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Schvoerer E, Moenne-Loccoz R, Murray JM, Velay A, Turek M, Fofana I, Fafi-Kremer S, Erba AC, Habersetzer F, Doffoël M, Gut JP, Donlin MJ, Tavis JE, Zeisel MB, Stoll-Keller F, Baumert TF. Hepatitis C virus envelope glycoprotein signatures are associated with treatment failure and modulation of viral entry and neutralization. J Infect Dis 2013; 207:1306-15. [PMID: 23335805 DOI: 10.1093/infdis/jit032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND A major challenge for antiviral treatment of hepatitis C virus (HCV) infection is viral resistance, potentially resulting from the high variability of HCV envelope glycoproteins and subsequent selection of strains with enhanced infectivity and/or immune escape. METHODS We used a bioinformatics and functional approach to investigate whether E1/E2 envelope glycoprotein structure and function were associated with treatment failure in 92 patients infected with HCV genotype 1. RESULTS Bioinformatics analysis identified 1 sustain virological response (R)-related residue in E1 (219T) and 2 non-SVR (NR)-related molecular signatures in E2 (431A and 642V) in HCV genotype 1a. Two of these positions also appeared in minimal networks separating NR patients from R patients. HCV pseudoparticles (HCVpp) expressing 431A and 642V resulted in a decrease in antibody-mediated neutralization by pretreatment sera. 431A/HCVpp entry into Huh7.5 cells increased with overexpression of CD81 and SR-BI. Moreover, an association of envelope glycoprotein signatures with treatment failure was confirmed in an independent cohort (Virahep-C). CONCLUSIONS Combined in silico and functional analyses demonstrate that envelope glycoprotein signatures associated with treatment failure result in an alteration of host cell entry factor use and escape from neutralizing antibodies, suggesting that virus-host interactions during viral entry contribute to treatment failure.
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Butt S, Idrees M, Rehman IU, Ali L, Hussain A, Ali M, Ahmed N, Saleem S, Fayyaz M. Establishment of stable Huh-7 cell lines expressing various hepatitis C virus genotype 3a protein: an in-vitro testing system for novel anti-HCV drugs. GENETIC VACCINES AND THERAPY 2011; 9:12. [PMID: 21711509 PMCID: PMC3164222 DOI: 10.1186/1479-0556-9-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/28/2011] [Indexed: 02/08/2023]
Abstract
Background Hepatitis C virus (HCV) infection is the leading cause of chronic hepatitis which progresses to hepatocellular carcinoma (HCC) afflicting > 170 million people worldwide. HCV 3a is the most common genotype (about 70% of all genotypes) circulating in Pakistan. Expression of HCV individual gene of 3a would facilitate therapeutic and vaccines strategies against chronic HCV and liver Cirrhosis. The aim of the present study was the establishment of stable Huh-7 cell lines expressing structural and non structural proteins of HCV Genotype 3a Pakistani isolate obtained from chronic HCV patients. Methods Blood samples were obtained from chronic HCV-3a positive patients. HCV individual genes were amplified using PCR with gene specific primers having restriction sites. These gene amplicons were cloned in mammalian expression vector PcDNA3.1+. Huh-7 cell lines were transfected with these constructed plasmids having structural or non-structural HCV genes in confluent cells with lipofectamine. Positive clones were selected with G418 and then confirmed by genome PCR. Subsequently, transcription and expression of the integrated genes were demonstrated by RT-PCR, sequencing and Western blot analysis. Results We successfully cloned and express five HCV-3a genes in PcDNA3.1+ mammalian expression vector. Results of western blot and sequencing PCR confirmed the stable expression of these five genes. Conclusion The stable cell-lines expressing HCV-3a individual genes would be a useful tool to investigate the role of various HCV proteins on HCV disease outcome and testing of new therapeutic strategies against HCV.
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Affiliation(s)
- Sadia Butt
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Irshad-Ur Rehman
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Liaqat Ali
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Abrar Hussain
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ali
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Naveed Ahmed
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Sana Saleem
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
| | - Madiha Fayyaz
- Molecular Virology Laboratory, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road ,Thokar Niaz Baig, Lahore-53700, University of the Punjab, Lahore, Pakistan
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Fan X, Xu Y, Di Bisceglie AM. Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun 2006; 346:1163-72. [PMID: 16793008 PMCID: PMC7092855 DOI: 10.1016/j.bbrc.2006.06.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 06/02/2006] [Indexed: 11/27/2022]
Abstract
Long RT-PCR (LRP) amplification of RNA templates is sometimes difficult compared to long PCR of DNA templates. Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. The only source for viral genome amplification is clinical samples in which HCV is usually present at low titers. We have created a comprehensive optimization protocol that allows robust amplification of a 9.1 kb fragment of HCV, followed by efficient cloning into a novel vector. Detailed analyses indicate the lack of potential LRP-mediated recombination and the preservation of viral diversity. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics.
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Affiliation(s)
- Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Saint Louis University Liver Center, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63110, USA.
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Chinchai T, Noppornpanth S, Bedi K, Theamboonlers A, Poovorawan Y. 222 base pairs in NS5B region and the determination of hepatitis C virus genotype 6. Intervirology 2006; 49:224-9. [PMID: 16491017 DOI: 10.1159/000091469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 08/17/2005] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE The present study was performed to genotype hepatitis C virus (HCV) by direct sequencing of a 222-bp nucleotide in the NS5B region and comparing the results with those of direct sequencing in the core region. We investigated a new region for HCV genotyping which gave the best performance to discriminate HCV genotype 6a, the unique genotype found in Southeast Asia. METHODS Plasma samples taken from 57 HCV-infected blood donors were used in this study. RT-PCR products were amplified using primers located in the NS5B region. The 222-bp PCR products were purified and sequenced. The genotype of HCV isolates were obtained by phylogenetic analysis and compared with HCV reference strains stored in the GenBank database. The HCV sequences clustering in the same node were considered to be of the same genotype. RESULTS Thirty-one, 22 and 4 samples of HCV genotype 3a, 1a and 1b, respectively, were analyzed by this method. Upon comparison with genotyping in the core region, 86 and 14% of the samples yielded concordant and discordant genotype results, respectively. The majority of discordant results (63%; 5 of 8) was observed with HCV genotype 6a which yielded 6a upon core sequencing as opposed to 1a or 3a upon NS5B sequencing. CONCLUSION HCV genotype 6a obtained by direct sequencing in the core region could not be unequivocally arrived at by sequencing 222 bp in the NS5B region. Hence, sequencing in the core region is preferable for genotyping our specimens, even though longer PCR products are required as this method enables discrimination between genotype 6a and the remaining genotypes.
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Affiliation(s)
- Teeraporn Chinchai
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
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