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Practices of Sequencing Quality Assurance. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Di Lello FA, Culasso ACA, Parodi C, Baré P, Campos RH, García G. New evidence of replication of hepatitis C virus in short-term peripheral blood mononuclear cell cultures. Virus Res 2014; 191:1-9. [PMID: 25087877 DOI: 10.1016/j.virusres.2014.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Even though hepatocytes are the main site for hepatitis C virus (HCV) replication, peripheral blood mononuclear cells (PBMC) have also been proposed as a suitable site for HCV replication. However, this issue still remains under discussion. We have previously developed an innovative system where HCV-RNA can be recovered during PBMC culture from HCV infected patients. Thus, the aim of this work was to use this novel approach in order to observe the evolution and replication of HCV genotype 1b in the PBMC of an HIV-HCV coinfected patient. METHODS HCV-RNA was extracted from serum, uncultured PBMC and PBMC culture at day 6, 20 and 33. The evolutionary analysis was performed using the direct sequences of three viral regions: 5'UTR, E2 and NS5A. Additionally, E2 region was cloned in order to extend the evolutive analysis. RESULTS In the present work, the molecular characterization of HCV along the culture showed a clear dynamic evolving process with the appearance of several nucleotide or amino acid changes in the three regions analyzed. Furthermore, the population analysis of E2 clones showed emerging and loss of lineages which indicate the fast evolutive dynamics of this system. CONCLUSIONS Since evolution can take place only if the virus is replicating in the culture, this finding constitutes an important evidence of viral replication in PBMC. Moreover, this extrahepatic compartment could be very important due to the presence of distinctive variants that could be responsible for resistance to treatment, viral pathogenesis and other clinical implications.
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Affiliation(s)
- Federico Alejandro Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | | | - Cecilia Parodi
- Instituto de Investigaciones Hematológicas "Mariano R. Castex", Instituto de Medicina Experimental (IMEx), Academia Nacional de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Patricia Baré
- Instituto de Investigaciones Hematológicas "Mariano R. Castex", Instituto de Medicina Experimental (IMEx), Academia Nacional de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriel García
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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Blackard JT, Ma G, Sengupta S, Martin CM, Powell EA, Shata MT, Sherman KE. Evidence of distinct populations of hepatitis C virus in the liver and plasma of patients co-infected with HIV and HCV. J Med Virol 2014; 86:1332-41. [PMID: 24788693 DOI: 10.1002/jmv.23968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2014] [Indexed: 12/15/2022]
Abstract
Viral diversity is an important predictor of hepatitis C virus (HCV) treatment response and may influence viral pathogenesis. HIV influences HCV variability in the plasma; however, limited data on viral variability are available from distinct tissue/cell compartments in patients co-infected with HIV and HCV. Thus, this exploratory study evaluated diversity of the hypervariable region 1 (HVR1) of HCV in the plasma and liver for 14 patients co-infected with HIV and HCV. Median intra-patient genetic distances and entropy values were similar in the plasma and liver compartments. Positive immune selection pressure was observed in the plasma for five individuals and in the liver for three individuals. Statistical evidence supporting viral compartmentalization was found in five individuals. Linear regression identified ALT (P = 0.0104) and AST (P = 0.0130) as predictors of viral compartmentalization. A total of 12 signature amino acids that distinguish liver from plasma E1/HVR1 were identified. One signature amino acid was shared by at least two individuals. These findings suggest that HCV compartmentalization is relatively common among patients co-infected with HIV and HCV. These data also imply that evaluating viral diversity, including drug resistance patterns, in the serum/plasma only may not adequately represent viruses replicating with in the liver and, thus, deserves careful consideration in future studies.
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Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
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Blackard JT, Ma G, Welge JA, Martin CM, Sherman KE, Taylor LE, Mayer KH, Jamieson DJ. Analysis of a non-structural gene reveals evidence of possible hepatitis C virus (HCV) compartmentalization. J Med Virol 2012; 84:242-52. [PMID: 22170544 DOI: 10.1002/jmv.22269] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viral diversity is a hallmark of hepatitis C virus (HCV) infection; however, only limited data are available regarding HCV variability in extrahepatic sites, and none have systematically compared diversity in non-structural and structural genomic regions. Therefore, HCV diversity in the NS5B and envelope 1 (E1) hypervariable region 1 (HVR1) genes was evaluated in matched sera and peripheral blood mononuclear cells (PBMCs) obtained from 13 HCV-infected women. Multiple clonal sequences were compared to evaluate quasispecies diversity and viral compartmentalization in PBMCs. Genetic distances were higher for E1/HVR1 compared to NS5B in both the sera and PBMCs (P = 0.0511 and 0.0284). Genetic distances were higher in serum NS5B compared to PBMC NS5B (P = 0.0003); however, they were not different when comparing E1/HVR1 in sera to PBMCs. By phylogenetic analysis of NS5B, evidence of possible PBMC compartmentalization was observed for one woman, while statistical methods were consistent with PBMC compartmentalization for six women. Evidence of compartmentalization within a non-structural genomic region may suggest that viral adaptation to a unique extracellular microenvironment(s) may be required for efficient replication and could contribute to HCV persistence.
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Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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Cassino L, Laufer N, Giuliano SF, Bouzas M, Quarleri J. Short Communication: Hepatitis B Virus Harboring Nucleotide Deletions in the Basal Core Promoter in HBe-Positive HIV-Coinfected Patients Under Lamivudine Therapy. AIDS Res Hum Retroviruses 2011; 27:543-5. [PMID: 20919924 DOI: 10.1089/aid.2010.0096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The presence of HBV genomes with deletions at the basal core promoter (BCP) is associated with more aggressive liver disease. This 3-year longitudinal analysis of two HIV-HBV-coinfected patients allowed identification of three deletions with dissimilar abundance and permanence into the HBV quasispecies composition. These deletions may contribute to HBV pathogenesis in HIV-coinfected individuals.
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Affiliation(s)
- L. Cassino
- Centro Nacional de Referencia para el SIDA, Dto. Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - N. Laufer
- Centro Nacional de Referencia para el SIDA, Dto. Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Unidad de Enfermedades Infecciosas, Hospital Fernández, Buenos Aires, Argentina
| | - S. Fernández Giuliano
- Unidad de Virología, Hospital de Enfermedades Infecciosas “F.J. Muñiz,” Buenos Aires, Argentina
| | - M.B. Bouzas
- Unidad de Virología, Hospital de Enfermedades Infecciosas “F.J. Muñiz,” Buenos Aires, Argentina
| | - J. Quarleri
- Centro Nacional de Referencia para el SIDA, Dto. Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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Variability of the polymerase gene (NS5B) in hepatitis C virus-infected women. J Clin Microbiol 2010; 48:4256-9. [PMID: 20810773 DOI: 10.1128/jcm.01613-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
There are limited data on diversity within the hepatitis C virus polymerase (NS5B). In concordance with its key functional role during the life cycle, NS5B intrapatient variability was low. Moreover, differences between NS5B nonsynonymous (dN) and synonymous (dS) mutation rates (dN - dS) were positively correlated with CD4 cell count, while nonsynonymous mutations were strongly correlated with reduced replication in vivo.
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7
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Martin CM, Welge JA, Shire NJ, Rouster SD, Shata MT, Sherman KE, Blackard JT. Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals. J Viral Hepat 2010; 17:588-97. [PMID: 19889143 PMCID: PMC3032083 DOI: 10.1111/j.1365-2893.2009.01214.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Occult hepatitis B virus (O-HBV) infection is characterized by the presence of HBV DNA without detectable hepatitis B surface antigen (HBV DNA+/HBsAg-) in the serum. Although O-HBV is more prevalent during HBV/HIV co-infection, analysis of HBV mutations in co-infected patients is limited. In this preliminary study, HBV PreSurface (PreS) and surface (S) regions were amplified from 33 HIV-positive patient serum samples - 27 chronic HBV (C-HBV) and six O-HBV infections. HBV genotype was determined by phylogenetic analysis, while quasispecies diversity was quantified for the PreS, S and overlapping polymerase regions. C-HBV infections harboured genotypes A, D and G, compared to A, E, G and one mixed A/G infection for O-HBV. Interestingly, nonsynonymous-synonymous mutation values indicated positive immune selection in three regions for O-HBV vs one for C-HBV. Sequence analysis further identified new O-HBV mutations, in addition to several previously reported mutations within the HBsAg antigenic determinant. Several of these O-HBV mutations likely contribute to the lack of detectable HBsAg in O-HBV infection by interfering with detection in serologic assays, altering antigen secretion and/or decreasing replicative fitness.
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Affiliation(s)
- C. M. Martin
- Department of Internal Medicine, Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - J. A. Welge
- Departments of Psychiatry and Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - N. J. Shire
- Department of Internal Medicine, Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - S. D. Rouster
- Department of Internal Medicine, Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - M. T. Shata
- Department of Internal Medicine, Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - K. E. Sherman
- Department of Internal Medicine, Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - J. T. Blackard
- Department of Internal Medicine, Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Fan X, Mao Q, Zhou D, Lu Y, Xing J, Xu Y, Ray SC, Di Bisceglie AM. High diversity of hepatitis C viral quasispecies is associated with early virological response in patients undergoing antiviral therapy. Hepatology 2009; 50:1765-72. [PMID: 19937690 PMCID: PMC2911951 DOI: 10.1002/hep.23290] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
UNLABELLED Differential response patterns to optimal antiviral therapy, peginterferon alpha plus ribavirin, are well documented in patients with chronic hepatitis C virus (HCV) infection. Among many factors that may affect therapeutic efficiency, HCV quasispecies (QS) characteristics have been a major focus of previous studies, yielding conflicting results. To obtain a comprehensive understanding of the role of HCV QS in antiviral therapy, we performed the largest-ever HCV QS analysis in 153 patients infected with HCV genotype 1 strains. A total of 4,314 viral clones spanning hypervarible region 1 were produced from these patients during the first 12 weeks of therapy, followed by detailed genetic analyses. Our data show an exponential distribution pattern of intrapatient QS diversity in this study population in which most patients (63%) had small QS diversity with genetic distance (d) less than 0.2. The group of patients with genetic distance located in the decay region (d>0.53) had a significantly higher early virologic response (EVR) rate (89.5%), which contributed substantially to the overall association between EVR and increased baseline QS diversity. In addition, EVR was linked to a clustered evolutionary pattern in terms of QS dynamic changes. CONCLUSION EVR is associated with elevated HCV QS diversity and complexity, especially in patients with significantly higher HCV genetic heterogeneity.
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Affiliation(s)
- Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, Saint Louis, MO
- Saint Louis University Liver Center, Saint Louis University School of Medicine, Saint Louis, MO
| | - Qing Mao
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Donghui Zhou
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, Saint Louis, MO
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Lu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, Saint Louis, MO
| | - Jianwei Xing
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, Saint Louis, MO
| | - Yanjuan Xu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, Saint Louis, MO
| | - Stuart C. Ray
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Adrian M. Di Bisceglie
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, Saint Louis, MO
- Saint Louis University Liver Center, Saint Louis University School of Medicine, Saint Louis, MO
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Cassino L, Laufer N, Salomon H, Campos R, Quarleri J. Hepatitis B precore/core promoter mutations in isolates from HBV-monoinfected and HBV-HIV coinfected patients: a 3-yr prospective study. J Clin Virol 2009; 46:354-9. [PMID: 19800842 DOI: 10.1016/j.jcv.2009.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 09/09/2009] [Indexed: 01/12/2023]
Abstract
BACKGROUND The course of chronic HBV infection is modified by HIV-coexistence. OBJECTIVE To analyze the role of HBV genomic heterogeneity in basal core promoter (BCP) and precore (Pc) genomic regions. STUDY DESIGN In a 3-yr prospective study, 39 HBV infected patients (20 monoinfected and 19 HIV-coinfected) were included. Eighty-two HBV isolates were studied at quasispecies level in the BCP/Pc genomic region. Clinical records obtained include data on lamivudine therapy and resistance mutations, HBV and HIV-viral load. RESULTS HBV isolates were predominantly ascribed to genotype (Gt) A2 among HBV-monoinfected and HIV-coinfected patients. BCP mutations in isolates from monoinfected patients were significantly more frequent than in those from coinfected ones, irrespective of the HBe expression pattern (p<0.0001). Regardless of the HIV-coexistence, the Pc mutation at G1896A only barely appeared among clone-derived sequences of GtF1 isolates, mainly from HBe(-) HBV-monoinfected patients. CONCLUSIONS HBV isolates characterized from HIV-coinfected patients seem to be more prone to exhibit a wild type genomic pattern at BCP regulatory region with respect to those from HBV-monoinfected ones. Besides, mutations at Pc region might be genotype-dependent in their frequency but not on HIV co-presence related.
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Affiliation(s)
- Lucila Cassino
- Centro Nacional de Referencia para el SIDA, Dto. Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Argentina
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10
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Comparative analysis of nearly full-length hepatitis C virus quasispecies from patients experiencing viral breakthrough during antiviral therapy: clustered mutations in three functional genes, E2, NS2, and NS5a. J Virol 2008; 82:9417-24. [PMID: 18667493 DOI: 10.1128/jvi.00896-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral breakthrough is a recognized response pattern to interferon-based antiviral therapy in patients with chronic hepatitis C virus (HCV) infection. The emergence of drug-resistant HCV quasispecies variants is assumed to be a major mechanism responsible for viral breakthrough. By using a long reverse transcription-PCR protocol recently developed in our lab, multiple nearly full-length HCV quasispecies variants were generated from 9.1-kb amplicons at both the baseline and breakthrough points in two patients experiencing viral breakthrough. Comparative analyses of consensus dominant quasispecies variants revealed that most mutations, occurring at the time of breakthrough, involved three functional viral genes, E2, NS2, and NS5a. Interestingly, similar mutation patterns were also observed in minor quasispecies variants at baseline. These three genes had the highest values of average amino acid complexity at the HCV 1a population level. No single amino acids were identified to be associated with viral breakthrough. Taken together, at the near-full-length HCV genome level, our data suggested that viral breakthrough might be attributed to the selection of minor quasispecies variants at the baseline with or without additional mutations during antiviral therapy. Furthermore, the pattern for mutation clustering indicated potential mutation linkage among E2, NS2, and NS5a due to structural or functional relatedness in HCV replication.
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Scottà C, Garbuglia AR, Ruggeri L, Spada E, Laurenti L, Perrone MP, Girelli G, Mele A, Capobianchi MR, Folgori A, Nicosia A, Del Porto P, Piccolella E. Influence of specific CD4+ T cells and antibodies on evolution of hypervariable region 1 during acute HCV infection. J Hepatol 2008; 48:216-28. [PMID: 18180071 DOI: 10.1016/j.jhep.2007.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 09/24/2007] [Accepted: 09/25/2007] [Indexed: 01/29/2023]
Abstract
BACKGROUND/AIMS Several studies suggest that the evolutionary rate of HVR1 sequence in acute HCV hepatitis derives from the action of a continuous immune-driven positive selection. However, these studies have not been performed examining the relationship between HVR1 evolution and the development of specific immunity to autologous HVR1 sequences. METHODS We performed a longitudinal analysis of HVR1 sequences and specific antibodies and CD4+ T cells in ten HCV acutely infected patients with different clinical outcomes (recovery versus persistence). RESULTS We showed that although both recovered and chronically evolving individuals developed IFN-gamma+ T cells specific for Core and NS sequences, HVR1-specific CD4+ T cells were detected only in patients clearing the virus. On the contrary, all patients displayed anti-HVR1 antibodies that recognized sequences exclusively carried by autologous viruses. Measurements of genetic diversity and the number of non-synonymous per synonymous substitutions within HVR1 sequences before and after antibody appearance showed an increase of these parameters only in concomitance with the appearance of anti-HVR1 antibodies. CONCLUSIONS The evidence that anti-HVR1 antibodies favor HVR1 variant selection suggests that viral complexity in chronically infected patients could represent a virus adaptive strategy to escape the continuous selective process mediated by anti-HVR1 antibodies.
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Affiliation(s)
- Cristiano Scottà
- Department of Cellular and Developmental Biology,"La Sapienza" University of Rome, Italy
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Blackard JT, Hiasa Y, Smeaton L, Jamieson DJ, Rodriguez I, Mayer KH, Chung RT. Compartmentalization of hepatitis C virus (HCV) during HCV/HIV coinfection. J Infect Dis 2007; 195:1765-73. [PMID: 17492592 PMCID: PMC3210030 DOI: 10.1086/518251] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 01/04/2007] [Indexed: 12/17/2022] Open
Abstract
Extrahepatic replication has important implications for the transmission and treatment of hepatitis C virus (HCV). We analyzed longitudinal HCV diversity in peripheral-blood mononuclear cells (PBMCs) and serum during HCV monoinfection and HCV/HIV coinfection to determine whether distinct amino acid signatures characterized HCV replicating within PBMCs. Analysis of E1-HVR1 sequences demonstrated higher serum genetic distances among HCV/human immunodeficiency virus (HIV)-coinfected persons. Moreover, consensus PBMC sequences were rarely identical to those in the corresponding serum, suggesting divergence in these 2 compartments. Three of 5 HCV/HIV-coinfected participants showed evidence of HCV compartmentalization in PBMCs. Additionally, signature sequence analysis identified PBMC-specific amino acids in all HCV/HIV-coinfected persons. To our knowledge, this is the first study to identify specific amino acids that may distinguish HCV variants replicating in PBMCs. It is provocative to speculate that extrahepatic HCV diversity may be an important determinant of treatment response and thus warrants additional study, particularly during HCV/HIV coinfection.
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Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH 45267, and Gastrointestinal Unit, Massachusetts General Hospital, Boston, USA.
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Hraber PT, Fischer W, Bruno WJ, Leitner T, Kuiken C. Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes. Virol J 2006; 3:103. [PMID: 17169155 PMCID: PMC1764733 DOI: 10.1186/1743-422x-3-103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 12/14/2006] [Indexed: 01/06/2023] Open
Abstract
Background The duration of treatment for HCV infection is partly indicated by the genotype of the virus. For studies of disease transmission, vaccine design, and surveillance for novel variants, subtype-level classification is also needed. This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions. Results Different regions of the HCV genome yield inconsistent phylogenies, which can lead to erroneous conclusions about classification of a given infection. In particular, the highly conserved 5' untranslated region (UTR) yields phylogenetic trees with topologies that differ from the HCV polyprotein and complete genome phylogenies. Phylogenetic trees from the NS5B gene reliably cluster related subtypes, and yield topologies consistent with those of the whole genome and polyprotein. Conclusion These results extend those from previous studies and indicate that, unlike the NS5B gene, the 5' UTR contains insufficient variation to resolve HCV classifications to the level of viral subtype, and fails to distinguish genotypes reliably. Use of the 5' UTR for clinical tests to characterize HCV infection should be replaced by a subtype-informative test.
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Affiliation(s)
- Peter T Hraber
- Theoretical Biology and Biophysics, T-10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545 USA
| | - William Fischer
- Theoretical Biology and Biophysics, T-10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545 USA
| | - William J Bruno
- Theoretical Biology and Biophysics, T-10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545 USA
| | - Thomas Leitner
- Theoretical Biology and Biophysics, T-10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545 USA
| | - Carla Kuiken
- Theoretical Biology and Biophysics, T-10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545 USA
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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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15
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Gao G, Stuver SO, Okayama A, Tsubouchi H, Mueller NE, Tabor E. The minimum number of clones necessary to sequence in order to obtain the maximum information about hepatitis C virus quasispecies: a comparison of subjects with and without liver cancer. J Viral Hepat 2005; 12:46-50. [PMID: 15655047 DOI: 10.1111/j.1365-2893.2005.00546.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Most studies of hepatitis C virus (HCV) quasispecies have reported the results of sequencing only three to five clones per sample. The possibility that sequencing so few clones might not provide a representative picture of the quasispecies present in a sample has never been evaluated. The present study was conducted to evaluate whether sequencing greater numbers of clones results in better information about the HCV quasispecies number and distribution, and to compare the HCV quasispecies in liver cancer cases and controls. RNA was extracted from serial serum samples from six subjects with HCV-associated liver cancer and 11 age- and sex-matched HCV-infected controls without liver cancer. The hypervariable region 1 (HVR1) of the HCV genome was amplified, cloned, and sequenced. For further studies of 12 serum samples from two liver cancer cases and two matched controls, successive groups of 10 additional clones were sequenced up to a total of 50 clones per serum sample. When only 10 clones were sequenced from each specimen, no consistent differences were seen between the number of HCV quasispecies in the six liver cancer cases and the 11 controls. However, sequencing 40 clones from each of 12 samples from two liver cancer cases and two controls revealed a greater number of quasispecies in liver cancer cases than in controls. Testing an additional 10 clones (50 clones per sample) did not significantly increase the number of quasispecies detected.
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Affiliation(s)
- G Gao
- Division of Emerging and Transfusion Transmitted Diseases, Food and Drug Administration, Bethesda, MD, USA
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Bracho MA, García-Robles I, Jiménez N, Torres-Puente M, Moya A, González-Candelas F. Effect of oligonucleotide primers in determining viral variability within hosts. Virol J 2004; 1:13. [PMID: 15588294 PMCID: PMC543450 DOI: 10.1186/1743-422x-1-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Accepted: 12/09/2004] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR) based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. RESULTS To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV) populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient). Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. CONCLUSIONS Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.
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Affiliation(s)
- Maria Alma Bracho
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon "La Coma" s/n, Paterna (València) 46980 SPAIN
| | - Inmaculada García-Robles
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon "La Coma" s/n, Paterna (València) 46980 SPAIN
| | - Nuria Jiménez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon "La Coma" s/n, Paterna (València) 46980 SPAIN
| | - Manuela Torres-Puente
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon "La Coma" s/n, Paterna (València) 46980 SPAIN
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon "La Coma" s/n, Paterna (València) 46980 SPAIN
| | - Fernando González-Candelas
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon "La Coma" s/n, Paterna (València) 46980 SPAIN
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