186/1743-422x-9-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 01/12/2012] [Indexed: 12/25/2022] Open
Abstract
Background HCV is prevalent throughout the world. It is a major cause of chronic liver disease. There is no effective vaccine and the most common therapy, based on Peginterferon, has a success rate of ~50%. The mechanisms underlying viral resistance have not been elucidated but it has been suggested that both host and virus contribute to therapy outcome. Non-structural 5A (NS5A) protein, a critical virus component, is involved in cellular and viral processes. Methods The present study analyzed structural and functional features of 345 sequences of HCV-NS5A genotypes 1 or 3, using in silico tools. Results There was residue type composition and secondary structure differences between the genotypes. In addition, second structural variance were statistical different for each response group in genotype 3. A motif search indicated conserved glycosylation, phosphorylation and myristoylation sites that could be important in structural stabilization and function. Furthermore, a highly conserved integrin ligation site was identified, and could be linked to nuclear forms of NS5A. ProtFun indicated NS5A to have diverse enzymatic and nonenzymatic activities, participating in a great range of cell functions, with statistical difference between genotypes. Conclusion This study presents new insights into the HCV-NS5A. It is the first study that using bioinformatics tools, suggests differences between genotypes and response to therapy that can be related to NS5A protein features. Therefore, it emphasizes the importance of using bioinformatics tools in viral studies. Data acquired herein will aid in clarifying the structure/function of this protein and in the development of antiviral agents.
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Affiliation(s)
- Lilian Ht Yamasaki
- Department of Biology, Sao Paulo State University--UNESP, Sao Jose do Rio Preto, SP, Brazil.
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Brahim I, Akil A, Mtairag EM, Pouillot R, Malki AE, Nadir S, Alaoui R, Njouom R, Pineau P, Ezzikouri S, Benjelloun S. Morocco underwent a drift of circulating hepatitis C virus subtypes in recent decades. Arch Virol 2011; 157:515-20. [PMID: 22160625 DOI: 10.1007/s00705-011-1193-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 12/01/2011] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) isolates circulating in Morocco are poorly documented. To determine the subgenotype distribution of HCV in chronically infected patients, serum samples from 185 anti-HCV-positive patients were analyzed. Determination of the HCV genotype and subtype was performed by sequencing the 5'UTR, NS5B and core regions. According to the NS5B phylogeny, the HCV strains primarily belonged to subtypes 1b (75.2%), 2i (19.1%) and 2k (2.8%). Using a Bayesian approach, the mean date of appearance of the most recent common ancestor was estimated to be 1910 for HCV-1b and 1854 for HCV-2i. Although it is currently the most frequent genotype in Morocco and the dominant form in hepatocellular carcinoma, it thus appears that HCV-1b was introduced into the population subsequently to HCV-2i.
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Affiliation(s)
- Ikram Brahim
- Virology Unit, Viral Hepatitis Laboratory, Pasteur Institute of Morocco, 1, Place Louis Pasteur, 20360 Casablanca, Morocco
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78
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Raychoudhuri A, Shrivastava S, Steele R, Kim H, Ray R, Ray RB. ISG56 and IFITM1 proteins inhibit hepatitis C virus replication. J Virol 2011; 85:12881-9. [PMID: 21976647 PMCID: PMC3233139 DOI: 10.1128/jvi.05633-11] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/28/2011] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) often leads to persistent infection. Interferon (IFN) and IFN-stimulated genes (ISGs) are amplified during HCV infection but fail to eliminate virus from the liver in a large number of infected patients. We have observed previously that HCV infection induces IFN-β production in immortalized human hepatocytes (IHH) as early as 24 h after infection, although virus replication is not inhibited. To gain insights on possible countermeasures of virus for the suppression of host antiviral response, the cellular transcriptional profiles of ISGs were examined after various treatments of IHH. The majority of ISGs were upregulated in IFN-treated IHH from the level for mock-treated cells. However, the comparison of ISG expression in IFN-treated IHH and IFN-pretreated, HCV genotype 2a-infected IHH indicated that virus infection suppresses the upregulation of a subset of effector molecules, including ISG56 and IFITM1. Similar results were observed for HCV-infected Huh7 cells. Subsequent study suggested that the exogenous expression of ISG56 or IFITM1 inhibits HCV replication in IHH or Huh7 cells, and the knockdown of these genes enhanced HCV replication. Further characterization revealed that the overexpression of these ISGs does not block HCV pseudotype entry into Huh7 cells. Taken together, our results demonstrated that ISG56 and IFITM1 serve as important molecules to restrict HCV infection, and they may have implications in the development of therapeutic modalities.
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Affiliation(s)
| | | | | | - Hangeun Kim
- Internal Medicine, Saint Louis University, St. Louis, Missouri
| | - Ranjit Ray
- Internal Medicine, Saint Louis University, St. Louis, Missouri
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Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A. HCVpro: Hepatitis C virus protein interaction database. INFECTION GENETICS AND EVOLUTION 2011; 11:1971-7. [DOI: 10.1016/j.meegid.2011.09.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/24/2011] [Accepted: 09/02/2011] [Indexed: 02/07/2023]
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80
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Origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b. J Virol 2011; 86:2212-20. [PMID: 22114341 DOI: 10.1128/jvi.06184-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Since its initial identification in St. Petersburg, Russia, the recombinant hepatitis C virus (HCV) 2k/1b has been isolated from several countries throughout Eurasia. The 2k/1b strain is the only recombinant HCV to have spread widely, raising questions about the epidemiological background in which it first appeared. In order to further understand the circumstances by which HCV recombinants might be formed and spread, we estimated the date of the recombination event that generated the 2k/1b strain using a Bayesian phylogenetic approach. Our study incorporates newly isolated 2k/1b strains from Amsterdam, The Netherlands, and has employed a hierarchical Bayesian framework to combine information from different genomic regions. We estimate that 2k/1b originated sometime between 1923 and 1956, substantially before the first detection of the strain in 1999. The timescale and the geographic spread of 2k/1b suggest that it originated in the former Soviet Union at about the time that the world's first centralized national blood transfusion and storage service was being established. We also reconstructed the epidemic history of 2k/1b using coalescent theory-based methods, matching patterns previously reported for other epidemic HCV subtypes. This study demonstrates the practicality of jointly estimating dates of recombination from flanking regions of the breakpoint and further illustrates that rare genetic-exchange events can be particularly informative about the underlying epidemiological processes.
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81
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Garrone P, Fluckiger AC, Mangeot PE, Gauthier E, Dupeyrot-Lacas P, Mancip J, Cangialosi A, Du Chéné I, LeGrand R, Mangeot I, Lavillette D, Bellier B, Cosset FL, Tangy F, Klatzmann D, Dalba C. A prime-boost strategy using virus-like particles pseudotyped for HCV proteins triggers broadly neutralizing antibodies in macaques. Sci Transl Med 2011; 3:94ra71. [PMID: 21813755 DOI: 10.1126/scitranslmed.3002330] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chronic hepatitis C virus (HCV) infection, with its cohort of life-threatening complications, affects more than 200 million persons worldwide and has a prevalence of more than 10% in certain countries. Preventive and therapeutic vaccines against HCV are thus much needed. Neutralizing antibodies (NAbs) are the foundation for successful disease prevention for most established vaccines. However, for viruses that cause chronic infection such as HIV or HCV, induction of broad NAbs from recombinant vaccines has remained elusive. We developed a vaccine platform specifically aimed at inducing NAbs based on pseudotyped virus-like particles (VLPs) made with retroviral Gag. We report that VLPs pseudotyped with E2 and/or E1 HCV envelope glycoproteins induced high-titer anti-E2 and/or anti-E1 antibodies, as well as NAbs, in both mouse and macaque. The NAbs, which were raised against HCV 1a, cross-neutralized the five other genotypes tested (1b, 2a, 2b, 4, and 5). Thus, the described VLP platform, which can be pseudotyped with a vast array of virus envelope glycoproteins, represents a new approach to viral vaccine development.
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82
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Bhattacharya D, Accola MA, Ansari IH, Striker R, Rehrauer WM. Naturally occurring genotype 2b/1a hepatitis C virus in the United States. Virol J 2011; 8:458. [PMID: 21967740 PMCID: PMC3205070 DOI: 10.1186/1743-422x-8-458] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/03/2011] [Indexed: 12/20/2022] Open
Abstract
Background Hepatitis C Virus (HCV) infected patients are frequently repeatedly exposed to the virus, but very few recombinants between two genotypes have been reported. Findings We describe the discovery of an HCV recombinant using a method developed in a United States clinical lab for HCV genotyping that employs sequencing of both 5' and 3' portions of the HCV genome. Over twelve months, 133 consecutive isolates were analyzed, and a virus from one patient was found with discordant 5' and 3' sequences suggesting it was a genotype 2b/1a recombinant. We ruled out a mixed infection and mapped a recombination point near the NS2/3 cleavage site. Conclusions This unique HCV recombinant virus described shares some features with other recombinant viruses although it is the only reported recombinant of a genotype 2 with a subtype 1a. This recombinant represents a conundrum for current clinical treatment guidelines, including treatment with protease inhibitors. This recombinant is also challenging to detect by the most commonly employed methods of genotyping that are directed primarily at the 5' structural portion of the HCV genome.
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Affiliation(s)
- Dipankar Bhattacharya
- University of Wisconsin-Madison, School of Medicine and Public Health, Department of Medicine, Madison, WI 53706, USA
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Zhang X, Ryu SH, Xu Y, Elbaz T, Zekri ARN, Abdelaziz AO, Abdel-Hamid M, Thiers V, Elena SF, Fan X, Di Bisceglie AM. The Core/E1 domain of hepatitis C virus genotype 4a in Egypt does not contain viral mutations or strains specific for hepatocellular carcinoma. J Clin Virol 2011; 52:333-8. [PMID: 21925935 DOI: 10.1016/j.jcv.2011.08.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/16/2011] [Accepted: 08/22/2011] [Indexed: 12/17/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a well-documented etiological factor for hepatocellular carcinoma (HCC). As HCV shows remarkable genetic diversity, an interesting and important issue is whether such a high viral genetic diversity plays a role in the incidence of HCC. Prior data on this subject are conflicting. OBJECTIVES Potential association between HCV genetic mutations or strain variability and HCC incidence has been examined through a comparative genetic analysis merely focused on a single HCV subtype (genotype 4a) in a single country (Egypt). STUDY DESIGN The study focused on three HCV sequence datasets with explicit sampling dates and disease patterns. An overlapping HCV Core/E1 domain from three datasets was used as the target for comparative analysis through genetic and phylogenetic approaches. RESULTS Based on partial Core/E1 domain (387 bp), genetic and phylogenetic analysis did not identify any HCC-specific viral mutations and strains, respectively. CONCLUSIONS The Core/E1 domain of HCV genotype 4a in Egypt does not contain HCC-specific mutations or strains. Additionally, sequence errors resulting from the polymerase chain reaction, together with a strong evolutionary pressure on HCV in patients with end-stage liver disease, have significant potential to bias data generation and interpretation.
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Affiliation(s)
- Xiaoan Zhang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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Chan DPC, Lee SS, Lee KCK. The effects of widespread methadone treatment on the molecular epidemiology of hepatitis C virus infection among injection drug users in Hong Kong. J Med Virol 2011; 83:1187-94. [PMID: 21567422 DOI: 10.1002/jmv.22099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The distribution of HCV genotypes among injection drug users in Hong Kong was assessed in context of methadone treatment availability. Three time periods were defined by the year of initiating injection-on or before 1980, 1981-1994, and 1995-2006-with methadone becoming widely available since the second period. Of the 273 HCV RNA-positive cases, the most prevalent subtype was HCV 6a (52.4%), followed by HCV 1b (38.5%). The new variants of HCV subtypes 6e and 6h were detected. Both subtypes 1b and 6a were prevalent among older injectors, while subtype 3a was more common in young injectors and those initiating injection recently during the third time period. Age (P < 0.05) and recent injection frequency (P < 0.01) were independently associated with HCV 6a infection. Subtype 1b was predominant in the first period, whereas 6a was more common in the second and third. Subtype 1b sequences appeared to have originated at two positions on the phylogenetic tree, while 6a showed a more disperse distribution suggestive of multiple introductions. Phylogenetic analysis on the NS5B region did not reveal specific clustering of any subtype/genotype. Overall, there was no suggestion of outbreaks of HCV. The extensive use of methadone may have protected Hong Kong from the emergence of HCV clusters among injection drug users.
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Affiliation(s)
- Denise P C Chan
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, Hong Kong
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85
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Robinson M, Tian Y, Pagratis N, Delaney WE. Screening of Hepatitis C Virus Inhibitors Using Genotype 1a HCV Replicon Cell Lines. ACTA ACUST UNITED AC 2011; Chapter 17:Unit17.7. [DOI: 10.1002/9780471729259.mc1707s22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | - Yang Tian
- Gilead Sciences Foster City California
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86
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Martró E, Valero A, Jordana-Lluch E, Saludes V, Planas R, González-Candelas F, Ausina V, Bracho MA. Hepatitis C virus sequences from different patients confirm the existence and transmissibility of subtype 2q, a rare subtype circulating in the metropolitan area of Barcelona, Spain. J Med Virol 2011; 83:820-6. [PMID: 21412791 DOI: 10.1002/jmv.22054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The hepatitis C virus (HCV) has been classified into six genotypes and more than 70 subtypes with distinct geographical and epidemiological distributions. While 18 genotype 2 subtypes have been proposed, only 5 have had their complete sequence determined. The aim of this study was to characterize HCV isolates from three patients from the Barcelona metropolitan area of Spain for whom commercial genotyping methods provided discordant results. Full-length genome sequencing was carried out for 2 of the 3 patients; for the third patient only partial NS5B sequences could be obtained. The generated sequences were subjected to phylogenetic, recombination, and identity analyses. Sequences covering most of the HCV genome (9398 and 9566 nt in length) were obtained and showed a 90.3% identity to each other at the nucleotide level, while both sequences differed by 17.5-22.6% from the other fully sequenced genotype 2 subtypes. No evidence of recombination was found. The NS5B phylogenetic tree showed that sequences from the three patients cluster together with the only representative sequence of the provisionally designed 2q subtype, which also corresponds to a patient from Barcelona. Phylogenetic analysis of the full coding sequence showed that subtype 2q was more closely related to subtype 2k. The results obtained in this study suggest that subtype 2q now meets the requirements for confirmed designation status according to consensus criteria for HCV classification and nomenclature, and its epidemiological value is ensured as it has spread among several patients in the Barcelona metropolitan area.
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Affiliation(s)
- Elisa Martró
- Microbiology Service, Health Sciences Research Institute of Germans Trias i Pujol Foundation, Germans Trias i Pujol Hospital, Autonoma University of Barcelona, Badalona, Spain.
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87
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Wang QQ, Zhang J, Hu JS, Chen HT, Du L, Wu LQ, Ding YZ, Xiong SH, Huang XC, Zhang YH, Liu YS. Rapid detection of hepatitis C virus RNA by a reverse transcription loop-mediated isothermal amplification assay. ACTA ACUST UNITED AC 2011; 63:144-7. [PMID: 21635570 DOI: 10.1111/j.1574-695x.2011.00828.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The usefulness of reverse transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid diagnosis of hepatitis C virus (HCV) RNA was evaluated. This assay showed higher sensitivities than that of nested RT-PCR, with a detection limit of 600 IU mL(-1) , and no cross-reactivity was observed with hepatitis A virus, hepatitis B virus and hepatitis E virus. Furthermore, 106 stored sera from recently diagnosed cases were retrospectively investigated with real-time RT-PCR, the nested RT-PCR, in parallel with this new assay. The general detection rates of HCV RT-LAMP, real-time PCR and the nested RT-PCR for 106 stored sera samples were 95%, 96% and 88%, respectively. This study provides the first data on the usefulness of HCV RT-LAMP in the diagnosis of HCV RNA, especially in the early clinical diagnosis of acute HCV infection.
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Affiliation(s)
- Qin-qin Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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88
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Khattab MA, Ferenci P, Hadziyannis SJ, Colombo M, Manns MP, Almasio PL, Esteban R, Abdo AA, Harrison SA, Ibrahim N, Cacoub P, Eslam M, Lee SS. Management of hepatitis C virus genotype 4: recommendations of an international expert panel. J Hepatol 2011; 54:1250-62. [PMID: 21316497 DOI: 10.1016/j.jhep.2010.11.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/17/2010] [Accepted: 11/23/2010] [Indexed: 02/06/2023]
Abstract
HCV has been classified into no fewer than six major genotypes and a series of subtypes. Each HCV genotype is unique with respect to its nucleotide sequence, geographic distribution, and response to therapy. Genotypes 1, 2, and 3 are common throughout North America and Europe. HCV genotype 4 (HCV-4) is common in the Middle East and in Africa, where it is responsible for more than 80% of HCV infections. It has recently spread to several European countries. HCV-4 is considered a major cause of chronic hepatitis, cirrhosis, hepatocellular carcinoma, and liver transplantation in these regions. Although HCV-4 is the cause of approximately 20% of the 170 million cases of chronic hepatitis C in the world, it has not been the subject of widespread research. Therefore, this document, drafted by a panel of international experts, aimed to review current knowledge on the epidemiology, natural history, clinical, histological features, and treatment of HCV-4 infections.
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89
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Li H, Hughes AL, Bano N, McArdle S, Livingston S, Deubner H, McMahon BJ, Townshend-Bulson L, McMahan R, Rosen HR, Gretch DR. Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time. PLoS One 2011; 6:e19562. [PMID: 21573177 PMCID: PMC3088699 DOI: 10.1371/journal.pone.0019562] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 04/09/2011] [Indexed: 01/06/2023] Open
Abstract
Infection with hepatitis C virus (HCV) is one of the leading causes of chronic hepatitis, liver cirrhosis and end-stage liver disease worldwide. The genetics of HCV infection in humans and the disease course of chronic hepatitis C are both remarkably variable. Although the response to interferon treatment is largely dependent on HCV genotypes, whether or not a relationship exists between HCV genome variability and clinical course of hepatitis C disease still remains unknown. To more thoroughly understand HCV genome evolution over time in association with disease course, near genome-wide HCV genomes present in 9 chronically infected participants over 83 total study years were sequenced. Overall, within HCV genomes, the number of synonymous substitutions per synonymous site (d(S)) significantly exceeded the number of non-synonymous substitutions per site (d(N)). Although both d(S) and d(N) significantly increased with duration of chronic infection, there was a highly significant decrease in d(N)/d(S) ratio in HCV genomes over time. These results indicate that purifying selection acted to conserve viral protein structure despite persistence of high level of nucleotide mutagenesis inherent to HCV replication. Based on liver biopsy fibrosis scores, HCV genomes from participants with advanced fibrosis had significantly greater d(S) values and lower d(N)/d(S) ratios compared to participants with mild liver disease. Over time, viral genomes from participants with mild disease had significantly greater annual changes in d(N), along with higher d(N)/d(S) ratios, compared to participants with advanced fibrosis. Yearly amino acid variations in the HCV p7, NS2, NS3 and NS5B genes were all significantly lower in participants with severe versus mild disease, suggesting possible pathogenic importance of protein structural conservation for these viral gene products.
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Affiliation(s)
- Hui Li
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Nazneen Bano
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Susan McArdle
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Stephen Livingston
- Liver Disease and Hepatitis Program, Alaska Native Tribal Health Consortium, Anchorage, Alaska, United States of America
| | - Heike Deubner
- Department of Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Brian J. McMahon
- Liver Disease and Hepatitis Program, Alaska Native Tribal Health Consortium, Anchorage, Alaska, United States of America
| | - Lisa Townshend-Bulson
- Liver Disease and Hepatitis Program, Alaska Native Tribal Health Consortium, Anchorage, Alaska, United States of America
| | - Rachel McMahan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Hugo R. Rosen
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - David R. Gretch
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington Medical Center, Seattle, Washington, United States of America
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Bolcic F, Jones L, Laufer N, Quarleri J. Molecular characterization of hepatitis C virus genotype 4 sequences in HIV-coinfected patients from Argentina. J Med Virol 2011; 83:935-40. [DOI: 10.1002/jmv.22068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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91
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Clemente-Casares P, López-Jiménez AJ, Bellón-Echeverría I, Encinar JA, Martínez-Alfaro E, Pérez-Flores R, Mas A. De novo polymerase activity and oligomerization of hepatitis C virus RNA-dependent RNA-polymerases from genotypes 1 to 5. PLoS One 2011; 6:e18515. [PMID: 21490973 PMCID: PMC3072391 DOI: 10.1371/journal.pone.0018515] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/04/2011] [Indexed: 01/20/2023] Open
Abstract
Hepatitis C virus (HCV) shows a great geographical diversity reflected in the high number of circulating genotypes and subtypes. The response to HCV treatment is genotype specific, with the predominant genotype 1 showing the lowest rate of sustained virological response. Virally encoded enzymes are candidate targets for intervention. In particular, promising antiviral molecules are being developed to target the viral NS3/4A protease and NS5B polymerase. Most of the studies with the NS5B polymerase have been done with genotypes 1b and 2a, whilst information about other genotypes is scarce. Here, we have characterized the de novo activity of NS5B from genotypes 1 to 5, with emphasis on conditions for optimum activity and kinetic constants. Polymerase cooperativity was determined by calculating the Hill coefficient and oligomerization through a new FRET-based method. The Vmax/Km ratios were statistically different between genotype 1 and the other genotypes (p<0.001), mainly due to differences in Vmax values, but differences in the Hill coefficient and NS5B oligomerization were noted. Analysis of sequence changes among the studied polymerases and crystal structures show the αF helix as a structural component probably involved in NS5B-NS5B interactions. The viability of the interaction of αF and αT helixes was confirmed by docking studies and calculation of electrostatic surface potentials for genotype 1 and point mutants corresponding to mutations from different genotypes. Results presented in this study reveal the existence of genotypic differences in NS5B de novo activity and oligomerization. Furthermore, these results allow us to define two regions, one consisting of residues Glu128, Asp129, and Glu248, and the other consisting of residues of αT helix possibly involved in NS5B-NS5B interactions.
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Affiliation(s)
- Pilar Clemente-Casares
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
| | - Alberto J. López-Jiménez
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
- Infectious Disease Unit, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Itxaso Bellón-Echeverría
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
| | - José Antonio Encinar
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Elisa Martínez-Alfaro
- Infectious Disease Unit, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Ricardo Pérez-Flores
- Digestive Department, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Antonio Mas
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
- * E-mail:
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92
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Albecka A, Montserret R, Krey T, Tarr AW, Diesis E, Ball JK, Descamps V, Duverlie G, Rey F, Penin F, Dubuisson J. Identification of new functional regions in hepatitis C virus envelope glycoprotein E2. J Virol 2011; 85:1777-92. [PMID: 21147916 PMCID: PMC3028898 DOI: 10.1128/jvi.02170-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 11/29/2010] [Indexed: 01/21/2023] Open
Abstract
Little is known about the structure of the envelope glycoproteins of hepatitis C virus (HCV). To identify new regions essential for the function of these glycoproteins, we generated HCV pseudoparticles (HCVpp) containing HCV envelope glycoproteins, E1 and E2, from different genotypes in order to detect intergenotypic incompatibilities between these two proteins. Several genotype combinations were nonfunctional for HCV entry. Of interest, a combination of E1 from genotype 2a and E2 from genotype 1a was nonfunctional in the HCVpp system. We therefore used this nonfunctional complex and the recently described structural model of E2 to identify new functional regions in E2 by exchanging protein regions between these two genotypes. The functionality of these chimeric envelope proteins in the HCVpp system and/or the cell-cultured infectious virus (HCVcc) was analyzed. We showed that the intergenotypic variable region (IgVR), hypervariable region 2 (HVR2), and another segment in domain II play a role in E1E2 assembly. We also demonstrated intradomain interactions within domain I. Importantly, we also identified a segment (amino acids [aa] 705 to 715 [segment 705-715]) in the stem region of E2, which is essential for HCVcc entry. Circular dichroism and nuclear magnetic resonance structural analyses of the synthetic peptide E2-SC containing this segment revealed the presence of a central amphipathic helix, which likely folds upon membrane binding. Due to its location in the stem region, segment 705-715 is likely involved in the reorganization of the glycoprotein complexes taking place during the fusion process. In conclusion, our study highlights new functional and structural regions in HCV envelope glycoprotein E2.
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Affiliation(s)
- Anna Albecka
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Roland Montserret
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Thomas Krey
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Alexander W. Tarr
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Eric Diesis
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Jonathan K. Ball
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Véronique Descamps
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Gilles Duverlie
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Felix Rey
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - François Penin
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
| | - Jean Dubuisson
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019 Lille, France; Inserm U1019, F-59019 Lille, France; CNRS UMR8204, F-59021 Lille, France; and Université Lille Nord de France, F-59000 Lille, France, Institut de Biologie et Chimie des Protéines, UMR-5086-CNRS, Université de Lyon, Lyon, France, Institut Pasteur, CNRS URA3015, Unité de Virologie Structurale, Paris, France, School of Molecular Medical Sciences, the University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom, Laboratoire de Virologie EA4294, Centre Hospitalier Universitaire d'Amiens, Université de Picardie Jules Verne, Amiens, France
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93
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Eriksen MB, Jørgensen LB, Krarup H, Laursen AL, Christensen PB, Møller A, Schlichting P, Kuiken C, Bukh J, Weis N. Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark. J Med Virol 2011; 82:1869-77. [PMID: 20872713 DOI: 10.1002/jmv.21896] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The prevalence of hepatitis C virus (HCV) genotype 4 has increased throughout Europe. This is an epidemiological study of patients infected chronically with HCV genotype 4 in Denmark. The HCV strains analyzed originated from patient samples collected between 1999 and 2007 as part of the national Danish hepatitis B and C network, DANHEP. Sequence analyses were based on the envelope 1 region of HCV. Results from a total of 72 patients indicated a high degree of genetic heterogeneity. Fifty-six patients (78%) were infected with one of the three dominating subtypes: 4d, 4a, or 4r. The remaining 16 patients (22%) were infected with subtypes 4h, 4k, 4l, 4n, 4o, or 4Unclassified. Three epidemiological profiles were identified: (1) patients infected with HCV by intravenous drug use were infected solely with subtype 4d. They were all of European origin, and 15 of the 16 patients were ethnic Danes. No single transmission event could be confirmed, but the pairwise nucleotide identity within the patients of Danish origin was relatively high (∼95%), suggesting a recent introduction into Denmark. (2) The 21 patients infected with subtype 4a all came from Northern Africa, Egypt, Pakistan, or the Middle East. (3) Patients from Southern Africa dominated among patients infected with subtype 4r (10 of 12 patients). This study demonstrates that HCV genotype 4d has been introduced in and spread among Danish intravenous drug users. The remaining subtypes show restricted distribution, infecting almost exclusively patients from geographical areas with a relatively high prevalence of HCV genotype 4 infections.
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94
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Germano FN, dos Santos CA, Honscha G, Strasburg A, Gabbi B, Mendoza-Sassi RA, Soares EA, Seuánez HN, Soares MA, Martínez AMB. Prevalence of hepatitis C virus among users attending a voluntary testing centre in Rio Grande, southern Brazil: predictive factors and hepatitis C virus genotypes. Int J STD AIDS 2011; 21:466-71. [PMID: 20852195 DOI: 10.1258/ijsa.2009.009089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We estimated the prevalence of hepatitis C (HCV) infection and associated risk factors in 750 individuals attending the Voluntary Counseling and Testing Center of Rio Grande (VCT/RG), in Southern Brazil, and identified viral genotypes. Demographic data and risk factors for HCV transmission were also collected and analysed. Anti-HCV antibody-positive individuals were tested for HCV-RNA and genotyped by sequencing the 5' untranslated region of the viral genome. Prevalence estimates of anti-HCV and HCV-RNA were 6% and 5.5%, respectively. We identified genotypes 1 (67%), 2 (2%) and 3 (31%); the latter was more prevalent than in other regions of Brazil. Anti-HCV prevalence in VCT/RG users was similar to previous reports. Age, previous blood transfusion, sexual orientation and injecting drug use were independent predictors of HCV infection. The presence of multiple risk factors was also associated with a higher risk for HCV infection. HCV genotype was not associated with any variable analysed in this study.
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Affiliation(s)
- F N Germano
- Departamento de Patologia, Fundação Universidade Federal do Rio Grande, AV. General Osório S/N, Centro 96200-400 Rio Grande
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95
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Mujtaba G, Jahan S, Khaliq S, Mahmood N, Javed F, Choudhry N, Aslam A, Bashir T, Faiz M. Current Status of Transmission Risk Factors and Genotypes of Hepatitis C Virus, In Punjabi Population of Pakistan. ACTA ACUST UNITED AC 2011. [DOI: 10.5455/ijavms.20110526102003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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96
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Smith J, Aberle JH, Fleming VM, Ferenci P, Thomson EC, Karayiannis P, McLean AR, Holzmann H, Klenerman P. Dynamic coinfection with multiple viral subtypes in acute hepatitis C. J Infect Dis 2010; 202:1770-9. [PMID: 21067369 PMCID: PMC3107554 DOI: 10.1086/657317] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 07/19/2010] [Indexed: 01/28/2023] Open
Abstract
INTRODUCTION Acute hepatitis C virus (HCV) infection is rarely studied, but virus sequence evolution and host-virus dynamics during this early stage may influence the outcome of infection. Hypervariable region 1 (HVR1) is genetically diverse and under selective pressure from the host immune response. We analyzed HVR1 evolution by frequent sampling of an acutely infected HCV cohort. METHODS Three or more pretreatment samples were obtained from each of 10 acutely infected subjects. Polymerase chain reaction amplification was performed with multiple primer combinations to identify the full range of sequences present. Positive samples were cloned and sequenced. Phylogenetic analyses were used to assess viral diversity. RESULTS Eight of the 10 subjects were coinfected with at least 2 HCV subtypes. Multiple subtypes were detected in individual samples, and their relative proportions changed through acute infection. The subjects with the most complex subtype structure also had a dynamic viral load; however, changes in viral load were not directly linked to changes in subtype. CONCLUSIONS This well-sampled cohort with acute HCV infection was characterized by dynamic coinfection with multiple viral subtypes, representing a highly complex virologic landscape extremely early in infection.
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Affiliation(s)
- Jennifer Smith
- Institute for Emerging Infections, University of Oxford, Oxford
| | - Judith H. Aberle
- Institute of Virology, Medical University of Vienna, Vienna, Austria
| | - Vicki M. Fleming
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford
| | - Peter Ferenci
- Department of Internal Medicine, Gastroenterology, and Hepatology, Medical University of Vienna, Vienna, Austria
| | - Emma C. Thomson
- Department of Hepatology, Imperial College, London, United Kingdom
| | | | | | | | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford
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97
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Abstract
Lipid droplets (LDs) are cellular lipid storage organelles involved not only in lipid homeostasis but also in a variety of diseases. Chronic hepatitis C virus (HCV) infection affects host lipid metabolism, and thus induces LD accumulation in the liver. Recent studies have suggested that cellular LDs also play a crucial role in the HCV life cycle. Interactions between HCV proteins, especially the core protein, and LDs are required for the morphogenesis of infectious HCV. The present minireview will summarize the recent research progress about this unique relationship between LDs and the HCV life cycle.
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Affiliation(s)
- Masayoshi Fukasawa
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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98
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Ciotti M, Marcuccilli F, Guenci T, Babakir-Mina M, Chiodo F, Favarato M, Perno CF. A multicenter evaluation of the Abbott RealTime HCV Genotype II assay. J Virol Methods 2010; 167:205-7. [PMID: 20362009 DOI: 10.1016/j.jviromet.2010.03.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 03/16/2010] [Accepted: 03/22/2010] [Indexed: 12/12/2022]
Abstract
Genotype determination is recommended before starting anti-HCV therapy to determine the duration of treatment (PEG-Interferon+ribavirin). The Versant HCV Genotype 2.0 assay, based on the reverse hybridization of the 5'UTR segment and core region of hepatitis C virus (HCV), has been one of the assays used most widely for HCV genotyping. A multicenter evaluation of the more automated Abbott RealTime HCV Genotype II assay was carried out on 124 HCV positive sera tested previously with the Versant HCV Genotype 2.0 assay. There was good agreement between the two assays. Type concordance was 95.9% (117/122) while concordance at the subtype level for genotype 1 was 95.6% (43/45). The Abbott RealTime HCV Genotype II assay is automated, allowing a substantial reduction of time-to results and hands-on time. The combined features of full automation, objective interpretation and digital archiving make this assay useful in a diagnostic setting.
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Affiliation(s)
- Marco Ciotti
- Laboratory of Molecular Virology, Foundation University Hospital Tor Vergata, Viale Oxford, 81-00133, Rome, Italy.
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99
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Ramirez S, Perez-del-Pulgar S, Carrion JA, Coto-Llerena M, Mensa L, Dragun J, Garcia-Valdecasas JC, Navasa M, Forns X. Hepatitis C virus superinfection of liver grafts: a detailed analysis of early exclusion of non-dominant virus strains. J Gen Virol 2010; 91:1183-8. [DOI: 10.1099/vir.0.018929-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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100
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Koletzki D, Dumont S, Vermeiren H, Fevery B, De Smet P, Stuyver LJ. Development and evaluation of an automated hepatitis C virus NS5B sequence-based subtyping assay. Clin Chem Lab Med 2010; 48:1095-102. [DOI: 10.1515/cclm.2010.236] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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