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Rzymski P, Jibril AT, Rahmah L, Abarikwu SO, Hashem F, Lawati AA, Morrison FMM, Marquez LP, Mohamed K, Khan A, Mushtaq S, Minakova K, Poniedziałek B, Zarębska-Michaluk D, Flisiak R. Is there still hope for the prophylactic hepatitis C vaccine? A review of different approaches. J Med Virol 2024; 96:e29900. [PMID: 39234788 DOI: 10.1002/jmv.29900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/17/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024]
Abstract
Despite remarkable progress in the treatment of hepatitis C virus (HCV) infection, it remains a significant global health burden, necessitating the development of an effective prophylactic vaccine. This review paper presents the current landscape of HCV vaccine candidates and approaches, including more traditional, based on inactivated virus, and more modern, such as subunit protein, vectored, based on nucleic acids (DNA and mRNA) and virus-like particles. The concept of the HCV vaccine is first put in the context of viral genetic diversity and adaptive responses to HCV infection, an understanding of which is crucial in guiding the development of an effective vaccine against such a complex virus. Because ethical dimensions are also significant in vaccine research, development, and potential deployment, we also address them in this paper. The road to a safe and effective vaccine to prevent HCV infection remains bumpy due to the genetic variation of HCV and its ability to evade immune responses. The progress in cell-culture systems allowed for the production of an inactivated HCV vaccine candidate, which can induce cross-neutralizing antibodies in vitro, but whether this could prevent infection in humans is unknown. Subunit protein vaccine candidates that entered clinical trials elicited HCV-specific humoral and cellular responses, though it remains to be shown whether they translate into effective prevention of HCV infection or progression of infection to a chronic state. Such responses were also induced by a clinically tested vector-based vaccine candidate, which decreased the viral HCV load but did not prevent chronic HCV infection. These disappointments were not readily predicted from preclinical animal studies. The vaccine platforms employing virus-like particles, DNA, and mRNA provide opportunities for the HCV vaccine, but their potential in this context has yet to be shown. Ensuring the designed vaccine is based on conserved epitope(s) and elicits broadly neutralizing immune responses is also essential. Given failures in developing a prophylactic HCV vaccine, it is crucial to continue supporting national strategies, including funding for screening and treatment programs. However, these actions are likely insufficient to permanently control the HCV burden, encouraging further mobilization of significant resources for HCV vaccine research as a missing element in the elimination of viral hepatitis as a global public health.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland
- Universal Scientific Education and Research Network (USERN)
| | - Aliyu Tijani Jibril
- Universal Scientific Education and Research Network (USERN)
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Laila Rahmah
- Universal Scientific Education and Research Network (USERN)
- Faculty of Medicine, Universitas Muhammadiyah Surabaya, Surabaya, Indonesia
- Department of Digital Health, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sunny O Abarikwu
- Universal Scientific Education and Research Network (USERN)
- Department of Biochemistry, University of Port Harcourt, Choba, PMB, Port Harcourt, Rivers State, Nigeria
| | - Fareeda Hashem
- Universal Scientific Education and Research Network (USERN)
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdullah Al Lawati
- Universal Scientific Education and Research Network (USERN)
- Sultan Qaboos University Hospital, Al Khoud, Muscat, Oman
| | | | - Leander Penaso Marquez
- Universal Scientific Education and Research Network (USERN)
- University of the Philippines Diliman, Quezon City, Philippines
| | - Kawthar Mohamed
- Universal Scientific Education and Research Network (USERN)
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amjad Khan
- Universal Scientific Education and Research Network (USERN)
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saima Mushtaq
- Universal Scientific Education and Research Network (USERN)
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Kseniia Minakova
- Universal Scientific Education and Research Network (USERN)
- Micro- and Nanoelectronics Department, National Technical University "Kharkiv Polytechnic Institute", Kharkiv, Ukraine
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland
| | | | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, Białystok, Poland
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Tamura T, Yamamoto H, Ogino S, Morioka Y, Tsujino S, Suzuki R, Hiono T, Suzuki S, Isoda N, Sakoda Y, Fukuhara T. A rapid and versatile reverse genetics approach for generating recombinant positive-strand RNA viruses that use IRES-mediated translation. J Virol 2024; 98:e0163823. [PMID: 38353536 PMCID: PMC10949505 DOI: 10.1128/jvi.01638-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/24/2024] [Indexed: 03/20/2024] Open
Abstract
Reverse genetics systems have played a central role in developing recombinant viruses for a wide spectrum of virus research. The circular polymerase extension reaction (CPER) method has been applied to studying positive-strand RNA viruses, allowing researchers to bypass molecular cloning of viral cDNA clones and thus leading to the rapid generation of recombinant viruses. However, thus far, the CPER protocol has only been established using cap-dependent RNA viruses. Here, we demonstrate that a modified version of the CPER method can be successfully applied to positive-strand RNA viruses that use cap-independent, internal ribosomal entry site (IRES)-mediated translation. As a proof-of-concept, we employed mammalian viruses with different types (classes I, II, and III) of IRES to optimize the CPER method. Using the hepatitis C virus (HCV, class III), we found that inclusion in the CPER assembly of an RNA polymerase I promoter and terminator, instead of those from polymerase II, allowed greater viral production. This approach was also successful in generating recombinant bovine viral diarrhea virus (class III) following transfection of MDBK/293T co-cultures to overcome low transfection efficiency. In addition, we successfully generated the recombinant viruses from clinical specimens. Our modified CPER could be used for producing hepatitis A virus (HAV, type I) as well as de novo generation of encephalomyocarditis virus (type II). Finally, we generated recombinant HCV and HAV reporter viruses that exhibited replication comparable to that of the wild-type parental viruses. The recombinant HAV reporter virus helped evaluate antivirals. Taking the findings together, this study offers methodological advances in virology. IMPORTANCE The lack of versatility of reverse genetics systems remains a bottleneck in viral research. Especially when (re-)emerging viruses reach pandemic levels, rapid characterization and establishment of effective countermeasures using recombinant viruses are beneficial in disease control. Indeed, numerous studies have attempted to establish and improve the methods. The circular polymerase extension reaction (CPER) method has overcome major obstacles in generating recombinant viruses. However, this method has not yet been examined for positive-strand RNA viruses that use cap-independent, internal ribosome entry site-mediated translation. Here, we engineered a suitable gene cassette to expand the CPER method for all positive-strand RNA viruses. Furthermore, we overcame the difficulty of generating recombinant viruses because of low transfection efficiency. Using this modified method, we also successfully generated reporter viruses and recombinant viruses from a field sample without virus isolation. Taking these findings together, our adapted methodology is an innovative technology that could help advance virologic research.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Hirotaka Yamamoto
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Saho Ogino
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Takahiro Hiono
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Norikazu Isoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
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AbdElrahman M, Ibrahim MK, Tawfik S, Omran D, Bendary MM, Hassanin SO, Elbatae H. The relation between SNPs in the NME1 gene and response to sofosbuvir in Egyptian patients with chronic HCV. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2023. [DOI: 10.1186/s43088-022-00337-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Abstract
Background
Hepatitis C virus (HCV) infection is considered one of the most urgent health problems in the world, with an incidence of approximately 71 million patients and 399,000 deaths per year from related liver diseases. In this study, we examined the association between 2 single nucleotide polymorphisms (SNPs) in the nucleoside diphosphate kinase 1 (NME1) gene (encoding one of the sofosbuvir metabolizing enzymes) and the response to the sofosbuvir plus daclatasvir regimen in Egyptian HCV-infected patients.
Results
Our data showed a similarity in the distribution of the CC, CT, and TT genotypes of NME1 rs2302254 C/T (p = 0.847) and the CC, TC, and TT genotypes of NME1 rs16949649 T/C (p = 0.937) among patients who were either treatment responders or relapsers. Based on the univariate and multivariate logistic regression analyses of the significant predictors for sustained virological response (SVR), five factors showed a robust predictive potency for the treatment outcome: age, fasting blood glucose level, platelets, albumin, and alpha-fetoprotein. Strikingly, there was a significant correlation between the rs16949649T/C polymorphism and serum creatinine (p = 0.023). Higher creatinine levels were observed among the CC carriers than the TC or TT carriers.
Conclusions
The 2 studied SNPs of NME1 had no significant association with SVR in Egyptian HCV-infected patients; however, the noticeable relation between rs16949649T/C and creatinine level might represent a foundation for future studies on the renal extra-hepatic manifestation of HCV and SNPs of NME1 gene.
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Hazra M, Dubey RC. Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV. J Biomol Struct Dyn 2022:1-20. [PMID: 35993498 DOI: 10.1080/07391102.2022.2113823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.
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Affiliation(s)
- Mousumi Hazra
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
| | - Ramesh Chandra Dubey
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
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Valutite D, Ostankova Y, Semenov A, Lyalina L, Totolian A. Distribution of Primary Resistance Mutations in Saint Petersburg in Patients with Chronic Hepatitis C. Diagnostics (Basel) 2022; 12:diagnostics12051054. [PMID: 35626210 PMCID: PMC9139387 DOI: 10.3390/diagnostics12051054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/17/2022] Open
Abstract
The advent of direct-acting antiviral drugs (DAAs) was a breakthrough in the treatment of patients with chronic hepatitis C, yet high viral replication errors can lead to the development of resistance associated variants (RAVs). Thus, assessment of RAV in infected patients is necessary to monitor treatment effectiveness. The aim of our study was to investigate the presence of primary resistance mutations in the NS3 and NS5 regions of HCV in treatment-naive patients. Samples were taken from 42 patients with HCV who had not previously received DAA treatment. In the present study, we used the method for determining drug resistance mutations based on direct sequencing of the NS3, NS5A, and NS5B genes developed by the Saint Petersburg Pasteur Institute. Primary mutations associated with resistance were detected in 5 patients (12%). According to the Geno2pheno [hcv] 0.92 database, nucleotide substitutions were identified in various viral genes conferring resistance or decreased sensitivity to the respective inhibitors. This study has shown different mutations in the analyzed genes in patients with HCV who had not previously received DAA treatment. These mutations may increase the likelihood of treatment failure in the future.
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Affiliation(s)
- Diana Valutite
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (Y.O.); (L.L.); (A.T.)
- Correspondence: ; Tel.: +7-95-2395-8965
| | - Yulia Ostankova
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (Y.O.); (L.L.); (A.T.)
| | - Alexandr Semenov
- FSBI State Scientific Center of Virology and Biotechnology «Vector» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 620030 Ekaterinburg, Russia;
| | - Liudmila Lyalina
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (Y.O.); (L.L.); (A.T.)
| | - Areg Totolian
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (Y.O.); (L.L.); (A.T.)
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Gömer A, Brown RJP, Pfaender S, Deterding K, Reuter G, Orton R, Seitz S, Bock CT, Cavalleri JMV, Pietschmann T, Wedemeyer H, Steinmann E, Todt D. OUP accepted manuscript. Virus Evol 2022; 8:veac007. [PMID: 35242360 PMCID: PMC8887644 DOI: 10.1093/ve/veac007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Even 30 years after the discovery of the hepatitis C virus (HCV) in humans there is still no vaccine available. Reasons for this include the high mutation rate of HCV, which allows the virus to escape immune recognition and the absence of an immunocompetent animal model for vaccine development. Phylogenetically distinct hepaciviruses (genus Hepacivirus, family Flaviviridae) have been isolated from diverse species, each with a narrow host range: the equine hepacivirus (EqHV) is the closest known relative of HCV. In this study, we used amplicon-based deep-sequencing to investigate the viral intra-host population composition of the genomic regions encoding the surface glycoproteins E1 and E2. Patterns of E1E2 substitutional evolution were compared in longitudinally sampled EqHV-positive sera of naturally and experimentally infected horses and HCV-positive patients. Intra-host virus diversity was higher in chronically than in acutely infected horses, a pattern which was similar in the HCV-infected patients. However, overall glycoprotein variability was higher in HCV compared to EqHV. Additionally, selection pressure in HCV populations was higher, especially within the N-terminal region of E2, corresponding to the hypervariable region 1 (HVR1) in HCV. An alignment of glycoprotein sequences from diverse hepaciviruses identified the HVR1 as a unique characteristic of HCV: hepaciviruses from non-human species lack this region. Together, these data indicate that EqHV infection of horses could represent a powerful surrogate animal model to gain insights into hepaciviral evolution and HCVs HVR1-mediated immune evasion strategy.
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Affiliation(s)
| | | | - Stephanie Pfaender
- Department for Molecular and Medical Virology, Ruhr University Bochum, Universitätsstr. 150, Bochum 44801, Germany
| | - Katja Deterding
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
- German Center for Infectious Disease Research (DZIF), HepNet Study-House, Hannover 30625, Germany
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs 7624, Hungary
| | | | - Stefan Seitz
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg 69120, Germany
| | - C- Thomas Bock
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin 13353, Germany
| | - Jessika M V Cavalleri
- Clinical Unit of Equine Internal Medicine, University of Veterinary Medicine Vienna, Veterinärplatz 1, Vienna 1210, Austria
| | - Thomas Pietschmann
- Twincore, Centre for Experimental and Clinical Infection Research, Institute of Experimental Virology, Hannover 30625, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig Site, Hannover 30625, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
- German Center for Infectious Disease Research (DZIF), HepNet Study-House, Hannover 30625, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Universitätsstr. 150, Bochum 44801, Germany
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Ibrahim MK, AbdElrahman M, Bader El Din NG, Tawfik S, Abd-Elsalam S, Omran D, Barakat AZ, Farouk S, Elbatae H, El Awady MK. The impact of genetic variations in sofosbuvir metabolizing enzymes and innate immunity mediators on treatment outcome in HCV-infected patients. Microb Pathog 2021; 162:105311. [PMID: 34843922 DOI: 10.1016/j.micpath.2021.105311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) is the leading cause of liver diseases worldwide. At present, combinations of different classes of direct-acting antiviral agents (DAAs) are used as treatment options for HCV, in which sofosbuvir (SOF) is the common DAA among different therapeutic regimes. In Egypt, SOF plus daclatasvir (DCV) is the widely used anti-HCV treatment protocol. Herein, we aimed to assess the association between 3 single-nucleotide polymorphisms (SNPs) at the genes coding for 2 SOF metabolizing enzymes: histidine triad nucleotide-binding protein 1 (HINT1) rs4696/rs7728773 and nucleoside diphosphate kinase 1 (NME1) rs3760468, together with the most potent anti-HCV innate molecule, i.e., interferon lambda 3 (IFNL3) rs12979860 and the response to SOF/DCV in Egyptian patients chronically infected with genotype 4 (GT4). SNPs were genotyped using real-time PCR in DNA from patients who achieved sustained virological response (SVR) at 12 weeks post-SOF/DCV treatment (i.e., responders; n = 188), patients who failed to achieve SVR12 (i.e., non-responders; n = 109), and healthy controls (n = 62). Our results demonstrated that patients bearing HINT1 rs7728773 CT/TT (odds ratio 2.119, 95% CI 1.263-3.559, p = 0.005) and IFNL3 rs12979860 CC (odds ratio 3.995, 95% CI 2.126-7.740, p = 0.0001) were more likely to achieve SVR12. However, neither HINT1 rs4696 nor NME1 rs3760468 seems to contribute to the responsiveness to SOF/DCV. Binary regression analysis defined 5 predictor factors independently associated with SVR12: age, bilirubin, hemoglobin, early stages of fibrosis, and combined HINT1 rs7728773 and IFNL3 rs12979860 favorable and mixed genotypes (odds ratio 3.134, 95% CI 1.518-6.47, p = 0.002), and that was confirmed by the combined ROC curve for the 5 predictor factors (AUC = 0.91, 95% CI 0.869-0.95, P = 0.0001). In conclusion, these data suggest that the two SNPs have the potential in predicting the response rate to SOF/DCV treatment in patients infected with HCV GT4. This study is the first to investigate the pharmacogenetics of SOF metabolizing enzyme and introduce HINT1 rs7728773 as a novel SNP that predicts the treatment efficacy.
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Affiliation(s)
- Marwa K Ibrahim
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt.
| | - Mohamed AbdElrahman
- Department of Pharmacy, Al-Mustaqbal University College, Babylon, Iraq; Clinical Pharmacy Unit, Badr University Hospital, Faculty of Medicine, Helwan University, Egypt
| | - Noha G Bader El Din
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Salwa Tawfik
- Department of Internal Medicine, National Research Center, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Sherief Abd-Elsalam
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Dalia Omran
- Department of Endemic Medicine and Hepatology, Faculty of Medicine, Cairo University, Egypt
| | - Amal Z Barakat
- Department of Molecular Biology, Biotechnology Research Institute, National Research Center, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Sally Farouk
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Hassan Elbatae
- Department of Tropical Medicine, Faculty of Medicine, Kafer Elshiek University, Kafer Elshiek, Egypt
| | - Mostafa K El Awady
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
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Llorens-Revull M, Gregori J, Dopazo C, Rodriguez-Frías F, Garcia-Cehic D, Soria ME, Chen Q, Rando A, Perales C, Esteban JI, Quer J, Bilbao I. Study of Quasispecies Complexity and Liver Damage Progression after Liver Transplantation in Hepatitis C Virus Infected Patients. Genes (Basel) 2021; 12:genes12111731. [PMID: 34828337 PMCID: PMC8625210 DOI: 10.3390/genes12111731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cirrhosis derived from chronic hepatitis C virus (HCV) infection is still a common indication for liver transplantation (LT). Reinfection of the engrafted liver is universal in patients with detectable viral RNA at the time of transplant and causes fast progression of cirrhosis (within 5 years) in around one-third of these patients. To prevent damage to the liver graft, effective direct-acting antiviral (DAA) therapy is required as soon as possible. However, because of post-LT clinical instability, it is difficult to determine the optimal time to start DAAs with a low risk of complications. Evaluate changes in quasispecies complexity following LT and seek a predictive index of fast liver damage progression to determine the timing of DAA initiation. HCV genomes isolated from pre-LT and 15-day post-LT serum samples of ten patients, who underwent orthotopic LT, were quantified and sequenced using a next-generation sequencing platform. Sequence alignments, phylogenetic trees, quasispecies complexity measures, biostatistics analyses, adjusted R2 values, and analysis of variance (ANOVA) were carried out. Three different patterns of reinfection were observed (viral bottlenecking, conserved pre-LT population, and mixed populations), suggesting that bottlenecking or homogenization of the viral population is not a generalized effect after liver graft reinfection. None of the quasispecies complexity measures predicted the future degree of liver damage. Higher and more uniform viral load (VL) values were observed in all pre-LT samples, but values were more dispersed in post-LT samples. However, VL increased significantly from the pre-LT to 15-day post-LT samples in patients with advanced fibrosis at 1-year post-LT, suggesting that a VL increase on day 15 may be a predictor of fast liver fibrosis progression. HCV kinetics after LT differ between patients and are not fibrosis-dependent. Higher VL at day 15 post-LT versus pre-LT samples may predict fast liver fibrosis progression.
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Affiliation(s)
- Meritxell Llorens-Revull
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Roche Diagnostics SL, Avinguda de la Generalitat, 171-173, 08174 Sant Cugat del Vallès, Spain
| | - Cristina Dopazo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Hepatobiliopancreatic Surgery and Transplant Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Francisco Rodriguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
| | - Maria Eugenia Soria
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
| | - Qian Chen
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
| | - Ariadna Rando
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Celia Perales
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Medicine, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: or
| | - Itxarone Bilbao
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Hepatobiliopancreatic Surgery and Transplant Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Surgery, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
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9
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Isakov V, Hedskog C, Wertheim JO, Hostager RE, Parhy B, Schneider ADB, Suri V, Mo H, Geivandova N, Morozov V, Bessonova E, Gankina N, Zhdanov K, Abdurakhmanov D, Svarovskaia E. Prevalence of resistance-associated substitutions and phylogenetic analysis of hepatitis C virus infection in Russia. Int J Infect Dis 2021; 113:36-42. [PMID: 34560266 DOI: 10.1016/j.ijid.2021.09.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Due to limited hepatitis C virus (HCV) sequence availability from patients in Russia, the relationship between subtypes and baseline resistance-associated substitutions (RAS) to direct antiretroviral treatment outcome is not fully understood. METHODS Deep sequencing of HCV NS3, NS5A, and NS5B sequences was performed on plasma HCV samples from 412 direct-acting antiviral (DAA)-naïve patients from Russia. Phylogenetic analysis was performed to investigate sequence similarities between HCV strains from Russia, Asia, Europe, and North America. Pretreatment HCV RAS was assessed with a 15% cutoff. RESULTS HCV genotype GT1b and GT3a sequences in Russia were related to strains in Europe and Asia. The prevalence of GT1a and GT2a was low in Russia. In GT1b, the prevalence of NS5A Y93H was lower in Russia (6%) compared with Asia (15%). The prevalence of NS5B L159F was similar between Russia and Europe (26-39%). GT3a RAS prevalence was similar between Russia and Asia, Europe, and North America. The 2k/1b recombinant strain in Russia was related to strains from Europe. A higher prevalence of the NS5A RAS L31M (10%) was observed in 2k/1b sequences compared to GT1b (1-6%). CONCLUSIONS The prevalence of RASs and the phylogenetic analysis showed similarities in HCV strains between Russia, Europe, and North America. This information may be useful for HCV regimens in Russia.
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Affiliation(s)
- Vasily Isakov
- Federal Research Center of Nutrition, Biotechnology and Food Safety, Moscow, Russia
| | | | - Joel O Wertheim
- University of California San Diego, San Diego, California, USA
| | | | - Bandita Parhy
- Gilead Sciences, Inc., Foster City, California, USA.
| | | | - Vithika Suri
- Gilead Sciences, Inc., Foster City, California, USA
| | - Hongmei Mo
- Gilead Sciences, Inc., Foster City, California, USA
| | | | | | - Elena Bessonova
- Sverdlovsk Regional Clinical Hospital, Yekaterinburg, Russia
| | - Natalya Gankina
- Krasnoyarsk Regional Center of Prevention and Control of AIDS, Krasnoyarsk, Russia
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10
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Augestad EH, Bukh J, Prentoe J. Hepatitis C virus envelope protein dynamics and the link to hypervariable region 1. Curr Opin Virol 2021; 50:69-75. [PMID: 34403905 DOI: 10.1016/j.coviro.2021.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022]
Abstract
Conformational dynamics of viral envelope proteins seem to be involved in mediating evasion from neutralizing antibodies (NAbs) by mechanisms that limit exposure of conserved protein motifs. For hepatitis C virus (HCV), molecular studies have only recently begun to unveil how such dynamics of the envelope protein heterodimer, E1/E2, are linked to viral entry and NAb evasion. Here, we review data suggesting that E1/E2 exists in an equilibrium between theoretical 'open' (NAb-sensitive) and 'closed' (NAb-resistant) conformational states. We describe how this equilibrium is influenced by viral sequence polymorphisms and that it is critically dependent on the N-terminal region of E2, termed hypervariable region 1 (HVR1). Finally, we discuss how it appears that the virus binding site for the HCV entry co-receptor CD81 is less available in 'closed' E1/E2 states and that NAb-resistant viruses require a more intricate entry pathway involving also the entry co-receptor, SR-BI.
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Affiliation(s)
- Elias H Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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11
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Ullah S, Ali M, Shaheen A, Zia F, Rahman L, Rahman S, Ali H, Din M, Waris A, Shinwari ZK. Sofosbuvir Resistance-associated Substitutions in the Palm Domain of HCV-NS5B RNA Dependent RNA Polymerase; Study of two Sofosbuvir non-responders. Int J Infect Dis 2021:S1201-9712(21)00426-4. [PMID: 34000421 DOI: 10.1016/j.ijid.2021.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE In current study we performed sequencing of palm domain of HCV-NS5B gene, its ancestral analysis along with amino acids substitution analysis. These analysis were done to find the molecular basis of the viral resistance against Sofosbuvir drug. METHODS Blood samples from individuals with chronic Hepatitis C infection that were resistant to Sofosbuvir were collected. The samples were processed for their molecular characterization that included RNA extraction, Complementary DNA (cDNA) synthesize, nested PCR, gel elution, Sequencing, ancestral and 3D structure analysis. RESULTS Evolutionary analysis revealed that current study sequences (QAU-01, QAU-02) clustered with a previously studied sequence, KY971494.1. Moreover, we reports multiple novel amino acid substitutions in the palm domain of NS5B gene such as Ile116Val, Asn117Gly, Glu246Ala, Val252Ala, Glu258Gln, Cys262Leu, Ser269Arg, Ala272Thr, Ile293Leu, Lys304Arg, Asn307Gly, Ala338Val and Arg345Gly in our query sequence (QAU-01). At 246 and 269 position in (QAU-02), no substitution was observed. CONCLUSIONS We have noticed that the current sequences are relatively emerging and could have been originated from aforementioned sequence recently. Based on the current results, we suggests that these substitutions could be associated with structural or functional impairment of protein and could also be may be considered as resistance associated substitutions (RAS) to Sofosbuvir drug.
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Affiliation(s)
- Sana Ullah
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Asmat Shaheen
- Department of Biochemistry, Khyber Medical University-Institute of Medical Sciences, Kohat, Pakistan.
| | - Fatima Zia
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Lubna Rahman
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Sidra Rahman
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Hammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Misbahud Din
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Abdul Waris
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Zabta Khan Shinwari
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan.
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12
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Roger S, Ducancelle A, Le Guillou-Guillemette H, Gaudy C, Lunel F. HCV virology and diagnosis. Clin Res Hepatol Gastroenterol 2021; 45:101626. [PMID: 33636428 DOI: 10.1016/j.clinre.2021.101626] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) infection is a major cause of severe liver disease including chronic hepatitis, cirrhosis and hepatocellular carcinoma. The HCV burden in public health is estimated at about 71 million people worldwide by World Health Organization (WHO) with at least 400,000 people that died every year from HCV disease [1]. New hepatitis C treatments with oral direct-acting antivirals (DAAs) showing high rates of response, with short treatment duration [2] have been available. HCV can now be eradicated with minimal side effects. Unfortunately, there is no vaccine yet available, but the development of a safe prophylactic vaccine remains a medical priority [3]. For this purpose, Hepatitis B-C subviral envelope particles can be produced by industrialized procedure. It seems to be very promising as this HBV-HCV vaccine candidate has been shown to elicit a broadly cross neutralizing activity against HCV [4]. Despite this revolution in the HCV-treatment, one of major challenge to achieve a global eradication of HCV remains to reduce the under diagnosis. The low rate of diagnosis is a major obstacle in resources limited countries and is mainly due to the cost of molecular tools, that are essential to diagnose and follow chronic HCV infection. In another hand, the mild clinical symptoms observed in HCV chronic disease, may explain that the majority of HCV infected individuals are unaware of their infection, because HCV testing is not generalized, like it is for HIV. HCV was discovered in 1989 after many years of work, by several researchers, who recently obtained the Nobel price [5-7]. This major discovery allowed the description of the HCV genome and later on of the virus replication and cell cycle, and also, importantly, the development of diagnostic tests for the detection of HCV antibodies (Ab) and RNA who were a priority in transfusion. In this review, we will try to get into the virology and cell biology of HCV. Thereafter, we will discuss the different categories of laboratory tests to diagnose/explore HCV infected subjects.
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Affiliation(s)
- Steven Roger
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France
| | - Alexandra Ducancelle
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France
| | - Hélène Le Guillou-Guillemette
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France
| | - Catherine Gaudy
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, 37000 Tours, France; INSERM U1259, Université de Tours, 37000 Tours, France
| | - Françoise Lunel
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France.
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13
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Martinez MA, Franco S. Discovery and Development of Antiviral Therapies for Chronic Hepatitis C Virus Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:139-157. [PMID: 34258740 DOI: 10.1007/978-981-16-0267-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
At the beginning of this decade, an estimated 71 million people were living with chronic hepatitis C virus (HCV) infection worldwide. After the acute stage of HCV infection, 18-34% of individuals exhibit spontaneous clearance. However, the remaining 66-82% of infected individuals progress to chronic HCV infection and are at subsequent risk of progression to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Chronic hepatitis C progression is generally slow during the first two decades of infection, but can be accelerated during this time in association with advancing age and cofactors, such as heavy alcohol intake and human immunodeficiency virus (HIV) co-infection. Since acute HCV infection is generally asymptomatic, HCV goes undiagnosed in a significant percentage of infected individuals. In 2014, direct-acting antiviral (DAA) therapy for chronic HCV was developed, which has increased the cure rates to nearly 100%. DAA therapy is among the best examples of success in the fight against viral infections. DAAs have transformed HCV management and have opened the door for the global eradication of HCV.
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Affiliation(s)
- Miguel Angel Martinez
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Sandra Franco
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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14
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Hepatitis C Virus Infection and the New Therapeutical Approach. CURRENT HEALTH SCIENCES JOURNAL 2021; 47:353-360. [PMID: 35003766 PMCID: PMC8679141 DOI: 10.12865/chsj.47.03.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022]
Abstract
Hepatitis C virus represents one of the most important public health problems nowadays. Several epidemiological studies have shown a continuous increasing rate of prevalence and incidence with severe consequences in terms of mortality. During the last decades, the treatment of the liver infection has evolved, and now there are available new therapies with better side-effect' profiles and bigger efficiency. The needs for more therapeutically efficacy also stand behind the numerous comorbidities associated to the liver disease, and also for assuring better quality of life for patients and their families.
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15
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Martinez MA, Franco S. Therapy Implications of Hepatitis C Virus Genetic Diversity. Viruses 2020; 13:E41. [PMID: 33383891 PMCID: PMC7824680 DOI: 10.3390/v13010041] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is an important human pathogen with a high chronicity rate. An estimated 71 million people worldwide are living with chronic hepatitis C (CHC) infection, which carries the risk of progression to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Similar to other RNA viruses, HCV has a high rate of genetic variability generated by its high mutation rate and the actions of evolutionary forces over time. There are two levels of HCV genetic variability: intra-host variability, characterized by the distribution of HCV mutant genomes present in an infected individual, and inter-host variability, represented by the globally circulating viruses that give rise to different HCV genotypes and subtypes. HCV genetic diversity has important implications for virus persistence, pathogenesis, immune responses, transmission, and the development of successful vaccines and antiviral strategies. Here we will discuss how HCV genetic heterogeneity impacts viral spread and therapeutic control.
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Affiliation(s)
- Miguel Angel Martinez
- Miguel Angel Martínez, IrsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain;
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16
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Laugel E, Hartard C, Jeulin H, Berger S, Venard V, Bronowicki JP, Schvoerer E. Full-length genome sequencing of RNA viruses-How the approach can enlighten us on hepatitis C and hepatitis E viruses. Rev Med Virol 2020; 31:e2197. [PMID: 34260779 DOI: 10.1002/rmv.2197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/09/2022]
Abstract
Among the five main viruses responsible for human hepatitis, hepatitis C virus (HCV) and hepatitis E virus (HEV) are different while sharing similarities. Both viruses can be transmitted by blood or derivatives whereas HEV can also follow environmental or zoonotic routes. These highly variable RNA viruses can cause chronic hepatitis potentially leading to hepatocarcinoma. HCV and HEV can develop new structures and functions under selective pressure to adapt to host immunity, human tissues, treatments or even various animal reservoirs. Elsewhere, with directly acting antiviral treatments, HCV can be eradicated whereas HEV is an emerging pathogen against which specific treatments have to be improved. As a unique molecular tool able to explore viral genomic plasticity, full-length genome (FLG) sequencing has become easier, faster and cheaper. The present review will show how FLG sequencing can explore these RNA viruses with the aim to investigate key genomics data to improve basic knowledge, patients' healthcare and preventive tools.
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Affiliation(s)
- Elodie Laugel
- Université de Lorraine, Vandœuvre-lès-Nancy, France.,Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France.,Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564 CNRS-UL, Vandœuvre-lès-Nancy, France
| | - Cédric Hartard
- Université de Lorraine, Vandœuvre-lès-Nancy, France.,Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France.,Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564 CNRS-UL, Vandœuvre-lès-Nancy, France
| | - Hélène Jeulin
- Université de Lorraine, Vandœuvre-lès-Nancy, France.,Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France.,Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564 CNRS-UL, Vandœuvre-lès-Nancy, France
| | - Sibel Berger
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France
| | - Véronique Venard
- Université de Lorraine, Vandœuvre-lès-Nancy, France.,Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France
| | - Jean-Pierre Bronowicki
- Université de Lorraine, Vandœuvre-lès-Nancy, France.,Service d'hépato-gastroentérologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France
| | - Evelyne Schvoerer
- Université de Lorraine, Vandœuvre-lès-Nancy, France.,Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France.,Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564 CNRS-UL, Vandœuvre-lès-Nancy, France
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17
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Khan S, Soni S, Veerapu NS. HCV Replicon Systems: Workhorses of Drug Discovery and Resistance. Front Cell Infect Microbiol 2020; 10:325. [PMID: 32714881 PMCID: PMC7344236 DOI: 10.3389/fcimb.2020.00325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
The development of direct-acting antivirals (DAAs) has revolutionized the state-of-the art treatment of HCV infections, with sustained virologic response rates above 90%. However, viral variants harboring substitutions referred to as resistance-associated substitutions (RASs) may be present in baseline levels and confer resistance to DAAs, thereby posing a major challenge for HCV treatment. HCV replicons have been the primary tools for discovering and evaluating the inhibitory activity of DAAs against viral replication. Interest in replicon systems has further grown as they have become indispensable for discovering genotype-specific and cross-genotype RASs. Here, we review functional replicon systems for HCV, how these replicon systems have contributed to the development of DAAs, and the characteristics and distribution of RASs for DAAs.
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Affiliation(s)
- Shaheen Khan
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | - Shalini Soni
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | - Naga Suresh Veerapu
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
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18
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Substitution of the CD81 Binding Site and β-Sandwich Area in E2 of HCV in Cambodia. Viruses 2020; 12:v12050551. [PMID: 32429467 PMCID: PMC7290788 DOI: 10.3390/v12050551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
The high genetic variability of hepatitis C virus (HCV) is the main obstacle to developing a vaccine. E2 has attracted attention for vaccine development because targeting this protein could potentially overcome issues related to the genetic diversity of HCV. In this study, we analyzed HCV genes in the general population of Cambodia and investigated the E2 locus as a candidate for vaccine development. HCV sero-epidemiological surveys were conducted between the period 2010 and 2014, with an HCV RNA–positive rate of 1.3% (11/868). Follow-up blood samples were collected from four anti-HCV– and HCV RNA– positive patients (genotype 1b: 2 cases, 6e: 1 case, 6r: 1 case) after 4.12 years. Analysis of HCV full-length nucleotide sequences in paired specimens revealed that the mutation rates of HCV genotypes 1b and 6e/6r were 1.61–2.03 × 10−3 and 2.52–2.74 × 10−3 substitutions/site/year, respectively. Non-synonymous substitutions were detected in HVR1, the front layer of the CD81 binding site, and the β-sandwich, but not in the N-terminal region or adjacent to the CD81 binding site. Therefore, we conclude that the CD81 binding site is a promising locus for HCV vaccine development.
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19
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Mailly L, Baumert TF. Hepatitis C virus infection and tight junction proteins: The ties that bind. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183296. [PMID: 32268133 DOI: 10.1016/j.bbamem.2020.183296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
The hepatitis C virus (HCV) is a major cause of liver diseases ranging from liver inflammation to advanced liver diseases like cirrhosis and hepatocellular carcinoma (HCC). HCV infection is restricted to the liver, and more specifically to hepatocytes, which represent around 80% of liver cells. The mechanism of HCV entry in human hepatocytes has been extensively investigated since the discovery of the virus 30 years ago. The entry mechanism is a multi-step process relying on several host factors including heparan sulfate proteoglycan (HSPG), low density lipoprotein receptor (LDLR), tetraspanin CD81, Scavenger Receptor class B type I (SR-BI), Epidermal Growth Factor Receptor (EGFR) and Niemann-Pick C1-like 1 (NPC1L1). Moreover, in order to establish a persistent infection, HCV entry is dependent on the presence of tight junction (TJ) proteins Claudin-1 (CLDN1) and Occludin (OCLN). In the liver, tight junction proteins play a role in architecture and homeostasis including sealing the apical pole of adjacent cells to form bile canaliculi and separating the basolateral domain drained by sinusoidal blood flow. In this review, we will highlight the role of liver tight junction proteins in HCV infection, and we will discuss the potential targeted therapeutic approaches to improve virus eradication.
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Affiliation(s)
- Laurent Mailly
- Université de Strasbourg, INSERM, UMR-S1110, Institut de Recherche sur les Maladies Virales et Hépatiques, F-67000 Strasbourg, France.
| | - Thomas F Baumert
- Université de Strasbourg, INSERM, UMR-S1110, Institut de Recherche sur les Maladies Virales et Hépatiques, F-67000 Strasbourg, France; Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France; Institut Universitaire de France, F-75231 Paris, France.
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20
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Alter HJ, Farci P, Bukh J, Purcell RH. Reflections on the History of HCV: A Posthumous Examination. Clin Liver Dis (Hoboken) 2020; 15:S64-S71. [PMID: 32140215 PMCID: PMC7050949 DOI: 10.1002/cld.882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/01/2019] [Indexed: 02/04/2023] Open
Affiliation(s)
- Harvey J. Alter
- Department of Transfusion MedicineClinical CenterNational Institutes of HealthBethesdaMD
| | - Patrizia Farci
- Laboratory of Infectious DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD
| | - Jens Bukh
- Department of Immunology and MicrobiologyFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Robert H. Purcell
- Laboratory of Infectious DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD
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21
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Genome-Wide Mutagenesis of Hepatitis C Virus Reveals Ability of Genome To Overcome Detrimental Mutations. J Virol 2020; 94:JVI.01327-19. [PMID: 31723027 DOI: 10.1128/jvi.01327-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/17/2019] [Indexed: 01/10/2023] Open
Abstract
To gain insight into the impact of mutations on the viability of the hepatitis C virus (HCV) genome, we created a set of full-genome mutant libraries, differing from the parent sequence as well as each other, by using a random mutagenesis approach; the proportion of mutations increased across these libraries with declining template amount or dATP concentration. The replication efficiencies of full-genome mutant libraries ranged between 71 and 329 focus-forming units (FFU) per 105 Huh7.5 cells. Mutant libraries with low proportions of mutations demonstrated low replication capabilities, whereas those with high proportions of mutations had their replication capabilities restored. Hepatoma cells transfected with selected mutant libraries, with low (4 mutations per 10,000 bp copied), moderate (33 mutations), and high (66 mutations) proportions of mutations, and their progeny were subjected to serial passage. Predominant virus variants (mutants) from these mutant libraries (Mutantl, Mutantm, and Mutanth, respectively) were evaluated for changes in growth kinetics and particle-to-FFU unit ratio, virus protein expression, and modulation of host cell protein synthesis. Mutantm and Mutantl variants produced >3.0-log-higher extracellular progeny per ml than the parent, and Mutanth produced progeny at a rate 1.0-log lower. More than 80% of the mutations were in a nonstructural part of the mutant genomes, the majority were nonsynonymous, and a moderate to large proportion were in the conserved regions. Our results suggest that the HCV genome has the ability to overcome lethal/deleterious mutations because of the high reproduction rate but highly selects for random, beneficial mutations.IMPORTANCE Hepatitis C virus (HCV) in vivo displays high genetic heterogeneity, which is partly due to the high reproduction and random substitutions during error-prone genome replication. It is difficult to introduce random substitutions in vitro because of limitations in inducing mutagenesis from the 5' end to the 3' end of the genome. Our study has overcome this limitation. We synthesized full-length genomes with few to several random mutations in the background of an HCV clone that can recapitulate all steps of the life cycle. Our study provides evidence of the capability of the HCV genome to overcome deleterious mutations and remain viable. Mutants that emerged from the libraries had diverse phenotype profiles compared to the parent, and putative adaptive mutations mapped to segments of the conserved nonstructural genome. We demonstrate the potential utility of our system for the study of sequence variation that ensures the survival and adaptation of HCV.
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22
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Study of multiple genetic variations caused by persistent hepatitis C virus replication in long-term cell culture. Arch Virol 2019; 165:331-343. [PMID: 31832864 DOI: 10.1007/s00705-019-04461-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/04/2019] [Indexed: 12/23/2022]
Abstract
The most characteristic feature of the hepatitis C virus (HCV) genome in patients with chronic hepatitis C is its remarkable variability and diversity. To better understand this feature, we performed genetic analysis of HCV replicons recovered from two human hepatoma HuH-7-derived cell lines after 1, 3, 5, 7, and 9 years in culture: The cell lines 50-1 and sO harbored HCV 1B-1 and O strain-derived HCV replicons established in 2002 and 2003, respectively. The results revealed that genetic variations in both replicons accumulated in a time-dependent manner at a constant rate despite the maintenance of moderate diversity (less than 1.8% difference) between the clones and that the mutation rate in the 50-1 and sO replicons was 2.5 and 2.9 × 10-3 base substitutions/site/year, respectively. We found that the genetic distance of both replicons increased from 7.9% to 10.5% after 9 years in culture. In addition, we observed that the guanine + cytosine (GC) content of both replicon RNAs increased in a time-dependent manner, as observed in our previous studies. Finally, we demonstrated that the high sensitivity of both replicons to direct-acting antivirals was maintained even after 9 years in culture. Our results suggest that long-term cultured HCV replicon-harboring cells are a useful model for understanding the variability and diversity of the HCV genome and the drug sensitivity of HCV in patients with chronic hepatitis C.
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23
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El-Shabrawi M, Hassanin F. Paediatric hepatitis C virus infection and its treatment: Present, past, and future. Arab J Gastroenterol 2019; 20:163-174. [PMID: 31585703 DOI: 10.1016/j.ajg.2019.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/01/2019] [Accepted: 09/15/2019] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) infection is a major cause of chronic liver disease in the world. It is a challenging medico-social problem in the paediatric population. High HCV infection rates are reported in low and middle incomes countries. From the health economic point of view treatment of hepatitis C virus (HCV) with subsequent virus eradication is very effective as it eliminates the long-term sequelae of untreated or maltreated HCV. In this review we summarize the updates and highlight the historical approach of treatment of chronic HCV infection in children in the new era of directly acting antiviral (DAA) agents.
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24
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Pérez AB, Chueca N, Macías J, Pineda JA, Salmerón J, Rivero-Juárez A, Hidalgo-Tenorio C, Espinosa MD, Téllez F, Von-Wichmann MÁ, Omar M, Santos J, Hernández-Quero J, Antón JJ, Collado A, Lozano AB, García-Deltoro M, Casado M, Pascasio JM, Selfa A, Rosales JM, De la Iglesia A, Arenas JI, García-Bujalance S, Ríos MJ, Bernal E, Martínez O, García-Herola A, Vélez M, Rincón P, García F. Prevalence of resistance associated substitutions and efficacy of baseline resistance-guided chronic hepatitis C treatment in Spain from the GEHEP-004 cohort. PLoS One 2019; 14:e0221231. [PMID: 31469856 PMCID: PMC6716636 DOI: 10.1371/journal.pone.0221231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Treatment guidelines differ in their recommendation to determine baseline resistance associated substitutions (RAS) before starting a first-line treatment with direct-acting antivirals (DAAs). Here we analyze the efficacy of DAA treatment with baseline RAS information. We conducted a prospective study involving 23 centers collaborating in the GEHEP-004 DAA resistance cohort. Baseline NS5A and NS3 RASs were studied by Sanger sequencing. After issuing a comprehensive resistance report, the treating physician decided the therapy, duration and ribavirin use. Sustained virological response (SVR12) data are available in 275 patients. Baseline NS5A RAS prevalence was between 4.3% and 26.8% according to genotype, and NS3 RASs prevalence (GT1a) was 6.3%. Overall, SVR12 was 97.8%. Amongst HCV-GT1a patients, 75.0% had >800,000 IU/ml and most of those that started grazoprevir/elbasvir were treated for 12 weeks. In genotype 3, NS5A Y93H was detected in 9 patients. 42.8% of the HCV-GT3 patients that started sofosbuvir/velpatasvir included ribavirin, although only 14.7% carried Y93H. The efficacy of baseline resistance-guided treatment in our cohort has been high across the most prevalent HCV genotypes in Spain. The duration of the grazoprevir/elbasvir treatment adhered mostly to AASLD/IDSA recommendations. In cirrhotic patients infected with GT-3 there has been a high use of ribavirin.
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Affiliation(s)
- Ana Belén Pérez
- Clinical Microbiology Unit, University Hospital Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Natalia Chueca
- Clinical Microbiology Unit, University Hospital San Cecilio, Instituto de Investigacion Ibs. Granada, Granada, Spain
| | - Juan Macías
- Infectious Diseases Unit, University Hospital Nuestra Señora de Valme, Sevilla, Spain
| | - Juan Antonio Pineda
- Infectious Diseases Unit, University Hospital Nuestra Señora de Valme, Sevilla, Spain
| | - Javier Salmerón
- Hepatology Unit, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. CIBERehd, Granada, Spain
| | - Antonio Rivero-Juárez
- Infectious Diseases Unit, University Hospital Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, Córdoba, Spain
| | | | | | - Francisco Téllez
- Infectious Diseases Unit, Hospital Puerto Real, Puerto Real, Cádiz, Spain
| | | | - Mohamed Omar
- Infectious Diseases Unit, Complejo Hospitalario de Jaén, Jáen, Spain
| | - Jesús Santos
- Infectious Diseases Unit, University Hospital Virgen de la Victoria, Málaga, Spain
| | | | | | - Antonio Collado
- Infectious Diseases Unit, Complejo Hospitalario Torrecárdenas, Almería, Spain
| | - Ana Belén Lozano
- Infectious Diseases Unit, Hospital de Poniente, El Ejido, Almería, Spain
| | | | - Marta Casado
- Hepatology Unit, Complejo Hospitalario Torrecárdenas, Almería, Spain
| | | | - Aida Selfa
- Hepatology Unit, Hospital Comarcal Santa Ana, Motril Granada, Spain
| | | | | | | | | | - María José Ríos
- Infectious Diseases Unit, University Hospital Virgen Macarena, Seville, Spain
| | - Enrique Bernal
- Infectious Diseases Unit, Hospital General Reina Sofía, Murcia, Spain
| | - Onofre Martínez
- Infectious Diseases Unit, University Hospital Santa Lucía, Cartagena, Spain
| | | | - Mónica Vélez
- Infectious Diseases Unit, Hospital General de La Palma, La Palma, Spain
| | - Pilar Rincón
- Infectious Diseases Unit, University Hospital Nuestra Señora de Valme, Sevilla, Spain
| | - Federico García
- Clinical Microbiology Unit, University Hospital San Cecilio, Instituto de Investigacion Ibs. Granada, Granada, Spain
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25
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Nii-Trebi NI, Brown CA, Osei YD, Ampofo WK, Nyarko AK. Core encoding sequences of Hepatitis C virus in Ghanaian blood donors are predominantly mosaics of different genotype 2 strains and cannot distinguish subtypes. BMC Infect Dis 2019; 19:533. [PMID: 31208352 PMCID: PMC6580569 DOI: 10.1186/s12879-019-4155-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
Background Distribution of Hepatitis C virus (HCV) genotypes varies significantly worldwide. Genomic diversity between genotypes has implications for treatment, vaccine development and optimal design of HCV diagnostic assays. Molecular characterization of HCV in different geographical areas is therefore very essential for management and public health control of HCV infection. This study investigated the molecular epidemiology and characteristics of HCV genotypes in healthy individuals in Accra, Ghana. Methods An experimental study was carried out on blood samples obtained from voluntary blood donors. Two hundred samples were initially screened for HCV antibodies and infection was confirmed by RNA detection through RT-PCR of the 5′-untranslated region (5’UTR). The core gene sequences were analysed for HCV genotype determination by genotype-specific PCR; and then by cloning and direct sequencing followed by phylogenetic analysis. The sequences were further analysed in detail by similarity plotting. Results Molecular diagnosis confirmed the presence of HCV RNA in 2 out of 200 (1%) blood donors. Initial genotyping by genotype-specific PCR identified all two infections as subtypes 2a and 2b of genotype 2. Extensive evolutionary and genetic analyses indicated two epidemiological profiles. First, phylogenetic tree topologies clearly showed that, collectively, the core sequences of the Ghanaian HCV isolates belong to a single, distinct genetic group within HCV genotype 2 cluster, with high genetic similarity and rapid sequence variation in a single individual. Second, the sequences are mosaics comprising 2e and other genotype 2 subtype fragments. The analyses underscore a unique and complex HCV genotype 2 core sequence profile of the Ghanaian isolates. Conclusions Analysis of HCV core encoding sequences from Ghanaian blood donors in Accra confirmed predominance of genotype 2 HCV among healthy individuals. However, the isolates could not be classified into subtypes, possibly due to their complex sequence pattern that might suggest high mutability of the prevailing genotype. The core region of Ghanaian HCV therefore may not be suitable for distinguishing subtypes. These findings extend those from previous studies and thus underscore the need to search for subtype-informative region of Ghanaian HCV to elucidate the genetic diversity and factors determining outcome of HCV infections in Ghana.
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Affiliation(s)
- Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana.
| | - Charles Addoquaye Brown
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Yaa Difie Osei
- Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - William Kwabena Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Alexander Kwadwo Nyarko
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
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26
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Sharafi H, Ghalamkari S, Hassanshahi A, Alavian SM. Pooled Prevalence of NS5A Resistance-Associated Substitutions in Chronic HCV Genotype 3 Infection: A Study Based on Deposited Sequences in GenBank. Microb Drug Resist 2019; 25:1072-1079. [PMID: 31021305 DOI: 10.1089/mdr.2018.0358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Using direct-acting antiviral agents (DAAs) against hepatitis C virus (HCV) infection results in a high treatment response rate. However, several factors can significantly alter this outcome such as resistance-associated substitutions (RASs) in HCV NS5A gene. This study aimed to evaluate the prevalence of naturally occurring RASs of NS5A in HCV genotype 3 (HCV-3) sequences isolated from individuals with chronic HCV-3 infection. All the registered sequences in the GenBank under "NS5A" AND "Hepacivirus C" query were evaluated and screened, those which followed our inclusion criteria were enrolled in our pooled analysis. The retrieved sequences of included studies were evaluated for substitutions, RASs, and RASs conferring >100 resistance fold change (RASs >100 × ) in NS5A amino acid positions 24, 28, 30, 31, 62, 92, and 93. From 7 enrolled studies, a total of 370 HCV-3a isolates were retrieved and investigated. Forty-eight (13.0%, 95% CI = 9.9-16.8%) isolates harbored NS5A RASs. Moreover, Y93H was the only NS5A RAS >100 × observed in 13 (3.5%, 95% CI = 2.0-5.9%) retrieved sequences. The low frequency of naturally occurring NS5A RASs, especially those with clinical relevance (RASs >100 × ), among individuals with HCV-3 infection and the high rate of treatment response to DAAs suggest not to investigate every individual with HCV-3 infection for NS5A RASs before treatment.
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Affiliation(s)
- Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, the Islamic Republic of Iran.,Middle East Liver Diseases (MELD) Center, Tehran, the Islamic Republic of Iran
| | - Saman Ghalamkari
- Department of Biology, Islamic Azad University, Arsanjan Branch, Arsanjan, Iran
| | - Alireza Hassanshahi
- Department of Biology, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, the Islamic Republic of Iran.,Middle East Liver Diseases (MELD) Center, Tehran, the Islamic Republic of Iran
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27
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Alazard-Dany N, Denolly S, Boson B, Cosset FL. Overview of HCV Life Cycle with a Special Focus on Current and Possible Future Antiviral Targets. Viruses 2019; 11:v11010030. [PMID: 30621318 PMCID: PMC6356578 DOI: 10.3390/v11010030] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C infection is the leading cause of liver diseases worldwide and a major health concern that affects an estimated 3% of the global population. Novel therapies available since 2014 and 2017 are very efficient and the WHO considers HCV eradication possible by the year 2030. These treatments are based on the so-called direct acting antivirals (DAAs) that have been developed through research efforts by academia and industry since the 1990s. After a brief overview of the HCV life cycle, we describe here the functions of the different targets of current DAAs, the mode of action of these DAAs and potential future inhibitors.
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Affiliation(s)
- Nathalie Alazard-Dany
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Solène Denolly
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Bertrand Boson
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
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28
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Ashraf MU, Iman K, Khalid MF, Salman HM, Shafi T, Rafi M, Javaid N, Hussain R, Ahmad F, Shahzad-Ul-Hussan S, Mirza S, Shafiq M, Afzal S, Hamera S, Anwar S, Qazi R, Idrees M, Qureshi SA, Chaudhary SU. Evolution of efficacious pangenotypic hepatitis C virus therapies. Med Res Rev 2018; 39:1091-1136. [PMID: 30506705 DOI: 10.1002/med.21554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.
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Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Talha Shafi
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momal Rafi
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Nida Javaid
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | | | - Shaper Mirza
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shafiq
- Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sadia Hamera
- Department of Plant Genetics, Institute of Life Sciences, University of Rostock, Germany
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, Pakistan
| | - Muhammad Idrees
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Sohail A Qureshi
- Institute of Integrative Biosciences, CECOS-University of Information Technology and Emerging Sciences, Peshawar, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
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29
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Marohnic CC, Birkenmeyer LG, Bogdan MF, Frias EC, Otis KS, Palafox MAP, McSherry TD, Gregory SD, Zhao C, Gutierrez RA, Prostko JC, Muerhoff AS. Engineering of the hepatitis C virus helicase for enhanced seroreactivity. J Virol Methods 2018; 264:11-17. [PMID: 30381240 DOI: 10.1016/j.jviromet.2018.10.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
Abstract
Hepatitis C Virus c33, a recombinant protein comprising residues 1192-1457 of NS3 helicase, has been a mainstay of HCV serology for decades. With seven unpaired cysteines, seroreactivity of E. coli expressed c33 is dependant on reductants. While engineering a c33 replacement for new anti-HCV serological tests, we sought to reduce oxidation sensitivity, a liability for immunodiagnostic reagent stability. A series of cysteine-to-serine substituted variants of a c33-like antigen was constructed and evaluated for reactivity against a panel of HCV-positive sera. Several variants were essentially nonreactive while others exhibited reactivity similar to or better than the wild-type construct. One demonstrated equivalent potency to wild-type but also diminished DTT dependence. To explore enhanced anti-NS3 reactivity, we constructed and examined an expanded series of antigens comprising individual helicase domains, the full-length helicase, additional cysteine-to-serine variants, and variants at positions critical to catalytic activity. Immunoassays using these latter NS3 helicase recombinants demonstrated that domain 1 possessed significantly more seroreactivity than previously believed, that the use of soluble full-length helicase protein enhanced sensitivity by several-fold over c33, and that anti-NS3 helicase seroreactivity was further enhanced by the introduction of point mutations which altered the catalytic activity or oxidation sensitivity of the antigen.
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Affiliation(s)
- Christopher C Marohnic
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA.
| | - Larry G Birkenmeyer
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - M Felicia Bogdan
- Abbott Laboratories, Diagnostics Division, Research and Development Process Design, Abbott Park, IL, USA
| | - Edwin C Frias
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - Kathy S Otis
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - Mary Ann P Palafox
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - Troy D McSherry
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - Svetoslava D Gregory
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - Cheng Zhao
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - Robin A Gutierrez
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - John C Prostko
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
| | - A Scott Muerhoff
- Abbott Laboratories, Diagnostics Division, Applied Research and Technology, Abbott Park, IL, USA
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30
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Ahmed M. Era of direct acting anti-viral agents for the treatment of hepatitis C. World J Hepatol 2018; 10:670-684. [PMID: 30386460 PMCID: PMC6206157 DOI: 10.4254/wjh.v10.i10.670] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/10/2018] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C infection is universal and the most common indication of liver transplantation in the United States. The period of less effective interferon therapy with intolerable side effects has gone. Now we have stepped into the era of direct acting anti-viral agents (DAAs) against hepatitis C virus. Treatment of hepatitis C is now extremely effective, tolerable and requires a short duration of intake of oral agents. Less monitoring is required with the current therapy and drug-drug interactions are less than the previous regimen. The current treatment options of chronic hepatitis C with various DAAs are discussed in this article.
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Affiliation(s)
- Monjur Ahmed
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Thomas Jefferson University, Philadelphia, PA 19107, United States
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31
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Hepatitis C virus cell culture models: an encomium on basic research paving the road to therapy development. Med Microbiol Immunol 2018; 208:3-24. [PMID: 30298360 DOI: 10.1007/s00430-018-0566-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022]
Abstract
Chronic hepatitis C virus (HCV) infections affect 71 million people worldwide, often resulting in severe liver damage. Since 2014 highly efficient therapies based on directly acting antivirals (DAAs) are available, offering cure rates of almost 100%, if the infection is diagnosed in time. It took more than a decade to discover HCV in 1989 and another decade to establish a cell culture model. This review provides a personal view on the importance of HCV cell culture models, particularly the replicon system, in the process of therapy development, from drug screening to understanding of mode of action and resistance, with a special emphasis on the contributions of Ralf Bartenschlager's group. It summarizes the tremendous efforts of scientists in academia and industry required to achieve efficient DAAs, focusing on the main targets, protease, polymerase and NS5A. It furthermore underpins the importance of strong basic research laying the ground for translational medicine.
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32
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Akaberi D, Bergfors A, Kjellin M, Kameli N, Lidemalm L, Kolli B, Shafer RW, Palanisamy N, Lennerstrand J. Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach. Infect Ecol Epidemiol 2018; 8:1528117. [PMID: 30319736 PMCID: PMC6179053 DOI: 10.1080/20008686.2018.1528117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background: Current combination treatments with direct-acting antiviral agents (DAAs) can cure more than 95% of hepatitis C virus (HCV) infections. However, resistance-associated substitutions (RASs) may emerge and can also be present in treatment-naïve patients. Methods, results and discussion: In this study, a semi-pan-genotypic population sequencing method was developed and used to assess all NS5B amino acid variants between residue positions 310 and 564. Our method successfully sequenced more than 90% of genotype (GT) 1a, 1b, 2b and 3a samples. By using the population sequencing method with a cut-off of 20%, we found the dasabuvir RASs A553V and C445F to be a baseline polymorphism of GT 2b (8 out of 8) and GT 3a (18 out of 18) sequences, respectively. In GT 1a and 1b treatment-naïve subjects (n=25), no high-fold resistance polymorphism/RASs were identified. We further predicted dasabuvir’s binding pose with the NS5B polymerase using the in silico methods to elucidate the reasons associated with the resistance of clinically relevant RASs. Dasabuvir was docked at the palm-I site and was found to form hydrogen bonds with the residues S288, I447, Y448, N291 and D318. The RAS positions 316, 414, 448, 553 and 556 were found to constitute the dasabuvir binding pocket.
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Affiliation(s)
- Dario Akaberi
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Assar Bergfors
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Midori Kjellin
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Nader Kameli
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Microbiology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Louise Lidemalm
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Bhavya Kolli
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Robert W Shafer
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Navaneethan Palanisamy
- HBIGS, University of Heidelberg, Heidelberg, Germany.,Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Johan Lennerstrand
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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33
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Prentoe J, Bukh J. Hypervariable Region 1 in Envelope Protein 2 of Hepatitis C Virus: A Linchpin in Neutralizing Antibody Evasion and Viral Entry. Front Immunol 2018; 9:2146. [PMID: 30319614 PMCID: PMC6170631 DOI: 10.3389/fimmu.2018.02146] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection is the cause of about 400,000 annual liver disease-related deaths. The global spread of this important human pathogen can potentially be prevented through the development of a vaccine, but this challenge has proven difficult, and much remains unknown about the multitude of mechanisms by which this heterogeneous RNA virus evades inactivation by neutralizing antibodies (NAbs). The N-terminal motif of envelope protein 2 (E2), termed hypervariable region 1 (HVR1), changes rapidly in immunoglobulin-competent patients due to antibody-driven antigenic drift. HVR1 contains NAb epitopes and is directly involved in protecting diverse antibody-specific epitopes on E1, E2, and E1/E2 through incompletely understood mechanisms. The ability of HVR1 to protect HCV from NAbs appears linked with modulation of HCV entry co-receptor interactions. Thus, removal of HVR1 increases interaction with CD81, while altering interaction with scavenger receptor class B, type I (SR-BI) in a complex fashion, and decreasing interaction with low-density lipoprotein receptor. Despite intensive efforts this modulation of receptor interactions by HVR1 remains incompletely understood. SR-BI has received the most attention and it appears that HVR1 is involved in a multimodal HCV/SR-BI interaction involving high-density-lipoprotein associated ApoCI, which may prime the virus for later entry events by exposing conserved NAb epitopes, like those in the CD81 binding site. To fully elucidate the multifunctional role of HVR1 in HCV entry and NAb evasion, improved E1/E2 models and comparative studies with other NAb evasion strategies are needed. Derived knowledge may be instrumental in the development of a prophylactic HCV vaccine.
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Affiliation(s)
- Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Copenhagen, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Copenhagen, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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34
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Greczmiel U, Oxenius A. The Janus Face of Follicular T Helper Cells in Chronic Viral Infections. Front Immunol 2018; 9:1162. [PMID: 29887868 PMCID: PMC5982684 DOI: 10.3389/fimmu.2018.01162] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
Chronic infections with non-cytopathic viruses constitutively expose virus-specific adaptive immune cells to cognate antigen, requiring their numeric and functional adaptation. Virus-specific CD8 T cells are compromised by various means in their effector functions, collectively termed T cell exhaustion. Alike CD8 T cells, virus-specific CD4 Th1 cell responses are gradually downregulated but instead, follicular T helper (TFH) cell differentiation and maintenance is strongly promoted during chronic infection. Thereby, the immune system promotes antibody responses, which bear less immune-pathological risk compared to cytotoxic and pro-inflammatory T cell responses. This emphasis on TFH cells contributes to tolerance of the chronic infection and is pivotal for the continued maturation and adaptation of the antibody response, leading eventually to the emergence of virus-neutralizing antibodies, which possess the potential to control the established chronic infection. However, sustained high levels of TFH cells can also result in a less stringent B cell selection process in active germinal center reactions, leading to the activation of virus-unspecific B cells, including self-reactive B cells, and to hypergammaglobulinemia. This dispersal of B cell help comes at the expense of a stringently selected virus-specific antibody response, thereby contributing to its delayed maturation. Here, we discuss these opposing facets of TFH cells in chronic viral infections.
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Affiliation(s)
- Ute Greczmiel
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
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35
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Puchades Renau L, Berenguer M. Introduction to hepatitis C virus infection: Overview and history of hepatitis C virus therapies. Hemodial Int 2018; 22 Suppl 1:S8-S21. [DOI: 10.1111/hdi.12647] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lorena Puchades Renau
- Department of Gastroenterology, Hepatology Unit & Instituto de Investigación La Fe; Hospital Universitari i Politècnic La Fe; Valencia Spain
| | - Marina Berenguer
- Department of Gastroenterology, Hepatology Unit & Instituto de Investigación La Fe; Hospital Universitari i Politècnic La Fe; Valencia Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd); Valencia Spain
- School of Medicine; University of Valencia; Valencia Spain
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36
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Fabrizi F, Martin P, Lunghi G, Ponticelli C. Nosocomial Transmission of Hepatitis C virus Infection in Hemodialysis Patients: Clinical Perspectives. Int J Artif Organs 2018. [DOI: 10.1177/039139880002301205] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- F. Fabrizi
- Division of Nephrology and Dialysis, Maggiore Hospital IRCCS, Milano - Italy
| | - P. Martin
- Division of Digestive Diseases and Dumont-UCLA Transplant Center, UCLA School of Medicine, Los Angeles, California - USA
| | - G. Lunghi
- Institute of Hygiene and Preventive Medicine, Maggiore Hospital IRCCS, Milano - Italy
| | - C. Ponticelli
- Division of Nephrology and Dialysis, Maggiore Hospital IRCCS, Milano - Italy
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37
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Sorbo MC, Cento V, Di Maio VC, Howe AYM, Garcia F, Perno CF, Ceccherini-Silberstein F. Hepatitis C virus drug resistance associated substitutions and their clinical relevance: Update 2018. Drug Resist Updat 2018. [PMID: 29525636 DOI: 10.1016/j.drup.2018.01.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nowadays, due to the development of potent Direct-Acting Antiviral Agents (DAAs) that specifically target NS3, NS5A and NS5B viral proteins, several new and highly efficacious options to treat chronic Hepatitis C virus (HCV) infection are available. The natural presence of resistance associated substitutions (RASs), as well as their rapid emergence during incomplete drug-pressure, are intrinsic characteristics of HCV that greatly affect treatment outcome and the chances to achieve a virolgical cure. To date, a high number of RASs in NS3, NS5A, and NS5B have been associated in vivo and/or in vitro with reduced susceptibility to DAAs, but no comprehensive RASs list is available. This review thus provides an updated, systematic overview of the role of RASs to currently approved DAAs or in phase II/III of clinical development against HCV-infection, discriminating their impact in different HCV-genotypes and DAAs, providing assistance for a fruitful use of HCV resistance testing in clinical practice.
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Affiliation(s)
- Maria C Sorbo
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Valeria Cento
- Residency program in Microbiology and Virology, Università degli Studi di Milano. Milan, Italy.
| | - Velia C Di Maio
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Anita Y M Howe
- Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, BC, Canada
| | - Federico Garcia
- Clinical Microbiology Service, Hospital Universitario San Cecilio, Granada, Spain
| | - Carlo F Perno
- Department of Oncology and Oncohematology, Università degli Studi di Milano. Milan, Italy.
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38
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Starace M, Minichini C, De Pascalis S, Macera M, Occhiello L, Messina V, Sangiovanni V, Adinolfi LE, Claar E, Precone D, Stornaiuolo G, Stanzione M, Ascione T, Caroprese M, Zampino R, Parrilli G, Gentile I, Brancaccio G, Iovinella V, Martini S, Masarone M, Fontanella L, Masiello A, Sagnelli E, Punzi R, Salomone Megna A, Santoro R, Gaeta GB, Coppola N. Virological patterns of HCV patients with failure to interferon-free regimens. J Med Virol 2018; 90:942-950. [PMID: 29315640 DOI: 10.1002/jmv.25022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/29/2017] [Indexed: 01/02/2023]
Abstract
The study characterized the virological patterns and the resistance-associated substitutions (RASs) in patients with failure to IFN-free regimens enrolled in the real-life setting. All 87 consecutive HCV patients with failed IFN-free regimens, observed at the laboratory of the University of Campania, were enrolled. All patients had been treated with DAA regimens according to the HCV genotype, international guidelines, and local availability. Sanger sequencing of NS3, NS5A, and NS5B regions was performed at failure by home-made protocols. Of the 87 patients enrolled, 13 (14.9%) showed a misclassified HCV genotype, probably causing DAA failure, 16 had been treated with a sub-optimal DAA regimen, 19 with a simeprevir-based regimen and 39 with an optimal DAA regimen. A major RAS was identified more frequently in the simeprevir regimen group (68.4%) and in the optimal regimen group (74.4%) than in the sub-optimal regimen group (56.3%). The prevalence of RASs in NS3 was similar in the three groups (30.8-57.9%), that in NS5A higher in the optimal regimen group (71.8%) than in the sub-optimal regimen group (12.5%, P < 0.0001) and in the simeprevir regimen group (31.6%, P < 0.0005), and that in NS5B low in all groups (0-25%). RASs in two or more HCV regions were more frequently identified in the optimal regimen group (46.6%) than in the simeprevir-based regimen group (31.6%) and sub-optimal regimen group (18.7%). In our real-life population the prevalence of RASs was high, especially in NS3 and NS5A and in those treated with suitable DAA regimens.
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Affiliation(s)
- Mario Starace
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Carmine Minichini
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Stefania De Pascalis
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Margherita Macera
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Laura Occhiello
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | | | | | - Ernesto Claar
- Internal Medicine Unit, Evangelical Hospital Villa Betania, Naples, Italy
| | | | - Gianfranca Stornaiuolo
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Maria Stanzione
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Tiziana Ascione
- IX Interventional Ultrasound Unit for Infectious Diseases, AORN dei Colli, Naples, Italy
| | - Mara Caroprese
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Rosa Zampino
- Department of Medical, Surgical, Neurological, Metabolic, and Geriatric Sciences, University of Campania L. Vanvitelli, and Infectious and Transplant Medicine, AORN Ospedali dei Colli-Monaldi Hospital, Naples, Italy
| | - Gianpaolo Parrilli
- Gastroenterology Unit, AOU San Giovanni di Dio Ruggi d'Aragona, Salerno, Italy
| | - Ivan Gentile
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
| | - Giuseppina Brancaccio
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | | | - Mario Masarone
- Internal Medicine and Hepatology Unit, University of Salerno, Naples, Italy
| | - Luca Fontanella
- Internal Medicine Unit, AO Madonna del Buon Consiglio FATEBENEFRATELLI, Naples, Italy
| | | | - Evangelista Sagnelli
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Rodolfo Punzi
- Infectious Diseases Unit, AORN dei Colli, Naples, Italy
| | | | - Renato Santoro
- Infectious Diseases Unit, AOU San Giovanni di Dio Ruggi d'Aragona, Salerno, Italy
| | - Giovanni B Gaeta
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Nicola Coppola
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy.,Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
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39
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Li Z, Chen ZW, Li H, Ren H, Hu P. Prevalence of hepatitis C virus-resistant association substitutions to direct-acting antiviral agents in treatment-naïve hepatitis C genotype 1b-infected patients in western China. Infect Drug Resist 2017; 10:377-392. [PMID: 29184422 PMCID: PMC5673042 DOI: 10.2147/idr.s146595] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Direct-acting antivirals (DAAs) against hepatitis C virus (HCV) are potent and highly efficacious. However, resistance-associated substitutions (RASs) relevant to DAAs can impair treatment effectiveness even at baseline. Moreover, the prevalence of baseline RASs in HCV genotype 1b-infected patients in western China is still unclear. Materials and methods Direct sequencing of the HCV NS3, NS5A, and NS5B regions was performed in baseline serum samples of 70 DAAs treatment-naïve HCV 1b-infected patients in western China. The sequences were analyzed with MEGA version 5.05 software. Evolutionary patterns of RASs and amino-acid covariance patterns in the NS3, NS5A, and NS5B genes were analyzed by MEGA and Cytoscape (version 3.2.1), respectively. Results The presence of at least one RAS in the NS3 region (C16S, T54S, Q80R/L, A87T, R117H, S122G, V132I, V170I) was observed in 85.48% (53 of 62) of patients, RASs in the NS5A region (L28M, R30Q, Q54H, P58S/T, Q62H/R, Y93H) were observed in 42.42% (28 of 66) of patients, and RASs in the NS5B region (N142S, A300T, C316N, A338V, S365A, L392I, M414L, I424V, A442T, V499A, S556G) were observed in 100% (44 of 44) of patients. Evolutionary patterns of RASs and amino-acid covariance patterns for the NS3, NS5A, and NS5B genes are reported. Conclusion The prevalence of RASs relevant to DAAs detected in the NS3, NS5A, and NS5B regions of HCV 1b from DAA treatment-naïve patients is high. Therefore, more attention should be paid to RASs associated with DAAs in the upcoming DAA-treatment era in China.
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Affiliation(s)
- Zhao Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Wei Chen
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hu Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Ren
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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40
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Ali M, Khan T, Fatima K, Ali QUA, Ovais M, Khalil AT, Ullah I, Raza A, Shinwari ZK, Idrees M. Selected hepatoprotective herbal medicines: Evidence from ethnomedicinal applications, animal models, and possible mechanism of actions. Phytother Res 2017; 32:199-215. [PMID: 29047177 PMCID: PMC7167792 DOI: 10.1002/ptr.5957] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 08/30/2017] [Accepted: 09/26/2017] [Indexed: 02/06/2023]
Abstract
Insight into the hepatoprotective effects of medicinally important plants is important, both for physicians and researchers. Main reasons for the use of herbal medicine include their lesser cost compared with conventional drugs, lesser undesirable drug reactions and thus high safety, and reduced side effects. The present review focuses on the composition, pharmacology, and results of experimental trials of selected medicinal plants: Silybum marianum (L.) Gaertn., Glycyrrhiza glabra, Phyllanthus amarus Schumach. & Thonn., Salvia miltiorrhiza Bunge., Astragalus membranaceus (Fisch.) Bunge, Capparis spinosa (L.), Cichorium intybus (L.), Solanum nigrum (L.), Sapindus mukorossi Gaertn., Ginkgo biloba (L.), Woodfordia fruticosa (L.) Kurz, Vitex trifolia (L.), Schisandra chinensis (Turcz.) Baill., Cuscuta chinensis (Lam.), Lycium barbarum, Angelica sinensis (Oliv.) Diels, and Litsea coreana (H. Lev.). The probable modes of action of these plants include immunomodulation, stimulation of hepatic DNA synthesis, simulation of superoxide dismutase and glutathione reductase to inhibit oxidation in hepatocytes, reduction of intracellular reactive oxygen species by enhancing levels of antioxidants, suppression of ethanol-induced lipid accumulation, inhibition of nucleic acid polymerases to downregulate viral mRNA transcription and translation, free radical scavenging and reduction of hepatic fibrosis by decreasing the levels of transforming growth factor beta-1, and collagen synthesis in hepatic cells. However, further research is needed to identify, characterize, and standardize the active ingredients, useful compounds, and their preparations for the treatment of liver diseases.
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Affiliation(s)
- Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Tariq Khan
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan.,Department of Biotechnology, University of Malakand Chakdara Dir (L)-18000, Khyber Pakhtunkhwa, Pakistan
| | - Kaneez Fatima
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Qurat Ul Ain Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Muhammad Ovais
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Ali Talha Khalil
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Ikram Ullah
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Abida Raza
- National Institute of Laser and Optronics, Nilore, 45650, Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Muhammad Idrees
- Hazara University Mansehra, Khyber Pakhtunkhwa, 21120, Pakistan.,Center for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, 53700, Pakistan
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41
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Raj VS, Hundie GB, Schürch AC, Smits SL, Pas SD, Le Pogam S, Janssen HLA, de Knegt RJ, Osterhaus ADME, Najera I, Boucher CA, Haagmans BL. Identification of HCV Resistant Variants against Direct Acting Antivirals in Plasma and Liver of Treatment Naïve Patients. Sci Rep 2017; 7:4688. [PMID: 28680115 PMCID: PMC5498547 DOI: 10.1038/s41598-017-04931-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Current standard-of-care treatment of chronically infected hepatitis C virus (HCV) patients involves direct-acting antivirals (DAA). However, concerns exist regarding the emergence of drug -resistant variants and subsequent treatment failure. In this study, we investigate potential natural drug-resistance mutations in the NS5B gene of HCV genotype 1b from treatment-naïve patients. Population-based sequencing and 454 deep sequencing of NS5B gene were performed on plasma and liver samples obtained from 18 treatment- naïve patients. The quasispecies distribution in plasma and liver samples showed a remarkable overlap in each patient. Although unique sequences in plasma or liver were observed, in the majority of cases the most dominant sequences were shown to be identical in both compartments. Neither in plasma nor in the liver codon changes were detected at position 282 that cause resistance to nucleos(t)ide analogues. However, in 10 patients the V321I change conferring resistance to nucleos(t)ide NS5B polymerase inhibitors and in 16 patients the C316N/Y/H non-nucleoside inhibitors were found mainly in liver samples. In conclusion, 454-deep sequencing of liver and plasma compartments in treatment naïve patients provides insight into viral quasispecies and the pre-existence of some drug-resistant variants in the liver, which are not necessarily present in plasma.
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Affiliation(s)
- V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Viroclinics Biosciences BV, Rotterdam, The Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sophie Le Pogam
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Harry L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands.,Division of Gastroenterology, University Health Network, Toronto, Canada
| | - Rob J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Artemis One health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - Isabel Najera
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Charles A Boucher
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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Holmes JA, Yu ML, Chung RT. Hepatitis B reactivation during or after direct acting antiviral therapy - implication for susceptible individuals. Expert Opin Drug Saf 2017; 16:651-672. [PMID: 28471314 DOI: 10.1080/14740338.2017.1325869] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The FDA issued a warning following 24 cases of HBV reactivation during DAA therapy for HCV, including individuals with inactive, occult and past HBV infection. Clinical presentations ranged from asymptomatic fluctuations in HBV DNA to fulminant hepatic failure, liver transplantation and death. The mechanism is unknown. Areas covered: HCV/HBV coinfection is common, particularly in regions endemic for HBV. HCV and HBV utilize host factors to support replication; both viruses evade/impair host immunity. Clinical presentations of HBV reactivation during DAAs are summarized. Other causes of HBV reactivation are revisited and recent data regarding HBV reactivation are presented. Expert opinion: HBV reactivation during DAAs for HCV occurs, with life-threatening consequences in some individuals. The risk of HBV reactivation is observed in all HBV stages. The rapid removal of HCV likely alters and liberates host-viral ± viral-viral interactions that lead to increased HBV replication. As immune reconstitution occurs with HCV removal, host recognition of HBV DNA likely ensues followed by vigorous host immune responses leading to liver injury (HBV flare). These cases highlight the importance of HBV testing prior to initiating DAA therapy, the need for close monitoring of HBV during therapy and timely administration of anti-HBV therapy to prevent serious sequelae.
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Affiliation(s)
- Jacinta A Holmes
- a Gastrointestinal Unit , Massachusetts General Hospital , Boston , MA , USA.,b Department of Gastroenterology , St Vincent's Hospital, University of Melbourne , Fitzroy , Australia
| | - Ming-Lung Yu
- a Gastrointestinal Unit , Massachusetts General Hospital , Boston , MA , USA.,c Division of Hepatobiliary, Department of Internal Medicine and Hepatitis Center , Kaohsiung Medical University Hospital , Kaohsiung , Taiwan.,d Graduate Institute of Medicine, College of Medicine , Kaohsiung Medical University , Kaohsiung , Taiwan
| | - Raymond T Chung
- a Gastrointestinal Unit , Massachusetts General Hospital , Boston , MA , USA.,e Department of Medicine , Harvard Medical School , Boston , MA , USA
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Daniel HD, David J, Raghuraman S, Gnanamony M, Chandy GM, Sridharan G, Abraham P. Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India. J Clin Lab Anal 2017; 31:e22045. [PMID: 27580956 PMCID: PMC6816979 DOI: 10.1002/jcla.22045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/28/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis. METHODS In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing. RESULTS Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P < 0.00) and 96% (κ = 0.794, P < 0.00) correlated with NS5b sequencing, respectively. Sixty percent and 75% of discordant samples by 5'NCR PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods. CONCLUSION This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing.
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Affiliation(s)
| | - Joel David
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
| | | | - Manu Gnanamony
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
| | - George M. Chandy
- Department of Gastrointestinal SciencesChristian Medical CollegeVelloreIndia
| | - Gopalan Sridharan
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
| | - Priya Abraham
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
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Guinoiseau T, Moreau A, Hohnadel G, Ngo-Giang-Huong N, Brulard C, Vourc’h P, Goudeau A, Gaudy-Graffin C. Deep sequencing is an appropriate tool for the selection of unique Hepatitis C virus (HCV) variants after single genomic amplification. PLoS One 2017; 12:e0174852. [PMID: 28362878 PMCID: PMC5376297 DOI: 10.1371/journal.pone.0174852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/16/2017] [Indexed: 01/19/2023] Open
Abstract
Hepatitis C virus (HCV) evolves rapidly in a single host and circulates as a quasispecies wich is a complex mixture of genetically distinct virus’s but closely related namely variants. To identify intra-individual diversity and investigate their functional properties in vitro, it is necessary to define their quasispecies composition and isolate the HCV variants. This is possible using single genome amplification (SGA). This technique, based on serially diluted cDNA to amplify a single cDNA molecule (clonal amplicon), has already been used to determine individual HCV diversity. In these studies, positive PCR reactions from SGA were directly sequenced using Sanger technology. The detection of non-clonal amplicons is necessary for excluding them to facilitate further functional analysis. Here, we compared Next Generation Sequencing (NGS) with De Novo assembly and Sanger sequencing for their ability to distinguish clonal and non-clonal amplicons after SGA on one plasma specimen. All amplicons (n = 42) classified as clonal by NGS were also classified as clonal by Sanger sequencing. No double peaks were seen on electropherograms for non-clonal amplicons with position-specific nucleotide variation below 15% by NGS. Altogether, NGS circumvented many of the difficulties encountered when using Sanger sequencing after SGA and is an appropriate tool to reliability select clonal amplicons for further functional studies.
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Affiliation(s)
- Thibault Guinoiseau
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
- * E-mail:
| | - Alain Moreau
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
| | - Guillaume Hohnadel
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement (IRD) UMI 174 PHPT-Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Celine Brulard
- UMR INSERM U930, Université François Rabelais, Tours, France
| | - Patrick Vourc’h
- UMR INSERM U930, Université François Rabelais, Tours, France
| | - Alain Goudeau
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
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Current therapy for chronic hepatitis C: The role of direct-acting antivirals. Antiviral Res 2017; 142:83-122. [PMID: 28238877 PMCID: PMC7172984 DOI: 10.1016/j.antiviral.2017.02.014] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/07/2017] [Accepted: 02/22/2017] [Indexed: 12/12/2022]
Abstract
One of the most exciting developments in antiviral research has been the discovery of the direct-acting antivirals (DAAs) that effectively cure chronic hepatitis C virus (HCV) infections. Based on more than 100 clinical trials and real-world studies, we provide a comprehensive overview of FDA-approved therapies and newly discovered anti-HCV agents with a special focus on drug efficacy, mechanisms of action, and safety. We show that HCV drug development has advanced in multiple aspects: (i) interferon-based regimens were replaced by interferon-free regimens; (ii) genotype-specific drugs evolved to drugs for all HCV genotypes; (iii) therapies based upon multiple pills per day were simplified to a single pill per day; (iv) drug potency increased from moderate (∼60%) to high (>90%) levels of sustained virologic responses; (v) treatment durations were shortened from 48 to 12 or 8 weeks; and (vi) therapies could be administered orally regardless of prior treatment history and cirrhotic status. However, despite these remarkable achievements made in HCV drug discovery, challenges remain in the management of difficult-to-treat patients. HCV genotype-specific drugs evolve to pan-genotypic drugs. Drug potency increases from moderate (∼60%) to high (>90%) levels of sustained virologic response. Treatment durations are shortened from a 48-week to 12-week or 8-week period. HCV therapies based upon multiple pills per day are simplified to a single pill per day. HCV therapies are administered orally regardless of prior treatment history and cirrhotic status.
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Elevation of Alanine Aminotransferase Activity Occurs after Activation of the Cell-Death Signaling Initiated by Pattern-Recognition Receptors but before Activation of Cytolytic Effectors in NK or CD8+ T Cells in the Liver During Acute HCV Infection. PLoS One 2016; 11:e0165533. [PMID: 27788241 PMCID: PMC5082795 DOI: 10.1371/journal.pone.0165533] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023] Open
Abstract
Pattern-recognition receptors (PRRs) promote host defenses against HCV infection by binding to their corresponding adapter molecules leading to the initiation of innate immune responses including cell death. We investigated the expression of PRR genes, biomarkers of liver cell-death, and T cell and NK cell activation/inhibition-related genes in liver and serum obtained from three experimentally infected chimpanzees with acute HCV infection, and analyzed the correlation between gene expression levels and clinical profiles. Our results showed that expression of hepatic RIG-I, TLR3, TLR7, 2OAS1, and CXCL10 mRNAs was upregulated as early as 7 days post-inoculation and peaked 12 to 83 days post-inoculation. All of the three HCV infected chimpanzees exhibited significant elevations of serum alanine aminotransferase (ALT) activity between 70 and 95 days after inoculation. Elevated levels of serum cytokeratin 18 (CK-18) and caspases 3 and 7 activity coincided closely with the rise of ALT activity, and were preceded by significant increases in levels of caspase 3 and caspase 7 mRNAs in the liver. Particularly we found that significant positive auto-correlations were observed between RIG-I, TLR3, CXCL10, 2OAS1, and PD-L1 mRNA and ALT activity at 3 to 12 days before the peak of ALT activity. However, we observed substantial negative auto-correlations between T cell and NK cell activation/inhibition-related genes and ALT activity at 5 to 32 days after the peak of ALT activity. Our results indicated cell death signaling is preceded by early induction of RIG-I, TLR3, 2OAS1, and CXCL10 mRNAs which leads to elevation of ALT activity and this signaling pathway occurs before the activation of NK and T cells during acute HCV infection. Our study suggests that PRRs and type I IFN response may play a critical role in development of liver cell injury related to viral clearance during acute HCV infection.
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Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach. INFECTION GENETICS AND EVOLUTION 2016; 44:61-68. [DOI: 10.1016/j.meegid.2016.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 01/05/2023]
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Biochemical Characterization of the Active Anti-Hepatitis C Virus Metabolites of 2,6-Diaminopurine Ribonucleoside Prodrug Compared to Sofosbuvir and BMS-986094. Antimicrob Agents Chemother 2016; 60:4659-69. [PMID: 27216050 DOI: 10.1128/aac.00318-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/12/2016] [Indexed: 12/20/2022] Open
Abstract
Ribonucleoside analog inhibitors (rNAI) target the hepatitis C virus (HCV) RNA-dependent RNA polymerase nonstructural protein 5B (NS5B) and cause RNA chain termination. Here, we expand our studies on β-d-2'-C-methyl-2,6-diaminopurine-ribonucleotide (DAPN) phosphoramidate prodrug 1 (PD1) as a novel investigational inhibitor of HCV. DAPN-PD1 is metabolized intracellularly into two distinct bioactive nucleoside triphosphate (TP) analogs. The first metabolite, 2'-C-methyl-GTP, is a well-characterized inhibitor of NS5B polymerase, whereas the second metabolite, 2'-C-methyl-DAPN-TP, behaves as an adenosine base analog. In vitro assays suggest that both metabolites are inhibitors of NS5B-mediated RNA polymerization. Additional factors, such as rNAI-TP incorporation efficiencies, intracellular rNAI-TP levels, and competition with natural ribonucleotides, were examined in order to further characterize the potential role of each nucleotide metabolite in vivo Finally, we found that although both 2'-C-methyl-GTP and 2'-C-methyl-DAPN-TP were weak substrates for human mitochondrial RNA (mtRNA) polymerase (POLRMT) in vitro, DAPN-PD1 did not cause off-target inhibition of mtRNA transcription in Huh-7 cells. In contrast, administration of BMS-986094, which also generates 2'-C-methyl-GTP and previously has been associated with toxicity in humans, caused detectable inhibition of mtRNA transcription. Metabolism of BMS-986094 in Huh-7 cells leads to 87-fold higher levels of intracellular 2'-C-methyl-GTP than DAPN-PD1. Collectively, our data characterize DAPN-PD1 as a novel and potent antiviral agent that combines the delivery of two active metabolites.
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Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents. PLoS One 2016; 11:e0155869. [PMID: 27196673 PMCID: PMC4873220 DOI: 10.1371/journal.pone.0155869] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/05/2016] [Indexed: 12/18/2022] Open
Abstract
The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR) rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs). RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2pheno[HCV] (g2p[HCV]) to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir), the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir), and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir). Upon submission of up to eight sequences, g2p[HCV] aligns the input sequences, identifies the genomic region(s), predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2p[HCV] offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant, phenotypic cell culture assays obtained from patients’ virus variants.
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Trémeaux P, Caporossi A, Thélu MA, Blum M, Leroy V, Morand P, Larrat S. Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges. Crit Rev Clin Lab Sci 2016; 53:341-51. [PMID: 27068766 DOI: 10.3109/10408363.2016.1163663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.
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Affiliation(s)
- Pauline Trémeaux
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
| | - Alban Caporossi
- c Centre d'investigation clinique, Santé publique, CHU Grenoble-Alpes , Grenoble , France .,d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and
| | - Marie-Ange Thélu
- e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France
| | - Michael Blum
- d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and
| | - Vincent Leroy
- e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France
| | - Patrice Morand
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
| | - Sylvie Larrat
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
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