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Sulbarán MZ, Di Lello FA, Sulbarán Y, Cosson C, Loureiro CL, Rangel HR, Cantaloube JF, Campos RH, Moratorio G, Cristina J, Pujol FH. Genetic history of hepatitis C virus in Venezuela: high diversity and long time of evolution of HCV genotype 2. PLoS One 2010; 5:e14315. [PMID: 21179440 PMCID: PMC3001475 DOI: 10.1371/journal.pone.0014315] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/19/2010] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The subtype diversity of the hepatitis C virus (HCV) genotypes is unknown in Venezuela. METHODOLOGY/PRINCIPAL FINDINGS Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1) was the most common genotype (63%), composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%), being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA) of G2j around 1785, before the introduction of G1b (1869) and G1a (1922). While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period. CONCLUSIONS/SIGNIFICANCE Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies.
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Affiliation(s)
| | - Federico A. Di Lello
- Cátedra de Virología de la Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Yoneira Sulbarán
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Clarisa Cosson
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
| | | | - Héctor R. Rangel
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Jean F. Cantaloube
- Unité Emergence et Co-évolution virale, Etablissement Français du Sang Alpes-Méditerranée, Marseille, France
| | - Rodolfo H. Campos
- Cátedra de Virología de la Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gonzalo Moratorio
- Departamento de Técnicas Nucleares Aplicadas, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
- Unidad de Biofísica de Proteínas, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan Cristina
- Departamento de Técnicas Nucleares Aplicadas, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
| | - Flor H. Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
- * E-mail:
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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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Sexually transmitted hepatitis C virus superinfection in HIV/hepatitis C virus co-infected men who have sex with men. AIDS 2008; 22:658-61. [PMID: 18317011 DOI: 10.1097/qad.0b013e3282f4e86f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report two cases of sexually transmitted hepatitis C virus (HCV) superinfection in HIV/HCV-co-infected patients with high-risk sexual behaviour. The two patients had chronic HCV and a history of sexually transmitted infections. HCV superinfection was confirmed by phylogenetic analysis. No risk factors for HCV were found except unprotected anal sex with multiple casual male partners. HCV serology and serum HCV RNA should be examined periodically in HIV-infected men who have sex with men engaging in high-risk sexual behaviours.
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Abstract
We sought evidence of viral recombination in five recently hepatitis C virus (HCV) infected young injection drug users who became superinfected with a distinguishable strain of HCV. The entire open reading frame of plasma HCV genomes was reverse transcribed, polymerase chain reaction amplified in two fragments, and directly sequenced. In two cases of same subtype (1a > 1a) superinfections the initial and later strains were both sequenced and compared for evidence of recombination. In three cases of superinfection with strains of different genotype/subtype (3a > 1a, 1a > 3a, 1b > 1a), the later time point HCV genomes were sequenced and compared with representative genomes of the initial genotype/subtype. No evidence of intra- or inter-genotype/subtype recombination was detected using six different programs for detecting recombination. We conclude that the generation of viable recombinant HCV genomes able to dominate in the viral quasispecies is a rare event.
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Affiliation(s)
- F Bernardin
- Blood Systems Research Institute, San Francisco, CA, USA
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Di Liberto G, Roque-Afonso AM, Kara R, Ducoulombier D, Fallot G, Samuel D, Feray C. Clinical and therapeutic implications of hepatitis C virus compartmentalization. Gastroenterology 2006; 131:76-84. [PMID: 16831592 DOI: 10.1053/j.gastro.2006.04.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 04/07/2006] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Blood mononuclear cells (BMCs) frequently are infected by hepatitis C virus (HCV) variants that are not found in plasma. The influence of this compartmentalization on the natural and therapeutic outcome of hepatitis C is unknown. METHODS We studied 119 patients with previously untreated chronic HCV infection. Sixty-five of these patients started first-line treatment with pegylated interferon-alfa and ribavirin after enrollment in the study. The internal ribosomal entry site (IRES) of HCV RNA was amplified and compared between plasma and BMCs by means of single-strand conformational polymorphism (SSCP) analysis, line-probe assay, and cloning sequencing. RESULTS The IRES SSCP patterns differed between plasma and BMCs in 54 (48%) of 113 assessable patients. Twenty-seven (24%) of these patients were co-infected by 2 HCV types or subtypes, only 1 of which was detectable in BMCs (n = 25) or in plasma (n = 2). SSCP-defined compartmentalization was more frequent in former drug users than in others (35/56 [60%] vs 19/56 [34%]; P < .01), and less frequent in patients with genotype 1 HCV in plasma (26/73 [24%] vs 28/40 [65%]; P < .01). The only variables that were independently predictive of a sustained virologic response were SSCP-defined compartmentalization (25/31 vs 10/32; P = .0001) and genotype 2 or 3 infection of BMCs (22/31 vs 8/34; P = .002). CONCLUSIONS A significant proportion of patients with hepatitis C are co-infected by 2 or more HCV variants with distinct IRES sequences and distinct cellular tropism. This compartmentalization is a strong independent predictor of treatment efficacy.
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Affiliation(s)
- Gaëtana Di Liberto
- Institut National de la Santé et de la Recherche Médicale, INSERM, Centre de Recherche Biomedicale Beaujon-Bichat, Faculté de Médecine Xavier Bichat, Paris, France
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Schultz AK, Zhang M, Leitner T, Kuiken C, Korber B, Morgenstern B, Stanke M. A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics 2006; 7:265. [PMID: 16716226 PMCID: PMC1525204 DOI: 10.1186/1471-2105-7-265] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 05/22/2006] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events. RESULTS We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states corresponding to these different subtypes, depending on which subtype is locally most similar to a database sequence. Jumps between different subtypes are indicative of intersubtype recombinations. We applied our method to a large set of genome sequences from human immunodeficiency virus (HIV) and hepatitis C virus (HCV) as well as to simulated recombined genome sequences. CONCLUSION Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences.
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Affiliation(s)
- Anne-Kathrin Schultz
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Ming Zhang
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas Leitner
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Carla Kuiken
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Burkhard Morgenstern
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Mario Stanke
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
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Abstract
1. Liver grafts from hepatitis C virus (HCV)-infected deceased donors can be used safely in HCV-infected recipients. 2. Histological assessment of the graft before orthotopic liver transplantation (OLT) is advised. 3. Recipients of these grafts should give consent accordingly. 4. The course of HCV disease after OLT parallels that in patients who received noninfected organs.
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Affiliation(s)
- Juan I Arenas
- Department of Medicine, Mayo Clinic Scottsdale, AZ, USA
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Rodriguez-Luna H, Arenas J, Vargas HE. The use of virologically compromised organs in liver transplantation. Clin Liver Dis 2003; 7:573-84, vi. [PMID: 14509527 DOI: 10.1016/s1089-3261(03)00056-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The present organ donor crisis has led to accepted use of organs from donors infected with hepatitis C virus (HCV) and hepatitis B virus (HBV). Although capable of transmitting disease, these grafts offer opportunities to expand the donor pool for certain populations. Anti-HBc positive grafts can be used if care is taken to provide prophylaxis. Good quality grafts from HCV+ donors may be used in recipients who are themselves HCV+ with good outcomes.
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Affiliation(s)
- Hector Rodriguez-Luna
- Mayo Clinic Scottsdale, Mayo Clinic Hospital, 5777 E. Mayo Boulevard, Phoenix, AZ 85054, USA
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Laporte J, Bain C, Maurel P, Inchauspe G, Agut H, Cahour A. Differential distribution and internal translation efficiency of hepatitis C virus quasispecies present in dendritic and liver cells. Blood 2003; 101:52-7. [PMID: 12393733 DOI: 10.1182/blood-2002-03-0818] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) is predominantly a hepatotropic virus. Nonetheless, there is mounting evidence that hematopoietic cells may support HCV replication. The HCV 5' untranslated region (5'UTR), responsible for initiation of viral translation, via an internal ribosome entry site (IRES), has been previously described to contain specific nucleotide substitutions when cultured in infected lymphoid cells. Our purpose was to establish whether the 5'UTR polymorphism of quasispecies from 3 cell compartments (liver, peripheral blood mononuclear cells [PBMG], and monocyte-derived dendritic cells [DCs]) of a patient chronically infected with HCV1b affects the corresponding translational efficiencies and thus the capacity for replication. The 5'UTR polymorphism was characterized by identification of changes at 3 crucial sites as compared with the reference nucleotide (nt) sequence: a G insertion between positions 19 and 20, a C>A substitution at position 204 and a G>A substitution at position 243. The quasispecies detected in DCs was unique and differed from those present in the liver, suggesting a particular tropism of HCV quasispecies for DCs. Moreover, its translational activity was significantly impaired when compared with those from liver and PBMCs in different cell lines. This impairment was thoroughly confirmed in primary cultures of both human hepatocytes and monocyte-derived DCs. Taken together, our data lend support both to a specific location and impaired replication of HCV quasispecies in DCs, which could be related to viral persistence and perturbation of DC function in chronically infected patients.
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Affiliation(s)
- Julien Laporte
- Laboratoire de virologie, C.E.R.VI., UPRES EA 2387, Hôpital Pitié-Salpêtrière, Paris, France
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A Bobak D, Yadavalli G. Update on the Management of Hepatitis C in Liver Transplant Recipients. Curr Infect Dis Rep 2002; 4:105-111. [PMID: 11927040 DOI: 10.1007/s11908-002-0049-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hepatic failure due to hepatitis C is the leading indicator for orthotopic liver transplantation (OLT) in the United States. Unfortunately, recurrent hepatitis C virus infection is essentially universal following orthotopic liver transplantation. Although significant advances have been made in the past decade for the treatment of hepatitis C, a similar level of success has not yet been achieved for most hepatitis C virus-infected liver transplant recipients. In addition, deleterious side effects of the currently available antiviral agents continue to significantly hamper their use. Several recent reports, however, indicate that newer immunosuppressive regimens combined with novel modifications of existing treatment paradigms will likely lead to improved clinical outcomes for the hepatitis C virus-infected liver transplant recipient.
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Affiliation(s)
- David A Bobak
- Division of Infectious Diseases, University Hospitals of Cleveland/CWRU School of Medicine, 11100 Euclid Avenue, Cleveland, OH 44106, USA.
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