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Le Guillou-Guillemette H, Ducancelle A, Bertrais S, Lemaire C, Pivert A, Veillon P, Bouthry E, Alain S, Thibault V, Abravanel F, Rosenberg AR, Henquell C, André-Garnier E, Petsaris O, Vallet S, Bour JB, Baazia Y, Trimoulet P, André P, Gaudy-Graffin C, Bettinger D, Larrat S, Signori-Schmuck A, Saoudin H, Pozzetto B, Lagathu G, Minjolle-Cha S, Stoll-Keller F, Pawlotsky JM, Izopet J, Payan C, Lunel-Fabiani F. Identification of a duplicated V3 domain in NS5A associated with cirrhosis and hepatocellular carcinoma in HCV-1b patients. J Clin Virol 2015. [PMID: 26209408 DOI: 10.1016/j.jcv.2015.06.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The NS5A protein of the hepatitis C virus has been shown to be involved in the development of hepatocellular carcinoma. OBJECTIVES In a French multicenter study, we investigated the clinical and epidemiological features of a new HCV genotype 1b strain bearing a wide insertion into the V3 domain. STUDY DESIGN We studied NS5A gene sequences in 821 French patients infected with genotype 1b HCV. RESULTS We identified an uncharacterized V3 insertion without ORF disruption in 3.05% of the HCV sequences. The insertion comprised 31 amino-acids for the majority of patients; 3 patients had 27 amino-acids insertions and 1 had a 12 amino-acids insertion. Sequence identity between the 31 amino-acids insertions and the V3 domain ranged from 48 to 96% with E-values above 4e(-5), thus illustrating sequence homology and a partial gene duplication event that to our knowledge has never been reported in HCV. Moreover we showed the presence of the duplication at the time of infection and its persistence at least during 12 years in the entire quasispecies. No association was found with extrahepatic diseases. Conversely, patients with cirrhosis were two times more likely to have HCV with this genetic characteristic (p=0.04). Moreover, its prevalence increased with liver disease severity (from 3.0% in patients without cirrhosis to 9.4% in patients with both cirrhosis and HCC, p for trend=0.045). CONCLUSIONS We identified a duplicated V3 domain in the HCV-1b NS5A protein for the first time. The duplication may be associated with unfavorable evolution of liver disease including a possible involvement in liver carcinogenesis.
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Affiliation(s)
- H Le Guillou-Guillemette
- Laboratoire de Virologie, CHU Angers, France; HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
| | - A Ducancelle
- Laboratoire de Virologie, CHU Angers, France; HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
| | - S Bertrais
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
| | - C Lemaire
- IRHS, PRES LUNAM, SFR QUASAV, Angers, France.
| | - A Pivert
- Laboratoire de Virologie, CHU Angers, France; HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
| | - P Veillon
- Laboratoire de Virologie, CHU Angers, France; HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
| | - E Bouthry
- Laboratoire de Virologie, CHU Angers, France; HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - S Alain
- Laboratoire de Virologie, CHU Limoges, France.
| | - V Thibault
- Laboratoire de Virologie, CHU Pitié-Salpêtrière, Paris, France.
| | - F Abravanel
- Laboratoire de Virologie, CNR VHE, Inserm U1043, CHU Purpan, Toulouse, France.
| | - A R Rosenberg
- AP-HP, GHU Cochin, Laboratoire de Virologie, Université Paris Descartes, EA 4474 "Hepatitis C Virology", Paris, France.
| | - C Henquell
- Laboratoire de Virologie, CHU Clermont-Ferrand, France.
| | | | - O Petsaris
- Département de Bactériologie-Virologie-Hygiène Hospitalière et Parasitologie-Mycologie, CHRU, LUBEM, EA3882, Brest, France.
| | - S Vallet
- Département de Bactériologie-Virologie-Hygiène Hospitalière et Parasitologie-Mycologie, CHRU, LUBEM, EA3882, Brest, France.
| | - J B Bour
- Laboratoire de Virologie, CHU, Dijon, France.
| | - Y Baazia
- Laboratoire de Virologie, CHU Avicenne, Bobigny, France.
| | - P Trimoulet
- Laboratoire de Virologie, Hôpital Pellegrin Tripode, CHU Bordeaux, France.
| | - P André
- Laboratoire de Virologie, Centre de Biologie Nord, Hôpital de la Croix Rousse, Lyon, France.
| | - C Gaudy-Graffin
- Université François Rabelais, Inserm U966, CHU Tours, France.
| | - D Bettinger
- Laboratoire de Virologie, CHU Besançon, France.
| | - S Larrat
- Laboratoire de Virologie, UMI 3265 UJF-EMBL-CNRS, CHU, Unit of Virus Host Cell Interactions, Grenoble, France.
| | - A Signori-Schmuck
- Laboratoire de Virologie, UMI 3265 UJF-EMBL-CNRS, CHU, Unit of Virus Host Cell Interactions, Grenoble, France.
| | - H Saoudin
- Laboratoire de Bactériologie-Virologie, CHU Saint-Etienne, France.
| | - B Pozzetto
- Laboratoire de Bactériologie-Virologie, CHU Saint-Etienne, France.
| | - G Lagathu
- Laboratoire de Virologie, CHU Rennes, France.
| | | | - F Stoll-Keller
- Institut de Virologie, CHU Strasbourg, Inserm U748, Strasbourg, France.
| | - J M Pawlotsky
- Laboratoire de Virologie-Bactériologie, CHU Henri-Mondor, Créteil, France.
| | - J Izopet
- Laboratoire de Virologie, CNR VHE, Inserm U1043, CHU Purpan, Toulouse, France.
| | - C Payan
- Département de Bactériologie-Virologie-Hygiène Hospitalière et Parasitologie-Mycologie, CHRU, LUBEM, EA3882, Brest, France.
| | - F Lunel-Fabiani
- Laboratoire de Virologie, CHU Angers, France; HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
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Revie D, Alberti MO, Prichard JG, Kelley AS, Salahuddin SZ. Analysis of the 5'UTR of HCV genotype 3 grown in vitro in human B cells, T cells, and macrophages. Virol J 2010; 7:155. [PMID: 20626910 PMCID: PMC2913957 DOI: 10.1186/1743-422x-7-155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/13/2010] [Indexed: 12/13/2022] Open
Abstract
Background Previously, we have reported the isolation and molecular characterization of human Hepatitis C virus genotype 1 (HCV-1) from infected patients. We are now reporting an analysis of HCV obtained from patients infected with HCV genotype 3 (HCV-3) as diagnosed by clinical laboratories. Results HCV was cultured in vitro using our system. HCV RNA was isolated from patients' blood and from HCV cultured in various cell types for up to three months. The 5'UTR of these isolates were used for comparisons. Results revealed a number of sequence changes as compared to the serum RNA. The HCV RNA produced efficiently by infected macrophages, B-cells, and T-cells had sequences similar to HCV-1, which suggests that selection of the variants was performed at the level of macrophages. Virus with sequences similar to HCV-1 replicated better in macrophages than HCV having a 5'UTR similar to HCV-3. Conclusions Although HCV-3 replicates in cell types such as B-cells, T-cells, and macrophages, it may require a different primary cell type for the same purpose. Therefore, in our opinion, HCV-3 does not replicate efficiently in macrophages, and patients infected with HCV-3 may contain a population of HCV-1 in their blood.
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Affiliation(s)
- Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
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Internal initiation stimulates production of p8 minicore, a member of a newly discovered family of hepatitis C virus core protein isoforms. J Virol 2009; 83:3104-14. [PMID: 19129450 DOI: 10.1128/jvi.01679-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The hepatitis C virus (HCV) core gene is more conserved at the nucleic acid level than is necessary to preserve the sequence of the core protein, suggesting that it contains information for additional functions. We used a battery of anticore antibodies to test the hypothesis that the core gene directs the synthesis of core protein isoforms. Infectious viruses, replicons, and RNA transcripts expressed a p8 minicore containing the C-terminal portion of the p21 core protein and lacking the N-terminal portion. An interferon resistance mutation, U271A, which creates an AUG at codon 91, upregulated p8 expression in Con1 replicons, suggesting that p8 is produced by an internal initiation event and that 91-AUG is the preferred, but not the required, initiation codon. Synthesis of p8 was independent of p21, as shown by the abundant production of p8 from transcripts containing an UAG stop codon that blocked p21 production. Three infectious viruses, JFH-1 (2a core), J6/JFH (2a core), and H77/JFH (1a core), and a bicistronic construct, Bi-H77/JFH, all expressed both p8 and larger isoforms. The family of minicores ranges in size from 8 to 14 kDa. All lack the N-terminal portion of the p21 core. In conclusion, the core gene contains an internal signal that stimulates the initiation of protein synthesis at or near codon 91, leading to the production of p8. Infectious viruses of both genotype 1 and 2 HCV express a family of larger isoforms, in addition to p8. Minicores lack significant portions of the RNA binding domain of p21 core. Studies are under way to determine their functions.
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Gottwein JM, Bukh J. Cutting the gordian knot-development and biological relevance of hepatitis C virus cell culture systems. Adv Virus Res 2008; 71:51-133. [PMID: 18585527 DOI: 10.1016/s0065-3527(08)00002-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Worldwide approximately 180 million people are chronically infected with hepatitis C virus (HCV). HCV isolates exhibit extensive genetic heterogeneity and have been grouped in six genotypes and various subtypes. Additionally, several naturally occurring intergenotypic recombinants have been described. Research on the viral life cycle, efficient therapeutics, and a vaccine has been hampered by the absence of suitable cell culture systems. The first system permitting studies of the full viral life cycle was intrahepatic transfection of RNA transcripts of HCV consensus complementary DNA (cDNA) clones into chimpanzees. However, such full-length clones were not infectious in vitro. The development of the replicon system and HCV pseudo-particles allowed in vitro studies of certain aspects of the viral life cycle, RNA replication, and viral entry, respectively. Identification of the genotype 2 isolate JFH1, which for unknown reasons showed an exceptional replication capability and resulted in formation of infectious viral particles in the human hepatoma cell line Huh7, led in 2005 to the development of the first full viral life cycle in vitro systems. JFH1-based systems now enable in vitro studies of the function of viral proteins, their interaction with each other and host proteins, new antivirals, and neutralizing antibodies in the context of the full viral life cycle. However, several challenges remain, including development of cell culture systems for all major HCV genotypes and identification of other susceptible cell lines.
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Affiliation(s)
- Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
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8
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Salahuddin SZ, Snyder KA, Godwin A, Grewal R, Prichard JG, Kelley AS, Revie D. The simultaneous presence and expression of human hepatitis C virus (HCV), human herpesvirus-6 (HHV-6), and human immunodeficiency virus-1 (HIV-1) in a single human T-cell. Virol J 2007; 4:106. [PMID: 17958914 PMCID: PMC2170440 DOI: 10.1186/1743-422x-4-106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 10/24/2007] [Indexed: 02/08/2023] Open
Abstract
We have developed a system that isolates and replicates HCV in vitro. These isolates are called CIMM-HCV. This system has made it possible to analyze the biology, nature, and extent of HCV variability, among other things. Individuals that are infected with HIV-1 are often also infected with HCV and HHV-6. In addition to HCV, our lab has systems for replicating HIV-1 and HHV-6. We asked whether all these viruses could infect the same cells. We report here the successful infection of a T-cell (CEM) by CIMM-HCV, HHV-6, and HIV-1. PCR analyses demonstrated that the CEM cells were productively infected by HHV-6A. RT-PCR showed that the same cell culture was positive for HCV and HIV-1. Co-infection of a T-cell by all three viruses was confirmed by transmission electron microscopy (TEM). All these viruses are highly cytolytic; therefore, triply-infected cells were short lived. However, HIV-1 and HCV co-infected cells unexpectedly lasted for several weeks. Viral replication was unhindered and the phenomenon of 'dominance' was not observed in our experiments. In addition, CIMM-HCV was present in the perinuclear space, suggesting their possible synthesis in the nucleus. This report is based entirely on viruses produced in vitro in our laboratories. As part of the determinations of host ranges of these viruses, studies were designed to demonstrate the infection of a single cell by these viruses and to study the consequences of this phenomenon. All measurements were made on cultured cells and cell culture supernatants.
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Affiliation(s)
- S Zaki Salahuddin
- Department of Basic Research, California Institute of Molecular Medicine, Ventura, California, USA.
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9
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Torres-Puente M, Cuevas JM, Jiménez-Hernández N, Bracho MA, García-Robles I, Carnicer F, Del Olmo J, Ortega E, Moya A, González-Candelas F. Contribution of insertions and deletions to the variability of hepatitis C virus populations. J Gen Virol 2007; 88:2198-2203. [PMID: 17622623 DOI: 10.1099/vir.0.82855-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Little is known about the potential effects of insertions and deletions (indels) on the evolutionary dynamics of hepatitis C virus (HCV). In fact, the consequences of indels on antiviral treatment response are a field of investigation completely unexplored. Here, an extensive sequencing project was undertaken by cloning and sequencing serum samples from 25 patients infected with HCV subtype 1a and 48 patients with subtype 1b. For 23 patients, samples obtained after treatment with alpha interferon plus ribavirin were also available. Two genome fragments containing the hypervariable regions in the envelope 2 glycoprotein and the PKR-BD domain in NS5A were sequenced, yielding almost 16 000 sequences. Our results show that insertions are quite rare, but they are often present in biologically relevant domains of the HCV genome. Moreover, their frequency distributions between different time samples reflect the quasispecies dynamics of HCV populations. Deletions seem to be subject to negative selection.
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Affiliation(s)
- Manuela Torres-Puente
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
| | - José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
| | - Nuria Jiménez-Hernández
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
| | - María A Bracho
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
| | - Inmaculada García-Robles
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
| | | | - Juan Del Olmo
- Servicio de Hepatologia, Hospital Clínico de Valencia, Spain
| | - Enrique Ortega
- Unidad de Enfermedades Infecciosas, Hospital General de Valencia, Spain
| | - Andrés Moya
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
| | - Fernando González-Candelas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
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Revie D, Alberti MO, Braich RS, Chelyapov N, Bayles D, Prichard JG, Salahuddin SZ. Analysis of in vitro replicated human hepatitis C virus (HCV) for the determination of genotypes and quasispecies. Virol J 2006; 3:81. [PMID: 17010197 PMCID: PMC1609102 DOI: 10.1186/1743-422x-3-81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 09/29/2006] [Indexed: 12/13/2022] Open
Abstract
Isolation and self-replication of infectious HCV has been a difficult task. However, this is needed for the purposes of developing rational drugs and for the analysis of the natural virus. Our recent report of an in vitro system for the isolation of human HCV from infected patients and their replication in tissue culture addresses this challenge. At California Institute of Molecular Medicine several isolates of HCV, called CIMM-HCV, were grown for over three years in cell culture. This is a report of the analysis of CIMM-HCV isolates for subtypes and quasispecies using a 269 bp segment of the 5'UTR. HCV RNA from three patients and eleven CIMM-HCV were analyzed for this purpose. All isolates were essentially identical. Isolates of HCV from one patient were serially transmitted into fresh cells up to eight times and the progeny viruses from each transmission were compared to each other and also to the primary isolates from the patient's serum. Some isolates were also transmitted to different cell types, while others were cultured continuously without retransmission for over three years. We noted minor sequence changes when HCV was cultured for extended periods of time. HCV in T-cells and non-committed lymphoid cells showed a few differences when compared to isolates obtained from immortalized B-cells. These viruses maintained close similarity despite repeated transmissions and passage of time. There were no subtypes or quasispecies noted in CIMM-HCV.
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Affiliation(s)
- Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
| | - Michael O Alberti
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
| | - Ravi S Braich
- California Institute of Molecular Medicine, Ventura, California, USA
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Nickolas Chelyapov
- California Institute of Molecular Medicine, Ventura, California, USA
- University of Southern California, Los Angeles, California, USA
| | - David Bayles
- California Institute of Molecular Medicine, Ventura, California, USA
| | | | - S Zaki Salahuddin
- California Institute of Molecular Medicine, Ventura, California, USA
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