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Alobaida A, Abouzied AS, Younes KM, Alzhrani RM, Alsaab HO, Huwaimel B. Analyzing energetics and dynamics of hepatitis C virus polymerase interactions with marine bacterial compounds: a computational study. Mol Divers 2024:10.1007/s11030-024-10904-x. [PMID: 38856834 DOI: 10.1007/s11030-024-10904-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
Hepatitis C Virus (HCV) is a significant health concern affecting a large portion of the global population and is a major cause of acute liver diseases, including cirrhosis. The variability in the HCV genome mainly results from the rapid replication facilitated by the NS5B polymerase, making it a prime target for anti-HCV drug development. This study explores potential compounds from marine bacteria that could inhibit the HCV NS5B polymerase by virtual screening, analyzing the energetics, and dynamic behavior of target-compound complexes. Virtual screening with the Lipinski filter was employed to select compounds from the marine bacteria database that demonstrated strong binding affinity to NS5B. The top four (CMNPD27216, CMNPD21066, CMNPD21065, and CMNPD27283) compounds, ranked by their re-docking scores, underwent additional evaluation. Molecular dynamics simulations for 200 ns were conducted to assess the dynamic stability of these complexes in a solvent environment. Furthermore, methods such as MM-GBSA, PCA, and free energy landscape analysis were used to analyze the system's energetics and identify stable conformations by locating transition states. The findings suggest that these compounds exhibit promising binding capabilities to HCV polymerase and could be considered for future experimental validation.
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Affiliation(s)
- Ahmed Alobaida
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, 81442, Ha'il, Saudi Arabia
| | - Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia.
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12311, Egypt.
| | - Kareem M Younes
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Rami M Alzhrani
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Ha'il, 55473, Hail, Saudi Arabia
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Gregori J, Colomer-Castell S, Ibañez-Lligoña M, Garcia-Cehic D, Campos C, Buti M, Riveiro-Barciela M, Andrés C, Piñana M, González-Sánchez A, Rodriguez-Frias F, Cortese MF, Tabernero D, Rando-Segura A, Pumarola T, Esteban JI, Antón A, Quer J. In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications. Microorganisms 2024; 12:1011. [PMID: 38792840 PMCID: PMC11124460 DOI: 10.3390/microorganisms12051011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic agents of HEV, suggests that quasispecies structure may play a crucial role beyond single point mutations. Quasispecies structured in a flat-like manner (referred to as flat-like) are considered to possess high average fitness, occupy a significant fraction of the functional genetic space of the virus, and exhibit a high capacity to evade specific or mutagenic treatments. In this paper, we studied HEV and HCV samples using high-depth next-generation sequencing (NGS), with indices scoring the different properties describing flat-like quasispecies. The significance of these indices was demonstrated by comparing the values obtained from these samples with those from acute infections caused by respiratory viruses (betacoronaviruses, enterovirus, respiratory syncytial viruses, and metapneumovirus). Our results revealed that flat-like quasispecies in HEV and HCV chronic infections without RAS are characterized by numerous low-frequency haplotypes with no dominant one. Surprisingly, these low-frequency haplotypes (at the nucleotide level) exhibited a high level of synonymity, resulting in much lower diversity at the phenotypic level. Currently, clinical approaches for managing flat-like quasispecies are lacking. Here, we propose methods to identifying flat-like quasispecies, which represents an essential initial step towards exploring alternative treatment protocols for viruses resistant to conventional therapies.
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Affiliation(s)
- Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (J.I.E.)
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain;
| | - Marta Ibañez-Lligoña
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain;
| | - Maria Buti
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Mar Riveiro-Barciela
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Cristina Andrés
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.A.); (M.P.); (A.G.-S.); (A.A.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Maria Piñana
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.A.); (M.P.); (A.G.-S.); (A.A.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Alejandra González-Sánchez
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.A.); (M.P.); (A.G.-S.); (A.A.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Francisco Rodriguez-Frias
- 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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Biochemistry Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Basic Science Department, International University of Catalonia, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Maria Francesca Cortese
- 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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - David Tabernero
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Biochemistry Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Ariadna Rando-Segura
- 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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Tomás Pumarola
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.A.); (M.P.); (A.G.-S.); (A.A.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Biochemistry Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Andrés Antón
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.A.); (M.P.); (A.G.-S.); (A.A.)
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (M.I.-L.); (D.G.-C.); (C.C.); (M.B.); (M.R.-B.); (D.T.); (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; (F.R.-F.); (M.F.C.); (A.R.-S.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain;
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
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3
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Nayak D, Rathnanand M, Tippavajhala VK. Unlocking the Potential of Bilosomes and Modified Bilosomes: a Comprehensive Journey into Advanced Drug Delivery Trends. AAPS PharmSciTech 2023; 24:238. [PMID: 37989979 DOI: 10.1208/s12249-023-02696-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023] Open
Abstract
Vesicular drug delivery systems have revolutionized the pharmaceutical field, offering a promising path for achieving targeted and sustained drug delivery. The oral, transdermal, and ocular routes of administration offer optimal ease in attaining desired therapeutic outcomes. However, conventional treatment strategies are all plagued with several challenges, such as poor skin permeability, ocular barriers, and gastrointestinal (GIT) degradation leading to vesicular disruption with the release of the encapsulated drug before reaching the targeted site of action. In recent years, bilosomes-stabilized nanovesicles containing bile salts have received considerable attention due to their versatility and adaptability for diverse applications. These bilayered vesicles enhance the solubility of lipophilic drugs and improve formulation stability in the gastrointestinal tract. They exhibit ultra-deformable properties, improving stratum corneum permeability, making them ideal candidates for oral and transdermal drug delivery. In addition, bilosomes find utility in topical drug delivery, making them applicable for ocular administration. Over the past decade, extensive research has highlighted bilosomes' potential as superior vesicular carriers surpassing liposomes and niosomes. Advances in this field have led to the development of modified bilosomes, such as probilosomes and surface-modified bilosomes, further enhancing their capabilities and therapeutic potential. Thus, the present review provides a comprehensive summary of bilosomes, modified bilosomes, surface modifications with their mechanism of action, formulation components, preparation methods, patents, and a wide array of recent pharmaceutical applications in oral, transdermal, and ocular drug delivery. The enhanced properties of bilosomes offer promising prospects for targeted and effective drug delivery, providing potential solutions for addressing various therapeutic challenges.
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Affiliation(s)
- Devika Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mahalaxmi Rathnanand
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India.
| | - Vamshi Krishna Tippavajhala
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India.
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Faiz S, Irfan M, Farooq S, Khan IA, Iqbal H, Wahab AT, Shakeel M, Gong P, Iftner T, Choudhary MI. Study of drug resistance-associated genetic mutations, and phylo-genetic analysis of HCV in the Province of Sindh, Pakistan. Sci Rep 2023; 13:12213. [PMID: 37500705 PMCID: PMC10374889 DOI: 10.1038/s41598-023-39339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
Current management of HCV infection is based on Direct-Acting Antiviral Drugs (DAAs). However, resistance-associated mutations, especially in the NS3 and NS5B regions are gradually decreasing the efficacy of DAAs. The aim of the current study was to identify such mutations in the NS3, and NS5B genes in DAAs treatment-naïve Pakistani chronic HCV 3a patients. Peripheral blood samples were collected from 233 chronic HCV 3a patients at different tertiary care hospitals in Karachi, Pakistan, between August 2020 to September 2021. PCR-amplified target regions of the NS3/NS5B gene were subjected to Sanger sequencing to identify resistance-associated mutations. Phylogenetic analysis of the identified amino acid sequences was performed using HCV3a sequences of the global population in the virus pathogen resource (VIPR) database. Sequence analysis identified five amino acid mutations, Leu36Pro, Gln41His, Gln80Lys/Arg, Ala156Tyr, and Gln168Arg in the NS3 region, and two mutations Leu159Phe and Cys316Arg in the NS5B region. Phylogenetic analysis revealed a high genetic diversity in the studied isolates. Overall, the prevalence of resistance-associated substitutions was almost similar to other geographic regions worldwide. This data could be helpful in selecting the most effective treatment regimen for HCV chronically infected people in Pakistan.
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Affiliation(s)
- Sirmast Faiz
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan
| | - Saba Farooq
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan.
| | - Ishtiaq Ahmad Khan
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan.
| | - Hana'a Iqbal
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
| | - Atia-Tul Wahab
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Shakeel
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan
| | - Peng Gong
- Wuhan Institute of Virology, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, 430071, Hubei, China
| | - Thomas Iftner
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital and Medical Faculty, Eberhard Karls University, Tuebingen, Germany
| | - M Iqbal Choudhary
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan.
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de Mariz E Miranda LS. The synergy between nucleotide biosynthesis inhibitors and antiviral nucleosides: New opportunities against viral infections? Arch Pharm (Weinheim) 2023; 356:e2200217. [PMID: 36122181 DOI: 10.1002/ardp.202200217] [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: 04/22/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/04/2023]
Abstract
5'-Phosphorylated nucleoside derivatives are molecules that can be found in all living organisms and viruses. Over the last century, the development of structural analogs that could disrupt the transcription and translation of genetic information culminated in the development of clinically relevant anticancer and antiviral drugs. However, clinically effective broad-spectrum antiviral compounds or treatments are lacking. This viewpoint proposes that molecules that inhibit nucleotide biosynthesis may sensitize virus-infected cells toward direct-acting antiviral nucleosides. Such potentially synergistic combinations might allow the repurposing of drugs, leading to the development of new combination therapies.
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Affiliation(s)
- Leandro S de Mariz E Miranda
- Department of Organic Chemistry, Chemistry Institute, Biocatalysis and Organic Synthesis Group, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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6
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Rodrigues JPV, Campos GRF, Bittar C, Martinelli ADLC, Campos MSDA, Pereira LRL, Rahal P, Souza FF. Selection dynamics of HCV genotype 3 resistance-associated substitutions under direct-acting antiviral therapy pressure. Braz J Infect Dis 2022; 26:102717. [PMID: 36410397 PMCID: PMC9706524 DOI: 10.1016/j.bjid.2022.102717] [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: 06/22/2022] [Revised: 10/07/2022] [Accepted: 10/30/2022] [Indexed: 11/21/2022] Open
Abstract
The chronic hepatitis C (CHC) treatment is currently based on the use of direct-acting antivirals (DAAs), and patients infected with hepatitis C virus genotype 3 (GT3) have emerged as a more difficult-to-cure population. The NS5A inhibitor daclatasvir (DCV) and sofosbuvir (SOF), an NS5B viral polymerase inhibitor, are among the drugs that compose more effective and safer treatment regimens. The virus genetic variability is related to resistance-associated substitutions (RASs) that adversely impact DAAs effectiveness. The aims of this study were to analyze the association of NS5A and NS5B RASs and other clinical factors with DAAs regimens effectiveness in patients with GT3 CHC infection. This was a prospective cohort study performed in a Brazilian university hospital. Individuals older than 18 years with GT3 CHC treated with SOF + DCV ± ribavirin (RBV) or SOF + peginterferon (PEG) + RBV were included. Blood samples were collected at baseline and post-treatment. A total of 121 patients were included. Sustained virological response rates were 87.6% for the SOF + DCV ± RBV group and 80.0% for the SOF + PEG + RBV arm. Cirrhosis, prior treatment with interferon/PEG + RBV, and baseline NS5A RAS were associated with higher risk of treatment failure. The NS5A analysis suggested that A30K, Y93H, and RAS at site 62 were related to failure. Interestingly, a likely compensatory effect was shown between A30K and A62T. Emergence of Y93H was always associated with RAS at position 62. The RASs dynamics comprehension is an important tool to indicate more effective treatment for GT3 patients.
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Affiliation(s)
- João Paulo Vilela Rodrigues
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil.
| | | | - Cintia Bittar
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | | | - Marília Silveira de Almeida Campos
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Leonardo Régis Leira Pereira
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Paula Rahal
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | - Fernanda Fernandes Souza
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
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Abstract
The virus-encoded RNA-dependent RNA polymerase (RdRp) is responsible for viral replication, and its fidelity is closely related to viral diversity, pathogenesis, virulence, and fitness. Hepatitis C virus (HCV) and the second human pegivirus (HPgV-2) belong to the family Flaviviridae and share some features, including similar viral genome structure. Unlike HCV, HPgV-2 preserves a highly conserved genome sequence and low intrahost variation. However, the underlying mechanism remains to be elucidated. In this study, we evaluated the fidelity of HPgV-2 and HCV RdRp in an in vitro RNA polymerase reaction system. The results showed higher fidelity of HPgV-2 RdRp than HCV NS5B with respect to the misincorporation rate due to their difference in recognizing nucleoside triphosphate (NTP) substrates. Furthermore, HPgV-2 RdRp showed lower sensitivity than HCV to sofosbuvir, a nucleotide inhibitor against HCV RdRp, which explained the insusceptibility of HPgV-2 to direct-acting antiviral (DAA) therapy against HCV infection. Our results indicate that HPgV-2 could be an excellent model for studying the mechanisms involved in viral polymerase fidelity as well as RNA virus diversity and evolution. IMPORTANCE RNA viruses represent the most important pathogens for humans and animals and exhibit rapid evolution and high adaptive capacity, which is due to the high mutation rates for using the error-prone RNA-dependent RNA polymerase (RdRp) during replication. The fidelity of RdRp is closely associated with viral diversity, fitness, and pathogenesis. Previous studies have shown that the second human pegivirus (HPgV-2) exhibits a highly conserved genome sequence and low intrahost variation, which might be due to the fidelity of HPgV-2 RdRp. In this work, we used a series of in vitro RNA polymerase assays to evaluate the in vitro fidelity of HPgV-2 RdRp and compared it with that of HCV RdRp. The results indicated that HPgV-2 RdRp preserves significantly higher fidelity than HCV RdRp, which might contribute to the conservation of the HPgV-2 genome. The unique feature of HPgV-2 RdRp fidelity provides a new model for investigation of viral RdRp fidelity.
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8
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Mangrio GR, Maneengam A, Khalid Z, Jafar TH, Chanihoon GQ, Nassani R, Unar A. RP-HPLC Method Development, Validation, and Drug Repurposing of Sofosbuvir Pharmaceutical Dosage Form: A Multidimensional Study. ENVIRONMENTAL RESEARCH 2022; 212:113282. [PMID: 35487258 DOI: 10.1016/j.envres.2022.113282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
A smooth, exceptionally sensitive, correct, and extra reproducible RP-HPLC technique was developed and demonstrated to estimate Sofosbuvir (SOF) in pharmaceutical dosage formulations. This process was carried out by Agilent High-Pressure Liquid Chromatograph 1260 with GI311C Quat. Pump, Phenomenex Luna C-18 (150 mm × 4.6 mm × 5 μm) (USA), and Photodiode Array Detector (PDA) G1315D. The cell section, including acetonitrile and methanol with 80:20 v/v and solution (B) 0.1% phosphoric acid (40:60), was used for the study. However, 10 μL of the sample was injected with a drift flow of 1 mL/min. The separation occurred at a column temperature of 30 °C, and the eluents used PDA set at 260 nm. The retention time of SOF was 5 min. The calibration curve was modified linearly within the range of 0.05-0.15 mg/mL with a correlation coefficient of 0.99 and genuine linear dating among top vicinity and consciousness in the calibration curve. The detection and quantification restrictions were 0.001 and 0.003 mg/mL, respectively. SOF recovery from pharmaceutical components ranged from 98% to 99%. The percentage assay of SOF was 99%. Analytical validation parameters, such as specificity, linearity, precision, accuracy, and selectivity, were studied, and the percentage relative standard deviation (%RSD) was less than 2%. All other key parameters were observed within the desired thresholds. Hence, the proposed RP-HPLC technique was proven effective for developing SOF in bulk and pharmaceutical pill dosage forms. SOF was found to interact with SARS-COV-2 nsp12, and molecular docking results revealed its high affinity and firm binding within the active site groove of nsp12. The key interacting residues include; LYS-72, GLN-75, MET-80 ALA-99, ASN-99, TRP-100, TYR-101 with ASN-99 and TRP-100 forming hydrogen bonds. Molecular Dynamics simulation of SOF and nsp12 complex elucidated that the system was stable throughout 20ns. Therefore, this drug repurposing strategy for SOF can be used for treating COVID-19 infections by performing animal experiments and accurate clinical trials in the future.
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Affiliation(s)
| | - Apichit Maneengam
- Department of Mechanical Engineering Technology, College of Industrial Technology, King Mongkut's University of Technology North Bangkok, Wongsawang, Bangsue, Bangkok, 10800, Thailand
| | - Zunera Khalid
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China
| | | | - Ghulam Qadir Chanihoon
- National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76090, Pakistan
| | - Rayan Nassani
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ahsanullah Unar
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China.
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9
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Younas S, Sumrin A, Hussain N, Bilal M. Identification of NS5B Resistance against SOFOSBUVIR in Hepatitis C Virus Genotype 3a, naive and treated Patients. J Appl Microbiol 2022; 133:2826-2834. [PMID: 35916643 DOI: 10.1111/jam.15754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022]
Abstract
AIMS Pakistan has the second highest prevalence of HCV with genotype 3a (GT-3a) being the most frequently circulating genotype. Currently resistance associated substitutions (RASs) are a major challenge in HCV treatment with direct acting antivirals (DAAs). Sofosbuvir (SOF) is an FDA-approved NS5B nucleotide inhibitor. The aim of this study was to identify these RASs in the NS5B gene in naive and treated Pakistani HCV 3a isolates against SOF. METHODS AND RESULTS Blood samples were collected from anti-HCV positive patients, followed by HCV RNA isolation and real time PCR quantification. HCV positive patients were processed for HCV RNA genotyping, Patients with genotype 3a were processed for NS5B gene amplification and sequencing. GT-3a was the most prevalent genotype (62.2%). S282T was identified in 2 (8.7%) patients, C316Y/G/R in 3 (13%), V321A, and L320P in 1 (4.3%) each in SOF/RBV resistant patients. Variants of S282 were detected in 3 (13%) of SOF/RBV treated patients. While INF/RBV associated mutations were also analyzed, D244N, A333R, and A334E were identified in 2 (9.5%), 3 (14.2%), and 7 (33.3%) in treatment-naive and 15 (65.2%), 7 (30.4%), and 5 (21.7%) treated patients respectively. Q309R was observed only in one treatment experienced patients. Some substitutions were present at higher frequency in both groups like N307G, K304R, A272D and R345H, considered that they do not have any role in Sofosbuvir resistance. CONCLUSION It was concluded that Sofosbuvir RASs are present in Pakistani HCV GT-3a isolates, and they should be monitored carefully, especially in treatment-experienced patients, for further selection of treatment regimens. SIGNIFICANCE AND IMPACT OF STUDY HCV RASs have been studied very well across the world but there is scarcity of data regarding this topic in Pakistani population, this study provides data regarding prevalence of these RASs in Pakistani HCV isolates emphasizing the fact that these RASs must be carefully monitored before starting HCV treatment especially in treatment failure patients.
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Affiliation(s)
- Saima Younas
- Centre for Applied Molecular Biology (CAMB), University of the Punjab Lahore, Pakistan
| | - Aleena Sumrin
- Centre for Applied Molecular Biology (CAMB), University of the Punjab Lahore, Pakistan
| | - Nazim Hussain
- Centre for Applied Molecular Biology (CAMB), University of the Punjab Lahore, Pakistan
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
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10
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Forgiveness of INSTI-Containing Regimens at Drug Concentrations Simulating Variable Adherence In Vitro. Antimicrob Agents Chemother 2022; 66:e0203821. [PMID: 35389236 PMCID: PMC9112893 DOI: 10.1128/aac.02038-21] [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] [Indexed: 12/02/2022] Open
Abstract
The integrase strand transfer inhibitor (INSTI)-based regimens bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF), dolutegravir (DTG)+FTC/TAF, DTG/lamivudine (3TC), and DTG/rilpivirine (RPV) are all approved for treatment of HIV-infected patients, with various limitations. Here, time to in vitro viral breakthrough (VB) and resistance barrier using simulated human drug exposures at either full or suboptimal treatment adherence to each regimen were compared. At drug concentrations corresponding to full adherence and 1 missed dose (Cmin and Cmin−1), no VB occurred with any regimen. At Cmin−2, VB occurred only with DTG+3TC, with emergent resistance to both drugs. At Cmin−3, VB occurred with all regimens: 100% of DTG+3TC cultures had VB by day 12, and <15% of BIC+FTC+TAF, DTG+FTC+TAF, and DTG+RPV cultures had VB. Emergent reverse transcriptase (RT) or integrase (IN) resistance was seen with DTG+RPV and DTG+3TC but not with BIC+FTC+TAF or DTG+FTC+TAF. At Cmin−4, 100% VB occurred with DTG+3TC and DTG+FTC+TAF by day 12, while 94% VB occurred with DTG+RPV by day 25 and only 50% VB occurred with BIC+FTC+TAF by day 35. Emergent Cmin−4 drug resistance was seen with all regimens but at differing frequencies; DTG+RPV had the most cultures with resistance. Emergent resistance was consistent with clinical observations. Overall, under high adherence conditions, no in vitro VB or resistance development occurred with these INSTI-based regimens. However, when multiple missed doses were simulated in vitro, BIC+FTC+TAF had the highest forgiveness and barrier to resistance of all tested regimens. Compared to DTG+3TC and DTG+FTC+TAF, DTG+RPV had higher forgiveness but lower resistance barrier after several simulated missed doses.
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11
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Loucks CM, Lin JJ, Trueman JN, Drögemöller BI, Wright GEB, Chang WC, Li KH, Yoshida EM, Ford JA, Lee SS, Crotty P, Kim RB, Al-Judaibi B, Schwarz UI, Ramji A, Farivar JF, Tam E, Walston LL, Ross CJD, Carleton BC. Patient-specific genetic factors predict treatment failure in sofosbuvir-treated patients with chronic hepatitis C. Liver Int 2022; 42:796-808. [PMID: 35107877 DOI: 10.1111/liv.15175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/12/2022] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS According to pivotal clinical trials, cure rates for sofosbuvir-based antiviral therapy exceed 96%. Treatment failure is usually assumed to be because of virological resistance-associated substitutions or clinical risk factors, yet the role of patient-specific genetic factors has not been well explored. We determined if patient-specific genetic factors help predict patients likely to fail sofosbuvir treatment in real-world treatment situations. METHODS We recruited sofosbuvir-treated patients with chronic hepatitis C from five Canadian treatment sites, and performed a case-control pharmacogenomics study assessing both previously published and novel genetic polymorphisms. Specifically studied were variants predicted to impair CES1-dependent production of sofosbuvir's active metabolite, interferon-λ signalling variants expected to impact a patient's immune response to the virus and an HLA variant associated with increased spontaneous and treatment-induced viral clearance. RESULTS Three hundred and fifty-nine sofosbuvir-treated patients were available for analyses after exclusions, with 34 (9.5%) failing treatment. We identified CES1 variants as novel predictors for treatment failure in European patients (rs115629050 or rs4513095; odds ratio (OR): 5.43; 95% confidence interval (CI): 1.64-18.01; P = .0057), replicated associations with IFNL4 variants predicted to increase interferon-λ signalling (eg rs12979860; OR: 2.25; 95% CI: 1.25-4.06; P = .0071) and discovered a novel association with a coding variant predicted to enhance the activity of IFNL4's receptor (rs2834167 in IL10RB; OR: 1.81; 95% CI: 1.01-3.24; P = .047). CONCLUSIONS Ultimately, this work demonstrates that patient-specific genetic factors could be used as a tool to identify patients at higher risk of treatment failure and allow for these patients to receive effective therapy sooner.
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Affiliation(s)
- Catrina M Loucks
- BC Children's Hospital Research Institute, Vancouver, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada.,Department of Anesthesiology, Pharmacology & Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Jennifer J Lin
- BC Children's Hospital Research Institute, Vancouver, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Jessica N Trueman
- BC Children's Hospital Research Institute, Vancouver, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Galen E B Wright
- Department of Pharmacy and Therapeutics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Wan-Chun Chang
- BC Children's Hospital Research Institute, Vancouver, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Kathy H Li
- BC Children's Hospital Research Institute, Vancouver, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Eric M Yoshida
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Jo-Ann Ford
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Samuel S Lee
- Liver Unit, University of Calgary Cumming School of Medicine, Calgary, Canada
| | - Pam Crotty
- Liver Unit, University of Calgary Cumming School of Medicine, Calgary, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Canada
| | - Bandar Al-Judaibi
- Division of Transplantation, University of Rochester, Rochester, New York, USA.,Department of Liver Transplantation and Hepatobiliary Surgery, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Canada
| | - Alnoor Ramji
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, Canada
| | | | | | | | - Colin J D Ross
- BC Children's Hospital Research Institute, Vancouver, Canada.,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada.,Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, Canada
| | - Bruce C Carleton
- BC Children's Hospital Research Institute, Vancouver, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada.,Pharmaceutical Outcomes Program (POPi), British Columbia Children's Hospital, Vancouver, Canada
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12
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Clement Dobbins G, Kimberlin D, Ross S. Cytomegalovirus variation among newborns treated with valganciclovir. Antiviral Res 2022; 203:105326. [DOI: 10.1016/j.antiviral.2022.105326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022]
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13
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Shoun AA, Abozahra R, Baraka K, Mehrez M, Abdelhamid SM. Identifying Different Mutation Sites Leading to Resistance to the Direct-Acting Antiviral (DAA) Sofosbuvir in Hepatitis C Virus Patients from Egypt. Microorganisms 2022; 10:microorganisms10040679. [PMID: 35456731 PMCID: PMC9024585 DOI: 10.3390/microorganisms10040679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
The hepatitis C virus (HCV) is a major global health challenge and a leading cause of morbidity and mortality. Many direct-acting antivirals (DAAs) target essential macromolecules involved in the virus’ life cycle. Although such DAAs achieve great success in reducing the viral load in genotype 1 infections, other genotypes demonstrate different levels of response. This study focused on mutation sites associated with patients with genotype 4a infections that failed to respond to treatment with sofosbuvir. The genotyping of HCV samples from patients with virological failure, and responder patients, was conducted using Geno2Pheno webserver-based full NS5B sequences. We constructed 3D structural models for all the samples and used structural analysis to investigate the effect of amino acid substitution on the observed resistance to SOF-based treatment, and the docking of sofosbuvir into the active sites of the 10 models was performed. Finally, 10 molecular dynamic (MD) simulation experiments were conducted to compare the stability of the 3D models of the resistant samples against the stability of the 3D models of the responder samples. The results highlighted the presence of HCV subtype 4a in all ten samples; in addition, an amino acid (aa) substitution in the palm region may hinder HCV polymerase activity. In this study, we provide evidence that a mutation in the NS5B gene that induces resistance to sofosbuvir in patients with the S282T/C/R mutant virus is present in the Egyptian population. Overall, the docking and MD results support our findings and highlight the significant impact of the identified mutations on the resistance of HCV NS5B RNA-dependent RNA polymerase to direct-acting antivirals (DAAs).
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Affiliation(s)
- Aly Atef Shoun
- Microbiology and Immunology Department, Faculty of Pharmacy, Sinai University, El Arish 45518, Egypt
- Correspondence:
| | - Rania Abozahra
- Microbiology and Immunology Department, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt; (R.A.); (K.B.); (S.M.A.)
| | - Kholoud Baraka
- Microbiology and Immunology Department, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt; (R.A.); (K.B.); (S.M.A.)
| | - Mai Mehrez
- National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo 11511, Egypt;
| | - Sarah M. Abdelhamid
- Microbiology and Immunology Department, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt; (R.A.); (K.B.); (S.M.A.)
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14
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Adeboyejo K, Grosche VR, José DP, Ferreira GM, Shimizu JF, King BJ, Tarr AW, Soares MMCN, Ball JK, McClure CP, Jardim ACG. Simultaneous determination of HCV genotype and NS5B resistance associated substitutions using dried serum spots from São Paulo state, Brazil. Access Microbiol 2022; 4:000326. [PMID: 35693474 PMCID: PMC9175972 DOI: 10.1099/acmi.0.000326] [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: 06/10/2021] [Accepted: 12/30/2021] [Indexed: 11/26/2022] Open
Abstract
Hepatitis C virus (HCV) is responsible for more than 180 million infections worldwide, and about 80 % of infections are reported in Low and Middle-income countries (LMICs). Therapy is based on the administration of interferon (INF), ribavirin (RBV) or more recently Direct-Acting Antivirals (DAAs). However, amino acid substitutions associated with resistance (RAS) have been extensively described and can contribute to treatment failure, and diagnosis of RAS requires considerable infrastructure, not always locally available. Dried serum spots (DSS) sampling is an alternative specimen collection method, which embeds drops of serum onto filter paper to be transported by posting to a centralized laboratory. Here, we assessed feasibility of genotypic analysis of HCV from DSS in a cohort of 80 patients from São Paulo state Brazil. HCV RNA was detected on DSS specimens in 83 % of samples of HCV infected patients. HCV genotypes 1a, 1b, 2a, 2c and 3a were determined using the sequence of the palm domain of NS5B region, and RAS C316N/Y, Q309R and V321I were identified in HCV 1b samples. Concerning therapy outcome, 75 % of the patients who used INF +RBV as a previous protocol of treatment did not respond to DAAs, and 25 % were end-of-treatment responders. It suggests that therapy with INF plus RBV may contribute for non-response to a second therapeutic protocol with DAAs. One patient that presented RAS (V321I) was classified as non-responder, and combination of RAS C316N and Q309R does not necessarily imply in resistance to treatment in this cohort of patients. Data presented herein highlights the relevance of studying circulating variants for a better understanding of HCV variability and resistance to the therapy. Furthermore, the feasibility of carrying out genotyping and RAS phenotyping analysis by using DSS card for the potential of informing future treatment interventions could be relevant to overcome the limitations of processing samples in several location worldwide, especially in LMICs.
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Affiliation(s)
- Kazeem Adeboyejo
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Victória Riquena Grosche
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Bioscience, Language and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | | | - Giulia Magalhães Ferreira
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Jacqueline Farinha Shimizu
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Bioscience, Language and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Barnabas J King
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK.,MRC/EPSRC Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
| | - Alexander W Tarr
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK.,MRC/EPSRC Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
| | | | - Jonathan K Ball
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK.,MRC/EPSRC Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
| | - C Patrick McClure
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK.,MRC/EPSRC Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Bioscience, Language and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
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15
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Smith DA, Fernandez-Antunez C, Magri A, Bowden R, Chaturvedi N, Fellay J, McLauchlan J, Foster GR, Irving WL, Simmonds P, Pedergnana V, Ramirez S, Bukh J, Barnes E, Ansari MA. Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure. Nat Commun 2021; 12:6105. [PMID: 34671027 PMCID: PMC8528821 DOI: 10.1038/s41467-021-25649-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.
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Affiliation(s)
- David A Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Graham R Foster
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - William L Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and 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 and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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16
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Malandris K, Kalopitas G, Theocharidou E, Germanidis G. The Role of RASs /RVs in the Current Management of HCV. Viruses 2021; 13:2096. [PMID: 34696525 PMCID: PMC8539246 DOI: 10.3390/v13102096] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022] Open
Abstract
The approval of combination therapies with direct-acting antiviral (DAA) regimens has led to significant progress in the field of hepatitis C virus (HCV) treatment. Although most patients treated with these agents achieve a virological cure, resistance to DAAs is a major issue. The rapid emergence of resistance-associated substitutions (RASs), in particular in the context of incomplete drug pressure, has an impact on sustained virological response (SVR) rates. Several RASs in NS3, NS5A and NS5B have been linked with reduced susceptibility to DAAs. RAS vary based on HCV characteristics and the different drug classes. DAA-resistant HCV variant haplotypes (RVs) are dominant in cases of virological failure. Viruses with resistance to NS3-4A protease inhibitors are only detected in the peripheral blood in a time frame ranging from weeks to months following completion of treatment, whereas NS5A inhibitor-resistant viruses may persist for years. Novel agents have been developed that demonstrate promising results in DAA-experienced patients. The recent approval of broad-spectrum drug combinations with a high genetic barrier to resistance and antiviral potency may overcome the problem of resistance.
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Affiliation(s)
- Konstantinos Malandris
- Second Department of Internal Medicine, Hippokration General Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (K.M.); (E.T.)
| | - Georgios Kalopitas
- First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Eleni Theocharidou
- Second Department of Internal Medicine, Hippokration General Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (K.M.); (E.T.)
| | - Georgios Germanidis
- First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
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17
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Liu Z, Mao X, Wu J, Yu K, Yang Q, Suo C, Lu M, Jin L, Zhang T, Chen X. World-wide Prevalence of Substitutions in HCV Genome Associated With Resistance to Direct-Acting Antiviral Agents. Clin Gastroenterol Hepatol 2021; 19:1906-1914.e25. [PMID: 31683059 DOI: 10.1016/j.cgh.2019.10.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/07/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The efficacy of direct-acting antiviral agents against hepatitis C virus (HCV) infection can be compromised by substitutions in the HCV genome that occur before treatment (resistance-associated substitutions [RASs]). We performed a meta-analysis to determine the prevalence of RASs and their effects. METHODS We searched publication databases for studies of HCV RNA substitutions that mediate resistance to direct-acting antiviral agents. Findings from 50 studies of the prevalence of RAS in HCV, from 32 countries, were used in a meta-analysis. We retrieved the HCV RNA sequence from the Los Alamos HCV sequence database to estimate the prevalence of the RASs. The degree of resistance to treatment conferred by each RAS was determined based on fold-change in the 50% effective concentration of the drugs. RESULTS Our final analysis included data from 49,744 patients with HCV infection and 12,612 HCV sequences. We estimated the prevalence of 56 RASs that encoded amino acids and 114 specific RASs. The average prevalence of RASs was highest in HCV genotype (GT) 6, followed by HCV GT1a, GT2, GT1b, GT3, and GT4. The highest prevalence of RASs observed encoded Q80K in NS3 to NS4A of HCV GT1a, Y93T in NS5A of GT1a, and C316N in NS5B of GT1b. The greatest number of RASs were observed at D168 in NS3 to NS4A, at Y93 in NS5A, and at C316 in NS5B. The prevalence of RASs and mutation burdens were high in Japan, the United States, Germany, Thailand, and the United Kingdom; low in Russia, Brazil, Egypt, and India; and intermediate in China, Canada, Australia, Spain, and France. CONCLUSIONS In a meta-analysis, we found evidence for 114 RASs in HCV of different genotypes. Patients with HCV infection should be tested for RASs before treatment is selected, especially in regions with a high prevalence of RASs.
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Affiliation(s)
- Zhenqiu Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Xianhua Mao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Jiaqi Wu
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Kangkang Yu
- Department of Infectious Diseases, Huashan Hospital, Shanghai, China
| | - Qin Yang
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Suo
- Department of Epidemiology, School of Public Health, Shanghai, China; Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Beijing, China
| | - Ming Lu
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, China; Human Phenome Institute, Fudan University, Shanghai, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Shanghai, China; Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Beijing, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, China; Human Phenome Institute, Fudan University, Shanghai, China.
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18
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Garcia-Cehic D, Rando A, Rodriguez-Frias F, Gregori J, Costa JG, Carrión JA, Macenlle R, Pamplona J, Castro-Iglesias A, Cañizares A, Tabernero D, Campos C, Buti M, Esteban JI, Quer J. Resistance-associated substitutions after sofosbuvir/velpatasvir/voxilaprevir triple therapy failure. J Viral Hepat 2021; 28:1319-1324. [PMID: 33720484 DOI: 10.1111/jvh.13497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/05/2023]
Abstract
Direct-acting antivirals (DAAs) resolve chronic HCV infection in >95% of patients, but a small percentage do not respond to DAA-based therapy. These may be difficult to treat because of resistance-associated substitutions (RAS) emerging after treatment failure. Triple therapy with sofosbuvir (SOF)/velpatasvir (VEL)/voxilaprevir (VOX) is the recommended retreatment after DAA-based failure. However, in rare cases, failure to triple therapy occurs, and there is little information characterizing the viruses that relapse. To determine the RAS profile after failing SOF/VEL/VOX, and seek suitable alternatives for retreatment, samples from 5 patients were analysed using MiSeq Illumina deep sequencing before and after triple therapy. All patients were men, aged 59-78 years, 2 HCV genotype (G) 1b and 3 G3a. The most prevalent NS3 substitutions after SOF/VEL/VOX failure were Y56F and A166T. Four patients had the NS5A RAS, Y93H, after triple failure, and Y93H was observed in both G1b patients before retreatment and after SOF/ledipasvir failure. In 2 G3a patients, Y93H appeared at triple failure, and on the other G3a, A30K persisted in 100% of viral genomes. Finally, G1b patients showed C316N in NS5B, associated with SOF failure, but G3a patients had no known NS5B substitutions. HCV RAS analysis identified the following substitutions present at higher rates after triple failure: Y56F in NS3 (G1b), A166T in NS3 (G3a), A30K or Y93H in NS5A, and C316N in NS5B (G1b). A RAS-based salvage treatment (SOF + glecaprevir/pibrentasvir + RBV) was successfully used in one G3a patient.
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Affiliation(s)
- 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, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Ariadna Rando
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 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, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain
| | - Juan Garcia Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - José Antonio Carrión
- Liver Section, Gastroenterology Department, Hospital del Mar, Parc de Salur Mar, Barcelona, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Javier Pamplona
- Gastroenterology Department, Hospital de Santa Caterina, Salt. Girona, Spain
| | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Buti
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - 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, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 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, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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19
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Kong F, Wen X, Wen X, Wang X, Wu G, Lin S, Wang L, Xing H, Yan X, Zheng S, Ning Q, Wang Z, Zhang L, Lin J, Tong Z, Huang C, Su M, Tong L, Jia J, Xin Y, Zhu Q, Wang J, Chen L, Li X, Wu X, Niu D, Liu Q, Wei W, Zhang Y, Li G, Niu J. Seraprevir and sofosbuvir for treatment of chronic hepatitis C virus infection: A single-arm, open-label, phase 3 trial. J Gastroenterol Hepatol 2021; 36:2375-2382. [PMID: 33491236 PMCID: PMC8518536 DOI: 10.1111/jgh.15412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/13/2020] [Accepted: 01/13/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND AND AIM This single-arm, open-label, multicenter, phase 3 trial evaluated the efficacy and safety of seraprevir, an hepatitis C virus (HCV) nonstructural protein 3/4A (NS3/4A) inhibitor, combined with sofosbuvir for treating Chinese patients with chronic HCV infection without cirrhosis. METHODS Treatment-naive or interferon-experienced adult patients without cirrhosis were treated with a universal, combinational regimen of seraprevir 100 mg, twice daily and sofosbuvir 400 mg, once daily, for 12 or 24 weeks. The primary efficacy endpoint was sustained virologic response at week 12 after treatment (SVR12). RESULTS Overall, 205 patients with genotype 1 HCV infection without cirrhosis were enrolled from 23 sites, 202 of whom completed the full treatment and post-treatment course and 3 discontinued follow-up. In total, 27 patients (13.2%) were interferon experienced. SVR12 was achieved by 201 out of 205 (98.0% [95% CI, 95.1%, 99.5%]) patients, 100.0% of patients with genotype 1a, and 98.0% of genotype 1b. In the other exploratory study, SVR 12 was achieved by 100% patients with genotype 2 (n = 21), genotype 3 (n = 7), and genotype 6 (n = 8). The majority of adverse events were mild to moderate and transient and did not require a specific medical intervention. CONCLUSIONS The all-oral, ribavirin-free regimen of seraprevir and sofosbuvir is an effective and well-tolerated treatment option for Chinese patients mono-infected with HCV, including those with a history of interferon treatment.
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Affiliation(s)
- Fei Kong
- Department of HepatologyThe First Hospital of Jilin UniversityChangchunChina,Department of Epidemiology and Biostatistics, School of Public HealthJilin UniversityChangchunChina
| | - Xiaoyu Wen
- Department of HepatologyThe First Hospital of Jilin UniversityChangchunChina
| | - Xiaofeng Wen
- Department of HepatologyLiuzhou People's HospitalLiuzhouChina
| | - Xiaozhong Wang
- Department of HepatologyXinjiang Uygur Autonomous Region Traditional Chinese Medicine HospitalUrumqiChina
| | - Guicheng Wu
- Department of HepatologyChongqing University Three Gorges Hosipital, Chongqing Three Gorges Central HospitalChongqingChina
| | - Shide Lin
- Department of Infectious DiseasesAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Li Wang
- Department of HepatologyPublic Health Clinical Center of ChengduChengduChina
| | - Huichun Xing
- Department of Hepatology Division 3Beijing Ditan Hospital, Capital Medical UniversityBeijingChina
| | - Xuebing Yan
- Department of Infectious DiseaseThe Affiliated Hospital of Xuzhou Medical UniversityXuzhouChina
| | - Sujun Zheng
- Difficult and Complicated Liver Diseases and Artificial Liver CenterBeijing YouAn Hospital, Capital Medical UniversityBeijingChina
| | - Qin Ning
- Department of Infectious Diseases, Tongji Hospital Affiliated to Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Zheng Wang
- Department of Infectious DiseasesWuxi No. 5 People's HospitalWuxiChina
| | - Liaoyun Zhang
- Department of Infectious DiseasesThe First Affiliated Hospital of Shanxi Medical UniversityTaiyuanChina
| | - Jianmei Lin
- Department of Infectious DiseasesSichuan Provincial People's HospitalChengduChina
| | - Zhaowei Tong
- Department of Infectious DiseasesHuzhou Central HospitalHuzhouChina
| | - Chengyu Huang
- Department of HepatologyChongqing Public Health Medical CenterChongqingChina
| | - Minghua Su
- Department of Infectious DiseaseThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Lixin Tong
- Center of Liver DiseasesThe First Affiliated Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Jidong Jia
- Liver Research Center, Beijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Yongning Xin
- Department of Infectious DiseaseQingdao Municipal HospitalQingdaoChina
| | - Qingjing Zhu
- Department of HepatologyWuhan Public Health Medical CenterWuhanChina
| | - Jing Wang
- Department of HepatologyThe Affiliated TCM Hospital of Southwest Medical UniversityLuzhouChina
| | - Li Chen
- General Manager OfficeShanghai Viromedicine Co., Ltd.ShanghaiChina
| | - Xiaowen Li
- General Manager OfficeShanghai Viromedicine Co., Ltd.ShanghaiChina
| | - Xuegang Wu
- Department of Clinical ResearchShanghai Viromedicine Co., Ltd.ShanghaiChina
| | - Duan Niu
- Department of Clinical ResearchShanghai Viromedicine Co., Ltd.ShanghaiChina
| | - Quan Liu
- Department of Emerging Infectious Diseases, Institute of Translational MedicineThe First Hospital of Jilin UniversityChangchunChina
| | - Wei Wei
- Institute of Virology and AIDS ResearchThe First Hospital of Jilin UniversityChangchunChina
| | - Yuexin Zhang
- Department of Infectious DiseasesFirst Affiliated Hospital of Xinjiang Medical UniversityUrumqiChina
| | - Guangming Li
- Cirrhosis DepartmentZhengzhou Sixth Municipal People's HospitalZhengzhouChina
| | - Junqi Niu
- Department of HepatologyThe First Hospital of Jilin UniversityChangchunChina
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20
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Lapointe HR, Dong W, Dong WWY, Kirkby D, Woods C, Poon AFY, Howe AYM, Harrigan PR, Brumme CJ. Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay. Viruses 2021; 13:v13091721. [PMID: 34578305 PMCID: PMC8473162 DOI: 10.3390/v13091721] [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: 06/18/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the effectiveness of direct-acting antiviral agents in treating hepatitis C virus (HCV), cases of treatment failure have been associated with the emergence of resistance-associated substitutions. To better guide clinical decision-making, we developed and validated a near-whole-genome HCV genotype-independent next-generation sequencing strategy. HCV genotype 1-6 samples from direct-acting antiviral agent treatment-naïve and -treated HCV-infected individuals were included. Viral RNA was extracted using a NucliSens easyMAG and amplified using nested reverse transcription-polymerase chain reaction. Libraries were prepared using Nextera XT and sequenced on the Illumina MiSeq sequencing platform. Data were processed by an in-house pipeline (MiCall). Nucleotide consensus sequences were aligned to reference strain sequences for resistance-associated substitution identification and compared to NS3, NS5a, and NS5b sequence data obtained from a validated in-house assay optimized for HCV genotype 1. Sequencing success rates (defined as achieving >100-fold read coverage) approaching 90% were observed for most genotypes in samples with a viral load >5 log10 IU/mL. This genotype-independent sequencing method resulted in >99.8% nucleotide concordance with the genotype 1-optimized method, and 100% agreement in genotype assignment with paired line probe assay-based genotypes. The assay demonstrated high intra-run repeatability and inter-run reproducibility at detecting substitutions above 2% prevalence. This study highlights the performance of a freely available laboratory and bioinformatic approach for reliable HCV genotyping and resistance-associated substitution detection regardless of genotype.
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Affiliation(s)
- Hope R. Lapointe
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Winnie W. Y. Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Don Kirkby
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Conan Woods
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Anita Y. M. Howe
- British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada;
| | - P. Richard Harrigan
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
| | - Chanson J. Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence:
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21
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Di Maio VC, Barbaliscia S, Teti E, Fiorentino G, Milana M, Paolucci S, Pollicino T, Morsica G, Starace M, Bruzzone B, Gennari W, Micheli V, Yu La Rosa K, Foroghi L, Calvaruso V, Lenci I, Polilli E, Babudieri S, Aghemo A, Raimondo G, Sarmati L, Coppola N, Pasquazzi C, Baldanti F, Parruti G, Perno CF, Angelico M, Craxì A, Andreoni M, Ceccherini-Silberstein F. Resistance analysis and treatment outcomes in hepatitis C virus genotype 3-infected patients within the Italian network VIRONET-C. Liver Int 2021; 41:1802-1814. [PMID: 33497016 DOI: 10.1111/liv.14797] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 12/20/2022]
Abstract
AIM This study aimed to investigate the role of resistance-associated substitutions (RASs) to direct-acting-antivirals (DAAs) in HCV genotype 3 (GT3). METHODS Within the Italian VIRONET-C network, a total of 539 GT3-infected patients (417 DAA-naïve and 135 DAA-failures, of them, 13 at both baseline and failure) were analysed. Sanger sequencing of NS3/NS5A/NS5B was performed following home-made protocols. RESULTS The majority of patients were male (79.4%), 91.4% were injection drug users, 49.3% were cirrhotic and 13.9% were HIV co-infected. Phylogenetic analysis classified sequences as GT3a-b-g-h (98%-0.4%-0.2%-1.2%) respectively. Overall, 135 patients failed a DAA regimen: sofosbuvir (SOF)/daclatasvir (DCV) or velpatasvir (VEL)±ribavirin (RBV) (N = 91/15) and glecaprevir (G)/pibrentasvir (P) (N = 9). Moreover, 14.8% of patients were treated with suboptimal regimens for GT3: 3D ± RBV (Paritaprevir/r + Ombitasvir+Dasabuvir, N = 15), SOF + Simeprevir (SIM) (N = 1) or SOF/Ledipasvir (LDV) ± RBV (N = 4). RAS prevalence was 15.8% in DAA-naïve patients. At failure, 81.5% patients showed at least one RAS: 11/25 (44.0%) in NS3, 109/135 (80.7%) in NS5A, 7/111 (6.3%) in NS5B SOF-failures. In NS5A-failures, Y93H RAS was the most prevalent (68.5% vs 5.1% DAA-naïve, P < .001) followed by A30K (12.7% vs 2.8% in DAA-naïve, P < .001). Analysing baseline samples, a higher prevalence of NS5A-RASs was observed before treatment in DAA-failures (5/13, 38.5%) vs DAA-naïves (61/393, 15.5%, P = .04). Regarding 228 DAA-naïve patients with an available outcome, 93.9% achieved a SVR. Interestingly, patients with baseline Y93H and/or A30K had SVR rate of 72.2% vs 95.7% for patients without NS5A-RASs (P = .002). CONCLUSIONS In this real-life GT3 cohort, the majority of failures harboured resistant variants carrying NS5A-RASs, the most frequent being Y93H. The presence of natural NS5A-RASs before treatment was associated with failure. Further analyses are needed to confirm this observation, particularly for the new current regimens.
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Affiliation(s)
- Velia Chiara Di Maio
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Barbaliscia
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Elisabetta Teti
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | | | - Martina Milana
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinic Foundation San Matteo, Pavia, Italy
| | - Teresa Pollicino
- Department of Internal Medicine, University Hospital of Messina, Messina, Italy
| | - Giulia Morsica
- Division of Infectious Diseases, IRCCS, Ospedale San Raffaele, Milan, Italy
| | - Mario Starace
- Laboratory for the identification of prognostic factors of response to the treatment against infectious diseases, University of Campania "L. Vanvitelli", Napoli, Italy
| | | | - William Gennari
- Microbiology Unit, University Hospital of Modena, Modena, Italy
| | - Valeria Micheli
- Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco University Hospital, Milan, Italy
| | - Katia Yu La Rosa
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Luca Foroghi
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | | | - Ilaria Lenci
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Ennio Polilli
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | - Sergio Babudieri
- Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Alessio Aghemo
- Division of Internal Medicine and Hepatology, Humanitas Clinical and Research Center IRCCS, Rozzano, Italy
| | - Giovanni Raimondo
- Department of Internal Medicine, University Hospital of Messina, Messina, Italy
| | - Loredana Sarmati
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Nicola Coppola
- Laboratory for the identification of prognostic factors of response to the treatment against infectious diseases, University of Campania "L. Vanvitelli", Napoli, Italy.,Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinic Foundation San Matteo, Pavia, Italy
| | - Giustino Parruti
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | | | - Mario Angelico
- Hepatology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Antonio Craxì
- Gastroenterology, "P. Giaccone" University Hospital, Palermo, Italy
| | - Massimo Andreoni
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
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22
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Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs. Sci Rep 2021; 11:9986. [PMID: 33976241 PMCID: PMC8113533 DOI: 10.1038/s41598-021-88132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Most individuals chronically infected with hepatitis C virus (HCV) are asymptomatic during the initial stages of infection and therefore the precise timing of infection is often unknown. Retrospective estimation of infection duration would improve existing surveillance data and help guide treatment. While intra-host viral diversity quantifications such as Shannon entropy have previously been utilized for estimating duration of infection, these studies characterize the viral population from only a relatively short segment of the HCV genome. In this study intra-host diversities were examined across the HCV genome in order to identify the region most reflective of time and the degree to which these estimates are influenced by high-risk activities including those associated with HCV acquisition. Shannon diversities were calculated for all regions of HCV from 78 longitudinally sampled individuals with known seroconversion timeframes. While the region of the HCV genome most accurately reflecting time resided within the NS3 gene, the gene region with the highest capacity to differentiate acute from chronic infections was identified within the NS5b region. Multivariate models predicting duration of infection from viral diversity significantly improved upon incorporation of variables associated with recent public, unsupervised drug use. These results could assist the development of strategic population treatment guidelines for high-risk individuals infected with HCV and offer insights into variables associated with a likelihood of transmission.
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Ahmed HR, Waly NGFM, Abd El-Baky RM, Yahia R, Hetta HF, Elsayed AM, Ibrahem RA. Distribution of naturally -occurring NS5B resistance-associated substitutions in Egyptian patients with chronic Hepatitis C. PLoS One 2021; 16:e0249770. [PMID: 33857212 PMCID: PMC8049381 DOI: 10.1371/journal.pone.0249770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Background NS5B polymerase inhibitors represent the cornerstone of the present treatment of Hepatitis C virus infection (HCV). Naturally occurring substitution mutations to NS5B inhibitors have been recorded. The current study intended to demonstrate possible natural direct acting antiviral (DAA)—mutations of the HCV NS5B region in HCV patients in Minia governorate, Egypt. Methods Samples were collected from 27 treatment-naïve HCV patients and 8 non-responders. Out of 27 treatment-naïve patients, 17 NS5B sequences (amino acids 221–345) from treatment-naïve patients and one sample of non-responders were successfully amplified. Nucleotide sequences have been aligned, translated into amino acids, and compared to drug resistance mutations reported in the literature. Results NS5B amino acid sequence analysis ensures several novel NS5B mutations existence (more than 40 substitution mutations) that have not been previously documented to be correlated with a resistant phenotype. It was found that K304R (82.4%), E327D and P300T (76.5% each) substitutions were the most distributed in the tested samples, respectively. S282T, the major resistance mutation that induces high sofosbuvir-resistance level in addition to other reported mutations (L320F/C) and (C316Y/N) were not recognized. Q309R mutation is a ribavirin-associated resistance, which was recognized in one strain (5.9%) of genotype 1g sequences. Besides, one substitution mutation (E237G) was identified in the successfully amplified non-responder sample. Conclusion Our study showed various combinations of mutations in the analyzed NS5B genes which could enhance the possibility of therapy failure in patients administered regimens including multiple DAA.
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Affiliation(s)
- Hala Rady Ahmed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Nancy G. F. M. Waly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Rehab Mahmoud Abd El-Baky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia, Egypt
- * E-mail: ,
| | - Ramadan Yahia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Merit University, Sohag, Egypt
| | - Amr M. Elsayed
- Tropical Medicine and Gastroenterology, Faculty of Medicine, Minia University, Minia, Egypt
| | - Reham Ali Ibrahem
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, Egypt
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Dar GA, Yattoo GN, Gulzar GM, Sodhi JS, Gorka S, Laway MA. Treatment of Chronic Hepatitis C Genotype 3 With Ledipasvir and Sofosbuvir: An Observational Study. J Clin Exp Hepatol 2021; 11:227-231. [PMID: 33746448 PMCID: PMC7953013 DOI: 10.1016/j.jceh.2020.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 06/14/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Sofosbuvir/ledipasvir (SOF/LED) is recommended for treatment of genotypes 1, 4, 5 and 6. Despite some preliminary data from the ELECTRON-2 trial regarding use of SOF/LED combination in chronic hepatitis C genotype 3, there are no guidelines recommending this combination in such patients. We conducted this study to evaluate the efficacy of the overall sustained virologic response at 12 weeks (SVR 12) and safety of SOF/LED in chronic hepatitis C genotype 3 infection in our population. METHODS It was a prospective, hospital-based observational study. All patients with chronic hepatitis C genotype 3 treated with SOF/LED were divided into two groups: patients with cirrhosis and without cirrhosis. Patients without cirrhosis received SOF/LED (90/400 mg) for 12 weeks; however, patients with cirrhosis received treatment for 24 weeks. RESULTS We enrolled 104 patients with chronic hepatitis C over a period of 24 months. Of the total, 66 were women (63.5%) and 38 were men (36.5%). The average age was 40 years (range: 18-76 years). Of 104 patients, 86 (82.7%) were of genotype 3, 15 (14.9%) were of genotype 1 and 3 (2.9%) were of genotype 4. Ninety-two (88%) were noncirrhotic and 12 (11.5%) were cirrhotic. Ninety-five (95.2%) were treatment naïve. Among genotype 1 and 4, all patients achieved rapid virologic response and SVR 12. Of 86 genotype 3 patients, 78 (90.6%) were noncirrhotic and 8 (9.3%) were cirrhotic. Among genotype 3 patients without cirrhosis, 75 (96%) achieved SVR 12 while 6 (75%) with cirrhosis achieved SVR 12. All patients tolerated the combination well; however, some patients experienced nausea (26%), headache (25%) and fatigue (21%). No patient had to discontinue therapy due to adverse drug reactions. CONCLUSIONS Single tablet LED and SOF combination is safe and effective in genotype 3 patients without cirrhosis even without ribavirin. Being effective in genotype 3, the combination can be used as a pangenotypic drug in patients without cirrhosis.
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Affiliation(s)
- Gulzar A. Dar
- Department of Gastroenterology, SKIMS, Srinagar, India
| | | | | | | | - Suresh Gorka
- Department of Gastroenterology, SKIMS, Srinagar, India
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Mulato A, Acosta R, Chang S, Martin R, Yant SR, Cihlar T, White K. Simulating HIV Breakthrough and Resistance Development During Variable Adherence to Antiretroviral Treatment. J Acquir Immune Defic Syndr 2021; 86:369-377. [PMID: 33196554 DOI: 10.1097/qai.0000000000002562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/26/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Barriers to lifelong HIV-1 suppression by antiretrovirals include poor adherence and drug resistance; regimens with higher tolerance to missed doses (forgiveness) would be beneficial to patients. To model short-term nonadherence, in vitro experiments monitoring viral breakthrough (VB) and resistance development were conducted. METHODS HIV breakthrough experiments simulated drug exposures at full adherence or suboptimal adherence to bictegravir+emtricitabine+tenofovir alafenamide (BIC+FTC+TAF) or dolutegravir + lamivudine (DTG+3TC). MT-2 cells were infected with wild-type or low frequency M184V HIV-1, exposed to drug combinations, monitored for VB, and rebound virus was deep sequenced. Drug concentrations were determined using human plasma-free adjusted clinical trough concentrations (Cmin), at simulated Cmin after missing 1 to 3 consecutive doses (Cmin - 1 or Cmin - 2, and Cmin - 3) based on drug or active metabolite half-lives. RESULTS Cultures infected with wild-type or low frequency M184V HIV-1 showed no VB with BIC+FTC+TAF at drug concentrations corresponding to Cmin, Cmin - 1, or Cmin - 2 but breakthrough did occur in 26 of 36 cultures at Cmin - 3, where the M184V variant emerged in one culture. Experiments using DTG + 3TC prevented most breakthrough at Cmin concentrations (9/60 had breakthrough) but showed more breakthroughs as drug concentrations decreased (up to 36/36) and variants associated with resistance to both drugs emerged in some cases. CONCLUSIONS These in vitro VB results suggest that the high potency, long half-lives, and antiviral synergy provided by the BIC/FTC/TAF triple therapy regimen may protect from viral rebound and resistance development after short-term lapses in drug adherence.
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Maheden K, Todd B, Gordon CJ, Tchesnokov EP, Götte M. Inhibition of viral RNA-dependent RNA polymerases with clinically relevant nucleotide analogs. Enzymes 2021; 49:315-354. [PMID: 34696837 PMCID: PMC8517576 DOI: 10.1016/bs.enz.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The treatment of viral infections remains challenging, in particular in the face of emerging pathogens. Broad-spectrum antiviral drugs could potentially be used as a first line of defense. The RNA-dependent RNA polymerase (RdRp) of RNA viruses serves as a logical target for drug discovery and development efforts. Herein we discuss compounds that target RdRp of poliovirus, hepatitis C virus, influenza viruses, respiratory syncytial virus, and the growing data on coronaviruses. We focus on nucleotide analogs and mechanisms of action and resistance.
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Affiliation(s)
- Kieran Maheden
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Brendan Todd
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, AB, Canada.
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El-Sokkary MMA, Gotina L, Al-Sanea MM, Pae AN, Elbargisy RM. Molecular Characterization of Hepatitis C Virus for Developed Antiviral Agents Resistance Mutations and New Insights into in-silico Prediction Studies. Infect Drug Resist 2020; 13:4235-4248. [PMID: 33262618 PMCID: PMC7696641 DOI: 10.2147/idr.s267809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/24/2020] [Indexed: 02/05/2023] Open
Abstract
Background Identification and characterization of developed antiviral drug resistance mutations are key to the success of antiviral therapies against hepatitis C virus (HCV), which remains a worldwide highly prevalent pathogenic disease. Although most studies focus on HCV genotypes 1, 2 or 3, the investigation of drug resistance in HCV genotype 4, predominant in North Africa, is especially significant in Egypt. Methods We performed mutational and genotypic analysis of the untranslated region (UTR) and nonstructural protein 5B (NS5B) drug resistance-associated regions of HCV for patients in the surrounding villages of Mansoura city, who were not responding to different antiviral treatments (sofosbuvir (SOF), ribavirin, and interferon). Furthermore, molecular modelling approaches (homology modelling and docking studies) were used to investigate the significance of the identified NS5B mutations for SOF and ribavirin binding in the HCV genotype 4a NS5B active site. Results Genotypic analysis confirmed all samples to have genotype 4 with sub-genotype 4a predominant. Partial sequencing of the UTR and NS5B resistance-associated regions identified D258E, T282S and A307G mutations in all isolates of NS5B. The UTR mutation site at position 243 was associated with interferon resistance, whereas the NS5B T282S mutation was considered as significant for SOF and ribavirin resistance. Docking studies in the HCV genotype 4a homology model predict SOF and ribavirin to accommodate a nucleotide-like binding mode, in which the T282 residue does interfere with the binding as it would in HCV genotypes 1 and 2. Mutation energy calculations predict T282S to moderately destabilize the binding of SOF and ribavirin by 0.57 and 0.47 kcal/mol, respectively. Conclusion The performed study identified and characterized several antiviral drug resistance mutations of HCV genotype 4a and proposed a mechanism by which the T282S mutation may contribute to SOF and ribavirin resistance.
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Affiliation(s)
- Mohamed M Adel El-Sokkary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Lizaveta Gotina
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Mohammad M Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Ae Nim Pae
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Rehab Mohammed Elbargisy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
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Joseph Naguib M, Moustafa Kamel A, Thabet Negmeldin A, Elshafeey AH, Elsayed I. Molecular docking and statistical optimization of taurocholate-stabilized galactose anchored bilosomes for the enhancement of sofosbuvir absorption and hepatic relative targeting efficiency. Drug Deliv 2020; 27:996-1009. [PMID: 32611266 PMCID: PMC8216436 DOI: 10.1080/10717544.2020.1787557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 02/08/2023] Open
Abstract
The work aimed to improve both absorption and hepatic availability of sofosbuvir. Bilosomes and galactose-anchored bilosomes were investigated as potential nanocarriers for this purpose. Sofosbuvir is a class III drug with high solubility and low permeability. Thus, the drug entrapment into lipid-based galactose-anchored carriers would enhance drug permeability and improve its liver availability. The galactosylated taurocholate was designed and synthesized based on molecular docking studies, where both galactose and taurocholate molecules were connected in a way to avoid affecting crucial interactions and avoid steric clashes with their cellular uptake receptors. The suggested nano-carriers were prepared using a thin-film hydration technique with sodium taurocholate and span 60 as stabilizers. The prepared formulae were statistically optimized using a central composite design. The optimized plain and galactosylated formulae, composed of SAA to drug ratio of 1:1 w/w and sodium taurocholate to span ratio of 10:1 w/w, have a vesicular size, zeta potential and entrapment efficiency in the range of 140-150 nm, -50 mV and 85%, respectively. The optimized formulae were lyophilized to increase their physical stability and facilitate accurate drug dosing. In vivo results showed that Sofosbuvir availability in the liver was significantly increased after oral administration of the plain and the galactosylated bilosomal formulae when compared to the oral drug solution with relative targeting efficiencies (RTIs) of 1.51 and 3.66, respectively. These findings confirmed the hypothesis of considering the galactosylated bilosomes a promising nanocarrier to efficiently target sofosbuvir to the liver.
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Affiliation(s)
- Marianne Joseph Naguib
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Ahmed Thabet Negmeldin
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Department of Pharmaceutical Sciences, College of Pharmacy and Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, UAE
| | - Ahmed Hassen Elshafeey
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ibrahim Elsayed
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Department of Pharmaceutical Sciences, College of Pharmacy and Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, UAE
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Soria ME, García-Crespo C, Martínez-González B, Vázquez-Sirvent L, Lobo-Vega R, de Ávila AI, Gallego I, Chen Q, García-Cehic D, Llorens-Revull M, Briones C, Gómez J, Ferrer-Orta C, Verdaguer N, Gregori J, Rodríguez-Frías F, Buti M, Esteban JI, Domingo E, Quer J, Perales C. Amino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus Infection. J Clin Microbiol 2020; 58:JCM.01985-20. [PMID: 32999010 PMCID: PMC7685896 DOI: 10.1128/jcm.01985-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Despite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide resistance-associated substitutions (RAS), from 220 patients who failed therapy. They were present frequently in basal and posttreatment virus of patients who failed different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. They also have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value for treatment response, are discussed.
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Affiliation(s)
- María Eugenia Soria
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Brenda Martínez-González
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Qian Chen
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Damir García-Cehic
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Meritxell Llorens-Revull
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Astrobiología (CAB, CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L., Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
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Lee J, Parvathareddy J, Yang D, Bansal S, O'Connell K, Golden JE, Jonsson CB. Emergence and Magnitude of ML336 Resistance in Venezuelan Equine Encephalitis Virus Depend on the Microenvironment. J Virol 2020; 94:e00317-20. [PMID: 32878897 PMCID: PMC7592223 DOI: 10.1128/jvi.00317-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is a New World Alphavirus that can cause neurological disease and death in humans and equines following transmission from infected mosquitoes. Despite the continued epidemic threat of VEEV, and its potential use as a bioterrorism agent, there are no FDA-approved antivirals or vaccines for treatment or prevention. Previously, we reported the discovery of a small molecule, ML336, with potent antiviral activity against VEEV. To further explore the population-level resistance profiles of ML336, we developed a whole-genome next-generation sequencing (NGS) approach to examine single nucleotide polymorphisms (SNPs) from virus passaged in dose escalation studies in a nonhuman primate kidney epithelial and a human astrocyte cell line, Vero 76 and SVGA, respectively. We passaged VEEV TC-83 in these two cell lines over seven concentrations of ML336, starting at 50 nM. NGS revealed several prominent mutations in the nonstructural protein (nsP) 3 and nsP4 genes that emerged consistently in these two distinct in vitro environments-notably, a mutation at Q210 in nsP4. Several of these mutations were stable following passaging in the absence of ML336 in Vero 76 cells. Network analyses showed that the trajectory of resistance differed between Vero and SVGA. Moreover, the penetration of SNPs was lower in SVGA. In conclusion, we show that the microenvironment influenced the SNP profile of VEEV TC-83. Understanding the dynamics of resistance in VEEV against newly developed antiviral compounds will guide the design of optimal drug candidates and dosing regimens for minimizing the emergence of resistant viruses.IMPORTANCE RNA viruses, including Venezuelan equine encephalitis virus (VEEV), have high mutation rates that allow for rapid adaptation to selective pressures in their environment. Antiviral compounds exert one such pressure on virus populations during infections. Next-generation sequencing allows for examination of viruses at the population level, which enables tracking of low levels of single-nucleotide polymorphisms in the population over time. Therefore, the timing and extent of the emergence of resistance to antivirals can be tracked and assessed. We show here that in VEEV, the trajectory and penetration of antiviral resistance reflected the microenvironment in which the virus population replicates. In summary, we show the diversity of VEEV within a single population under antiviral pressure and two distinct cell types, and we show that population dynamics in these viruses can be examined to better understand how they evolve over time.
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Affiliation(s)
- Jasper Lee
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Dong Yang
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Shruti Bansal
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Kathryn O'Connell
- Laboratory Animal Care Unit, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jennifer E Golden
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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31
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Rodriguez C, Mercier-Darty M, Soulier A, Poiteau L, Wlassow M, Fourati S, Hézode C, Pawlotsky JM, Chevaliez S. Performance assessment of a fully automated deep sequencing platform for HCV resistance testing. Antivir Ther 2020; 24:417-423. [PMID: 31112134 DOI: 10.3851/imp3318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND International liver society guidelines recommended to perform HCV resistance testing at baseline of first-line therapy with certain combination regimens or prior to retreatment in patients previously exposed to a direct-acting antiviral (DAA) containing regimen. Currently, no standardized assays have been developed as purchasable kits for HCV resistance testing. The aim of this study was to evaluate the performance of the Sentosa SQ HCV Genotyping Assay, a novel deep sequencing-based assay, to identify resistance-associated substitutions (RASs) in the NS3 protease, NS5A protein domain I and NS5B polymerase regions for patients infected with HCV genotypes-1a and 1b. METHODS Serum samples collected from patients with chronic hepatitis C infection who failed to achieve a sustained virological response after receiving a DAA-containing treatment regimen were extracted and sequenced by two methods including population sequencing of the NS3, NS5A and NS5B coding region reference method and the deep sequencing-based Sentosa SQ HCV Genotyping Assay. RESULTS A high concordance rate with Sanger sequencing, the reference method, was found for the NS3, NS5A and NS5 coding regions, regardless of the genotype-1 subtypes. The deep sequencing-based assay was more sensitive than population sequencing to detect minority variants, representing less than 10% of the viral populations, but also some variants representing up to 30% of the viral quasispecies, as expected. CONCLUSIONS The Sentosa SQ HCV Genotyping Assay can be confidently used in clinical practice in the indications of HCV resistance testing for these subtypes. Technical improvements are now required to allow for pangenotypic coverage.
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Affiliation(s)
- Christophe Rodriguez
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Mélanie Mercier-Darty
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Alexandre Soulier
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Lila Poiteau
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Mélanie Wlassow
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Slim Fourati
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Christophe Hézode
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Stéphane Chevaliez
- Department of Virology, National Reference Center for Viral Hepatitis B, C and Delta, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
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32
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El-Tahan RR, Ghoneim AM, Zaghloul H. Dissection of two drug-targeted regions of Hepatitis C virus subtype 4a infecting Egyptian patients. Virus Genes 2020; 56:564-581. [PMID: 32572756 PMCID: PMC7307947 DOI: 10.1007/s11262-020-01776-y] [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: 12/21/2019] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Recently, treatment of HCV infection has been improved after the development of direct acting antivirals (DAAs) which target different viral proteins (NS3-4A, NS5A and NS5B). The activity and effectiveness of these DAAs are affected by the presence of resistance associated substitutions (RASs). This study aimed to characterize HCV genotypes circulating among Egyptian HCV patients, to dissect the full sequences of HCV NS3-4A and NS5B regions, and to characterize RASs associated with NS3-4A and NS5B inhibitors in HCV treatment-naïve patients. Genotyping of 80 HCV samples from treatment-naïve patients was done using restriction fragment length polymorphism and phylogenetic analysis based on some full NS5B sequences. Results showed the prevalence of HCV subtype 4a. Twenty four new full sequences of NS3-4A and NS5B regions of subtype 4a were deposited in the GenBank database. In general, the substitutions associated with NS3-4A-targeting drugs were absent predicting possible responsiveness of Egyptian HCV patients to these drugs. In addition, the absence of amino acid substitutions associated with resistance to Sofosbuvir may predict good response to treatment with Sofosbuvir. Some amino acid substitutions associated with resistance to different classes of non-nucleoside inhibitors were detected. Further investigations on treated Egyptian HCV patients may evaluate the effectiveness of the massively used drugs. Many predicted T-cell-binding epitopes in NS3-4A and NS5B regions were found to be highly conserved in the currently studied isolates; a finding that might be important for HCV vaccine development. We demonstrated potential NS3 epitopes that could be used in engineering T cells against HCV epitopes.
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Affiliation(s)
- Radwa R El-Tahan
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt
| | - Ahmed M Ghoneim
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt.
| | - Hosam Zaghloul
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Sofosbuvir as a potential alternative to treat the SARS-CoV-2 epidemic. Sci Rep 2020; 10:9294. [PMID: 32518317 PMCID: PMC7283245 DOI: 10.1038/s41598-020-66440-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023] Open
Abstract
As of today, there is no antiviral for the treatment of the SARS-CoV-2 infection, and the development of a vaccine might take several months or even years. The structural superposition of the hepatitis C virus polymerase bound to sofosbuvir, a nucleoside analog antiviral approved for hepatitis C virus infections, with the SARS-CoV polymerase shows that the residues that bind to the drug are present in the latter. Moreover, a multiple alignment of several SARS-CoV-2, SARS and MERS-related coronaviruses polymerases shows that these residues are conserved in all these viruses, opening the possibility to use sofosbuvir against these highly infectious pathogens.
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Aguiar BF, Campos GRF, Rodrigues JPV, Marques NN, Molina BF, Bittar C, Souza FF, Martinelli ADLC, Rahal P, Pereira LRL. Baseline resistance associated substitutions in HCV genotype 1 infected cohort treated with Simeprevir, Daclatasvir and Sofosbuvir in Brazil. Clin Res Hepatol Gastroenterol 2020; 44:329-339. [PMID: 31523019 DOI: 10.1016/j.clinre.2019.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/18/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND The World Health Organization estimates that 1% of the world population (71 million) is infected with hepatitis C virus (HCV). In 2015, three direct-acting antivirals (DAAs), simeprevir (SMV), sofosbuvir (SOF) and daclatasvir (DCV) were included in the Brazilian protocol for the treatment of chronic hepatitis C. Despite the fact that the use of these drugs is associated with higher treatment response rates and with lower incidence of side effects, studies have shown the association between the presence of viral resistance mutations and the failure of pharmacological treatment. AIM This way, this study aimed to evaluate the safety and effectiveness of treatment for HCV genotypes 1a and 1b infected patients with these DAAs, also analyzing the occurrence and prevalence of baseline resistance associated substitutions (RAS), observing the impact of these mutations into the treatment success. METHODS Clinical data were collected from all the 262 HCV infected patients included for comparative analysis, while serum samples collected from 144 of these individuals, before treatment, were submitted to molecular biology approaches for mutation analysis into NS3, NS5A and NS5B regions. RESULTS Regarding the treatment regimens, 49.6% of the patients received SOF+DCV±ribavirin and 50.4% used SOF+SMV±ribavirin. The sustained virological response at 12 weeks post-treatment (SVR12) rate was 92.7% (93.9% for SOF plus DCV and 91.7% for SOF plus SMV). No clinical or laboratorial factor was statistically associated with SVR. The most common adverse reactions were haematological events, nausea/vomiting, headache and asthenia. Out of 144 blood samples, 70 (48.6%) had detected RAS, 34.8% treated with SOF+DCV±ribavirin and 61.3% SOF+SMV±ribavirin. The resistance mutations against SMV were detected into NS3: substitutions G122S (28%), I170V (22.7%), Y56F (17.3%) and V132I (14.7%). The mutations against DCV R30Q (9.1%), P58H (6.1%) and Q62E (6.1%) were observed into NS5A, and for SOF the mutations A421V (10.6%), L159F (6.4%) and C316N (6.4%) were present inside NS5B viral protein. Four patients did not reach SVR, three of them presented viruses carrying RAS (1 treated with SOF+DCV and 2 with SOF+SMV). Some of these mutations, like R30Q (present in relapsing samples) and L159F, are well known by their influence on antiviral resistance, while others, like C316N, have a compensatory effect on viral fitness, maintaining these baseline RAS. CONCLUSION The use of treatment regimens composed of SOF and DCV or SOF and SMV showed a high SVR rate, despite of a high rate of RAS, and a good tolerability profile in patients with HCV genotype 1. However, the high occurrence of baseline RAS observed in this casuistic is still a concern and studies like this show the necessity to understand how they are maintained in the population and to direct more efficiently the use of DAAs.
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Affiliation(s)
- Bruna Forte Aguiar
- FCFRP-USP - University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences-Café avenue, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Guilherme Rodrigues Fernandes Campos
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - João Paulo Vilela Rodrigues
- FCFRP-USP - University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences-Café avenue, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Nayara Nathie Marques
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Bárbara Floriano Molina
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Cintia Bittar
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Fernanda Fernandes Souza
- FMRP-USP-University of São Paulo, Ribeirão Preto School of Medicine, Bandeirantes Avenue, 3900, 14049-900 Ribeirão Preto, SP, Brazil.
| | - Ana de Lourdes Candolo Martinelli
- FMRP-USP-University of São Paulo, Ribeirão Preto School of Medicine, Bandeirantes Avenue, 3900, 14049-900 Ribeirão Preto, SP, Brazil.
| | - Paula Rahal
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Leonardo Régis Leira Pereira
- FCFRP-USP - University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences-Café avenue, 14040-903 Ribeirão Preto, SP, Brazil.
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Mawatari S, Oda K, Kumagai K, Tabu K, Ijuin S, Fujisaki K, Inada Y, Uto H, Saisyoji A, Hiramine Y, Hori T, Taniyama O, Toyodome A, Sakae H, Hashiguchi M, Kure T, Sakurai K, Tamai T, Moriuchi A, Ido A. Viral and host factors are associated with retreatment failure in hepatitis C patients receiving all-oral direct antiviral therapy. Hepatol Res 2020; 50:453-465. [PMID: 31846553 DOI: 10.1111/hepr.13474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/25/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022]
Abstract
AIM Direct-acting antiviral (DAA) therapy for hepatitis C virus is associated with high sustained virologic response rates. However, patients for whom DAA therapy fails acquire resistance-associated substitutions (RASs). We therefore evaluated the efficacy of DAA retreatment and factors associated with retreatment failure. METHODS Non-structural 5A RASs were investigated at the start of DAA therapy and at treatment failure in 64 patients with hepatitis C virus genotype 1b for whom DAA combination therapy had failed. A total of 59 patients were introduced to DAA retreatment. The factors associated with retreatment failure were investigated. RESULTS A total of 20 of 43 (46.5%) daclatasvir + asunaprevir-treated patients with virologic failure had no RASs at baseline, and three (15%) acquired P32 deletion RASs. Four of seven sofosbuvir/ledipasvir-treated patients with virologic failure had more than two RASs of NS5A at baseline. The sustained virologic response rates on retreatment were as follows: sofosbuvir/ledipasvir, 81.8%; with elbasvir + grazoprevir, 0%; and glecaprevir/pibrentasvir, 87.5%. Patients for whom sofosbuvir/ledipasvir or elbasvir + grazoprevir failed achieved sustained virologic response with glecaprevir/pibrentasvir. Two of three patients for whom glecaprevir/pibrentasvir retreatment failed had Q24/L28/R30 and A92K RASs; the other had P32 deletion RAS at baseline. Interestingly, 10 of 11 patients with retreatment failure had the interleukin (IL)-28B single-nucleotide polymorphism (SNP) minor allele. A multivariate analysis showed that the IL28B SNP minor allele (P = 0.005, odds ratio 28.291) was an independent risk factor for retreatment failure. CONCLUSIONS In addition to viral factors (e.g. Q24, L28, R30, and A92 or P32 deletion RASs), host factors (e.g. IL28B SNP) are associated with DAA retreatment failure.
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Affiliation(s)
- Seiichi Mawatari
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kohei Oda
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kotaro Kumagai
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuaki Tabu
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Sho Ijuin
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kunio Fujisaki
- Department of Hepatology, Kirishima Medical Center, Kagoshima, Japan
| | - Yukiko Inada
- Center for Digestive and Liver Diseases,, Miyazaki Medical Center Hospital, Miyazaki, Japan
| | - Hirofumi Uto
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Digestive and Liver Diseases,, Miyazaki Medical Center Hospital, Miyazaki, Japan
| | - Akiko Saisyoji
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Hepatology, Kagoshima Kouseiren Hospital, Kagoshima, Japan
| | - Yasunari Hiramine
- Department of Hepatology, Kagoshima Kouseiren Hospital, Kagoshima, Japan
| | - Takeshi Hori
- Department of Gastroenterology and Hepatology, Kagoshima City Hospital, Kagoshima, Japan
| | - Ohki Taniyama
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Ai Toyodome
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Haruka Sakae
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masafumi Hashiguchi
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Gastroenterology and Hepatology, Kagoshima City Hospital, Kagoshima, Japan
| | - Takeshi Kure
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Gastroenterology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Kazuhiro Sakurai
- Department of Gastroenterology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Tsutomu Tamai
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Gastroenterology and Hepatology, Kagoshima City Hospital, Kagoshima, Japan
| | - Akihiro Moriuchi
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Gastroenterology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Akio Ido
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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Hepatitis C Virus Translation Regulation. Int J Mol Sci 2020; 21:ijms21072328. [PMID: 32230899 PMCID: PMC7178104 DOI: 10.3390/ijms21072328] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
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Tojima H, Kakizaki S, Takakusagi S, Hoshino T, Naganuma A, Nagashima T, Namikawa M, Ueno T, Shimada Y, Hatanaka T, Takizawa D, Arai H, Sato K, Takagi H, Uraoka T. Favorable outcome of retreatment by direct-acting antivirals for hepatitis C patients with daclatasvir plus asunaprevir combination therapy failure. Hepatol Res 2020; 50:303-312. [PMID: 31750974 DOI: 10.1111/hepr.13462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/23/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
AIM In patients with hepatitis C virus, treatment failure of daclatasvir plus asunaprevir combination therapy (DCV + ASV) seems to become intractable due to the induction of resistance-associated substitutions. This study aimed to investigate the outcomes of retreatment with direct-acting antivirals (DAAs) in patients with DCV + ASV therapy failure, as well as changes in drug resistance mutations. METHODS We retrospectively analyzed 44 patients re-treated with DAAs after DCV + ASV failure between December 2015 and April 2018. All patients were analyzed for amino acid substitutions, and additional treatment regimens were selected based on the results and current treatment guidelines. RESULTS The sustained virological response rate with second-line treatment was 81.8% (36/44), and relapse occurred in five of 16 patients who received sofosbuvir/ledipasvir and three of seven patients who received DCV/ASV/beclabuvir. Third- and fourth-line treatments were also tried in relapsed cases, and the overall sustained virological response rates were 90.9% (40/44) and 93.2% (41/44), respectively. A high rate of viral clearance was eventually observed. Before second-line treatment, the prevalence of mutations in the NS5A and NS3/4A regions was 100% (44/44) and 86.4% (38/44), respectively. There was no significant increase in the number of amino acid substitutions in patients for whom second-line treatment failed. CONCLUSIONS Amino acid substitutions were frequently observed in patients with DCV + ASV failure, but most patients achieved a sustained virological response after retreatment with DAAs. Although the spread of drug-resistant viruses due to unsuccessful DAA treatment was a matter of concern, most cases of DCV + ASV failure were overcome with additional treatment.
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Affiliation(s)
- Hiroki Tojima
- Department of Gastroenterology and Hepatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Satoru Kakizaki
- Department of Gastroenterology and Hepatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | | | - Takashi Hoshino
- Department of Gastroenterology, National Hospital Organization Takasaki General Medical Center, Takasaki, Japan
| | - Atsushi Naganuma
- Department of Gastroenterology, National Hospital Organization Takasaki General Medical Center, Takasaki, Japan
| | - Tamon Nagashima
- Department of Gastroenterology, National Hospital Organization Shibukawa Medical Center, Shibukawa, Japan
| | - Masashi Namikawa
- Department of Internal Medicine, Kiryu Kosei General Hospital, Kiryu, Japan
| | - Takashi Ueno
- Department of Internal Medicine, Isesaki Municipal Hospital, Isesaki, Japan
| | - Yasushi Shimada
- Department of Internal Medicine, Isesaki Municipal Hospital, Isesaki, Japan
| | - Takeshi Hatanaka
- Department of Gastroenterology, Gunma Saiseikai Maebashi Hospital, Maebashi, Japan
| | - Daichi Takizawa
- Department of Gastroenterology, Maebashi Red Cross Hospital, Maebashi, Japan
| | - Hirotaka Arai
- Department of Gastroenterology, Maebashi Red Cross Hospital, Maebashi, Japan
| | - Ken Sato
- Department of Gastroenterology and Hepatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hitoshi Takagi
- Department of Gastroenterology, Kusunoki Hospital, Fujioka, Japan
| | - Toshio Uraoka
- Department of Gastroenterology and Hepatology, Gunma University Graduate School of Medicine, Maebashi, Japan
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Chen Q, Perales C, Soria ME, García-Cehic D, Gregori J, Rodríguez-Frías F, Buti M, Crespo J, Calleja JL, Tabernero D, Vila M, Lázaro F, Rando-Segura A, Nieto-Aponte L, Llorens-Revull M, Cortese MF, Fernandez-Alonso I, Castellote J, Niubó J, Imaz A, Xiol X, Castells L, Riveiro-Barciela M, Llaneras J, Navarro J, Vargas-Blasco V, Augustin S, Conde I, Rubín Á, Prieto M, Torras X, Margall N, Forns X, Mariño Z, Lens S, Bonacci M, Pérez-Del-Pulgar S, Londoño MC, García-Buey ML, Sanz-Cameno P, Morillas R, Martró E, Saludes V, Masnou-Ridaura H, Salmerón J, Quíles R, Carrión JA, Forné M, Rosinach M, Fernández I, García-Samaniego J, Madejón A, Castillo-Grau P, López-Núñez C, Ferri MJ, Durández R, Sáez-Royuela F, Diago M, Gimeno C, Medina R, Buenestado J, Bernet A, Turnes J, Trigo-Daporta M, Hernández-Guerra M, Delgado-Blanco M, Cañizares A, Arenas JI, Gomez-Alonso MJ, Rodríguez M, Deig E, Olivé G, Río OD, Cabezas J, Quiñones I, Roget M, Montoliu S, García-Costa J, Force L, Blanch S, Miralbés M, López-de-Goicoechea MJ, García-Flores A, Saumoy M, Casanovas T, Baliellas C, Gilabert P, Martin-Cardona A, Roca R, Barenys M, Villaverde J, Salord S, Camps B, Silvan di Yacovo M, Ocaña I, Sauleda S, Bes M, Carbonell J, Vargas-Accarino E, Ruzo SP, Guerrero-Murillo M, Von Massow G, Costafreda MI, López RM, González-Moreno L, Real Y, Acero-Fernández D, Viroles S, Pamplona X, Cairó M, Ocete MD, Macías-Sánchez JF, Estébanez A, Quer JC, Mena-de-Cea Á, Otero A, Castro-Iglesias Á, Suárez F, Vázquez Á, Vieito D, López-Calvo S, Vázquez-Rodríguez P, Martínez-Cerezo FJ, Rodríguez R, Macenlle R, Cachero A, Mereish G, Mora-Moruny C, Fábregas S, Sacristán B, Albillos A, Sánchez-Ruano JJ, Baluja-Pino R, Fernández-Fernández J, González-Portela C, García-Martin C, Sánchez-Antolín G, Andrade RJ, Simón MA, Pascasio JM, Romero-Gómez M, Antonio Del-Campo J, Domingo E, Esteban R, Esteban JI, Quer J. Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure. Antiviral Res 2020; 174:104694. [PMID: 31857134 DOI: 10.1016/j.antiviral.2019.104694] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/24/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) α-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of "extra-target" RAS suggests the need for RAS screening in all three DAA target regions.
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Affiliation(s)
- Qian Chen
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - María Eugenia Soria
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Roche Diagnostics SL, Sant Cugat del Valles, Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Crespo
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Marta Vila
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Fernando Lázaro
- Microbiology Department, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Meritxell Llorens-Revull
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Irati Fernandez-Alonso
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - José Castellote
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Jordi Niubó
- Microbiology Department, Hospital Universitari de Bellvitge, Barcelona
| | - Arkaitz Imaz
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Xavier Xiol
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Lluís Castells
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Riveiro-Barciela
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Llaneras
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Víctor Vargas-Blasco
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Augustin
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Conde
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Ángel Rubín
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Martín Prieto
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Xavier Torras
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Nuria Margall
- Digestive Pathology Unit, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Zoe Mariño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Martin Bonacci
- Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Maria Carlota Londoño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | | | | | - Rosa Morillas
- Liver Unit, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Elisa Martró
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Verónica Saludes
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | - Javier Salmerón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - Rosa Quíles
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - José Antonio Carrión
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Parc de Salut Mar - Hospital del Mar, Barcelona, Spain
| | - Montserrat Forné
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | - Mercè Rosinach
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | - Javier García-Samaniego
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Antonio Madejón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Pilar Castillo-Grau
- Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Carme López-Núñez
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - María José Ferri
- Clinical Laboratory, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Rosa Durández
- Laboratori Territorial - Hospital Santa Caterina, Girona, Spain
| | - Federico Sáez-Royuela
- Gastroenterology and Hepatology Depart., Hospital Universitario de Burgos, Burgos, Spain
| | - Moisés Diago
- Liver Unit, Hospital General de Valencia, Valencia, Spain
| | | | - Rafael Medina
- Microbiology Unit, Hospital General de Valencia, Valencia, Spain
| | - Juan Buenestado
- Medicine Department-Medical School, Hospital Univ. Arnau de Vilanova, Lleida, Spain
| | - Albert Bernet
- Microbiology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Juan Turnes
- Gastroenterology and Hepatology Department, Instituto de Investigación Sanitaria Galicia Sur (IISGS) - Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | - Matilde Trigo-Daporta
- Microbiology and Parasitology Department, Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Manuel Rodríguez
- Gastroenterology Depart., Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | | | - Gemma Olivé
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Oscar Del Río
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Joaquín Cabezas
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Ildefonso Quiñones
- Gastroenterology Department, Dr Negrin University Hospital of Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Mercè Roget
- Liver Unit, Consorci Sanitari de Terrassa - Hospital de Terrassa, Terrassa, Spain
| | - Silvia Montoliu
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Juan García-Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | | | - Silvia Blanch
- Hospital Universitari Sant Pau i Santa Tecla, Tarragona, Spain
| | - Miguel Miralbés
- Gastroenterology Department, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
| | | | | | - María Saumoy
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Teresa Casanovas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Carme Baliellas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Pau Gilabert
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Rosa Roca
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Mercè Barenys
- Liver Unit, Hospital de Viladecans, Barcelona, Spain
| | - Joana Villaverde
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Silvia Salord
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Blau Camps
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Imma Ocaña
- Infectious Disease Unit, HUVH, Barcelona, Spain
| | - Silvia Sauleda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Marta Bes
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Judit Carbonell
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Elena Vargas-Accarino
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Sofía P Ruzo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Georg Von Massow
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - María Isabel Costafreda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Rosa Maria López
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | | | - Yolanda Real
- Liver Unit, Hospital Universitario La Princesa, Madrid, Spain
| | | | - Silvia Viroles
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Xavier Pamplona
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Mireia Cairó
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | | | - Angel Estébanez
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Joan Carles Quer
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Álvaro Mena-de-Cea
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Alejandra Otero
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | - Francisco Suárez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Ángeles Vázquez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Vieito
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Soledad López-Calvo
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Raúl Rodríguez
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Alba Cachero
- Liver Unit, Hospital d'Igualada, Barcelona, Spain
| | | | | | - Silvia Fábregas
- Fundació Salut Empordà - Hospital de Figueres, Girona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Manolo Romero-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - José Antonio Del-Campo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Centro de Biología Molecular "Severo Ochoa" (CBMSO), Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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Dobbins GC, Patki A, Chen D, Tiwari HK, Hendrickson C, Britt WJ, Fowler K, Chen JY, Boppana SB, Ross SA. Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection. BMC Infect Dis 2019; 19:1046. [PMID: 31822287 PMCID: PMC6905059 DOI: 10.1186/s12879-019-4681-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Background Congenital cytomegalovirus (cCMV) infection is the most common congenital infection and a leading cause of long-term neurological and sensory sequelae, the most common being sensorineural hearing loss (SNHL). Despite extensive research, clinical or laboratory markers to identify CMV infected children with increased risk for disease have not been identified. This study utilizes viral whole-genome next generation-sequencing (NGS) of specimens from congenitally infected infants to explore viral diversity and specific viral variants that may be associated with symptomatic infection and SNHL. Methods CMV DNA from urine specimens of 30 infants (17 asymptomatic, 13 symptomatic) was target enriched and next generation sequenced resulting in 93% coverage of the CMV genome allowing analysis of viral diversity. Results Variant frequency distribution was compared between children with symptomatic and asymptomatic cCMV and those with (n = 13) and without (n = 17) hearing loss. The CMV genes UL48A, UL88, US19 and US22 were found to have an increase in nucleotide diversity in symptomatic children; while UL57, UL20, UL104, US14, UL115, and UL35 had an increase in diversity in children with hearing loss. An analysis of single variant differences between symptomatic and asymptomatic children found UL55 to have the highest number, while the most variants associated with SNHL were in the RL11 gene family. In asymptomatic infants with SNHL, mutations were observed more frequently in UL33 and UL20. Conclusion CMV genomes from infected newborns can be mapped to 93% of the genome at a depth allowing accurate and reproducible analysis of polymorphisms for variant and gene discovery that may be linked to symptomatic and hearing loss outcomes.
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Affiliation(s)
- G Clement Dobbins
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.
| | - Amit Patki
- Department of Biostatistics, The University of Alabama School of Public Health, Birmingham, AL, USA
| | - Dongquan Chen
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, The University of Alabama School of Public Health, Birmingham, AL, USA
| | - Curtis Hendrickson
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - William J Britt
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.,Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Karen Fowler
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA
| | - Jake Y Chen
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suresh B Boppana
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.,Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shannon A Ross
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA. .,Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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40
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Zhu X, Wang M, Liu M, Yu X, Huang P. Efficacy and safety of direct-acting antivirals for treatment-naive patients with genotype 1 hepatitis C virus infection. Per Med 2019; 16:421-429. [PMID: 31591934 DOI: 10.2217/pme-2018-0121] [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: 02/07/2023]
Abstract
This systematic review was performed on the basis of Preferred Reporting Items for Systematic Reviews and Meta-analyses and Cochrane recommendations to compare sustained virological response (SVR12) and the serious adverse events in patients treated by directing-acting antivirals. We conducted a literature search in PubMed/Medline, EBSCO, Embase and the Cochrane Library until 2018. A consistency model was used to get the relative effect of odds ratio among regimens and the possibility for the efficacy and safety of 13 regimen, and we divided these regimens into DUAL or TRIO regimens to conduct integrated data analysis. The results demonstrated that dual or triple directing-acting antiviral-combined regimens had higher SVR12 rates, Daclatasvir plus Asunaprevir may be a good choice for genotype 1 patients, and regimens without Ribavirin and interferon are safer.
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Affiliation(s)
- Xiaobo Zhu
- Department of Pharmacy, People's Hospital of Danyang, Danyang 212300, China
| | - Mingqi Wang
- Department of Epidemiology, Xu Zhou Medical University, Xuzhou 221000, China
| | - Mei Liu
- Department of Epidemiology, Nanjing Medical University, Nanjing 211166, China
| | - Xinghao Yu
- Department of Epidemiology, Xu Zhou Medical University, Xuzhou 221000, China
| | - Peng Huang
- Department of Epidemiology, Nanjing Medical University, Nanjing 211166, China.,Key Laboratory of Infectious Diseases, Nanjing Medical University, Nanjing 211166, China
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41
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Wu R, Geng D, Chi X, Wang X, Gao X, Xu H, Shi Y, Guan Y, Wang Y, Jin J, Ding Y, Niu J. Computational analysis of naturally occurring resistance-associated substitutions in genes NS3, NS5A, and NS5B among 86 subtypes of hepatitis C virus worldwide. Infect Drug Resist 2019; 12:2987-3015. [PMID: 31571951 PMCID: PMC6756830 DOI: 10.2147/idr.s218584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/22/2019] [Indexed: 12/14/2022] Open
Abstract
Background and objective Direct-acting antivirals (DAA) facing resistance continue to be used in some areas worldwide. Thus, identifying hepatitis C virus (HCV) genotypes/subtypes and loci with certain prevalent resistance-associated substitutions (RASs) deserves attention. We investigated the global and regional frequencies of naturally occurring RASs among all confirmed HCV subtypes (n=86) and explored co-occurring and mutually exclusive RAS pairs within and between genes NS3, NS5A, and NS5B. Methods A total of 213,908 HCV sequences available as of July 10, 2019 were retrieved from the NCBI nucleotide database. After curation, 17,312 NS3, 8,478 NS5A, and 25,991 NS5B sequence fragments from DAA-naïve patients were screened for RASs. MEGA 6.0 was used to translate aligned nucleotide sequences into amino acid sequences, and RAS pairs were identified by hypergeometric analysis. Results RAS prevalence varied significantly among HCV subtypes. For example, D168E, highly resistanct to all protease inhibitors except voxilaprevir, was nearly absent in all subtypes except in 43.48% of GT5a sequences. RASs in NS3 exhibiting significantly different global distribution included Q80K in GT1a with the highest frequency in North America (54.49%), followed by in Europe (22.66%), Asia (6.98%), Oceania (6.62%), and South America (1.03%). The prevalence of NS3 S122G in GT1b was highest in Asia (26.6%) and lowest in Europe (2.64%). NS5A L28M, R30Q, and Y93H in GT1b, L31M in GT2b, and NS5B C316N in GT1b was most prevalent in Asia. A150V in GT3a, associated with sofosbuvir treatment failure, was most prevalent in Asia (44.09%), followed by Europe (31.19%), Oceania (24.29%), and North America (19.05%). Multiple mutually exclusive or co-occurring RAS pairs were identified, including Q80K+R155K and R155K+D168G in GT1a and L159F+C316N and R30Q (NS5A)+C316N (NS5B) in GT1b. Conclusion Our data may be of special relevance for those countries where highly effective antivirals might not be available. Considering the specific RASs prevalence will help the clinicians to make optimal treatment choices. The RASs pairs would benefit anti-HCV drug development.
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Affiliation(s)
- Ruihong Wu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Dongfeng Geng
- Centre for Reproductive Medicine, Centre for Prenatal Diagnosis, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Xiumei Chi
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Xiaomei Wang
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Xiuzhu Gao
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Hongqin Xu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Ying Shi
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Yazhe Guan
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Yang Wang
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Jinglan Jin
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Yanhua Ding
- Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Junqi Niu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
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42
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Wing PA, Jones M, Cheung M, DaSilva S, Bamford C, Jason Lee WY, Aranday-Cortes E, Da Silva Filipe A, McLauchlan J, Smith D, Irving W, Cunningham M, Ansari A, Barnes E, Foster GR. Amino Acid Substitutions in Genotype 3a Hepatitis C Virus Polymerase Protein Affect Responses to Sofosbuvir. Gastroenterology 2019; 157:692-704.e9. [PMID: 31078622 PMCID: PMC6739484 DOI: 10.1053/j.gastro.2019.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 04/25/2019] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Sofosbuvir is a frequently used pan-genotype inhibitor of hepatitis C virus (HCV) polymerase. This drug eliminates most chronic HCV infections, and resistance-associated substitutions in the polymerase are rare. However, HCV genotype 3 responds slightly less well to sofosbuvir-based therapies than other genotypes. We collected data from England's National Health Service Early Access Program to search for virus factors associated with sofosbuvir treatment failure. METHODS We collected patient serum samples and used the capture-fusion assay to assess viral sensitivity to sofosbuvir in 14 HCV genotype 3 samples. We identified polymorphisms associated with reduced response and created modified forms of HCV and replicons containing the substitutions of interest and tested their sensitivity to sofosbuvir and ribavirin. We examined the effects of these polymorphisms by performing logistic regression multivariate analysis on their association with sustained virologic response in a separate cohort of 411 patients with chronic HCV genotype 3 infection who had been treated with sofosbuvir and ribavirin, with or without pegylated interferon. RESULTS We identified a substitution in the HCV genotype 3a NS5b polymerase at amino acid 150 (alanine [A] to valine [V]), V at position 150 was observed in 42% of patients) with a reduced response to sofosbuvir in virus replication assays. In patients treated with sofosbuvir-containing regimens, the A150V variant was associated with a reduced response to treatment with sofosbuvir and ribavirin, with or without pegylated interferon. In 326 patients with V at position 150, 71% achieved an sustained virologic response compared to 88% with A at position 150. In cells, V at position 150 reduced the response to sofosbuvir 7-fold. We found that another rare substitution, glutamic acid (E) at position 206, significantly reduced the response to sofosbuvir (8.34-fold reduction); the combinations of V at position 150 and E at position 206 reduced the virus response to sofosbuvir 35.77-fold. Additionally, in a single patient, we identified 5 rare polymorphisms that reduced sensitivity to sofosbuvir our cell system. CONCLUSIONS A common polymorphism, V at position 150 in the HCV genotype 3a NS5b polymerase, combined with other variants, reduces the virus response to sofosbuvir. Clinically, infection with HCV genotype 3 containing this variant reduces odds of sustained virologic response. In addition, we identified rare combinations of variants in HCV genotype 3 that reduce response to sofosbuvir.
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Affiliation(s)
- Peter A.C. Wing
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Meleri Jones
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Michelle Cheung
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Sampath DaSilva
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Connor Bamford
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Wing-Yiu Jason Lee
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Elihu Aranday-Cortes
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Ana Da Silva Filipe
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - John McLauchlan
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - David Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University National Health Service Trust, Oxford, UK
| | - William Irving
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, UK,University of Nottingham, Nottingham, UK
| | - Morven Cunningham
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University National Health Service Trust, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University National Health Service Trust, Oxford, UK
| | - Graham R. Foster
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK,Reprint requests Address requests for reprints to: Graham R. Foster, PhD, Barts Liver Centre, Blizard Institute, 4 Newark Street, London E1 2AT, UK.
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Uchida Y, Kouyama JI, Naiki K, Uemura H, Tsuji S, Sugawara K, Nakao M, Motoya D, Nakayama N, Imai Y, Tomiya T, Mochida S. A case of genotype-3b hepatitis C virus in which the whole genome was successfully analyzed using third-generation nanopore sequencing. Hepatol Res 2019; 49:1083-1087. [PMID: 30924272 DOI: 10.1111/hepr.13339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
Abstract
A 42-year-old Chinese man with chronic hepatitis C virus (HCV) infection visited our hospital for antiviral therapy. The subgenotype could not be determined using the HCV GENOTYPE Primer Kit (Institute of Immunology, Tokyo, Japan), which can identify genotype 3a HCV exclusively among genotype 3 HCV. Thus, the whole-genome sequence of HCV was analyzed using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK), a third-generation single-molecule sequencing platform. Consequently, a total of 9442 bases with a 73.6 mean depth, corresponding to the sequences between nt25 and PolyU/UC were determined (LC414155.2). The similarity analysis revealed that the obtained sequence was classified into genotype 3b HCV and showed nucleotide identities from 87.6% to 93.9% with those of 12 previously reported strains. Furthermore, possible resistance-associated substitutions in non-structural protein (NS)3, NS5A, and NS5B based on consensus sequences of 12 genotype 3b HCV strains, including NS5A-Y93H and NS5B-S282 T substitutions, were absent. In conclusion, the MinION nanopore sequencer is useful for analyzing the HCV genome, especially the genomes of genotype 3 HCV strains for which standardized real- time PCR methods for all subgenotypes have not been established.
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Affiliation(s)
- Yoshihito Uchida
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Jun-Ichi Kouyama
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Kayoko Naiki
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Hayato Uemura
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Shohei Tsuji
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Kayoko Sugawara
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Masamitsu Nakao
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Daisuke Motoya
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Nobuaki Nakayama
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Yukinori Imai
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Tomoaki Tomiya
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Satoshi Mochida
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
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Ishida H, Ishihara A, Tanaka S, Iwasaki T, Hasegawa H, Akasaka T, Sakakibara Y, Nakazuru S, Uehira T, Shirasaka T, Mita E. Favorable outcome with direct-acting antiviral treatment in hepatitis C patients coinfected with HIV. Hepatol Res 2019; 49:1076-1082. [PMID: 31074580 DOI: 10.1111/hepr.13360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/27/2019] [Accepted: 04/21/2019] [Indexed: 12/29/2022]
Abstract
AIM To investigate the efficacy and safety of all-oral direct-acting antiviral treatments in patients coinfected with hepatitis C virus (HCV) and HIV. METHODS In all, 35 patients with HCV/HIV coinfection (22 patients with HCV genotype 1 infection, 6 with genotype 2, and 7 with genotype 3) were treated with sofosbuvir and ledipasvir (for genotype 1 patients) or sofosbuvir and ribavirin (for genotypes 2 and 3). Sustained virological response (SVR) at 24 weeks after end of treatment and adverse events were assessed. RESULTS The overall SVR rate was 91.4% (32/35). One patient with genotype 1 infection discontinued treatment on day 2 due to severe headache, which subsided after the cessation of medication; all other patients completed their treatment without severe adverse events. Two patients who had a relapse of HCV were infected with a genotype 3 strain. We observed hyperbilirubinemia in a patient with genotype 3, who was under antiretroviral therapy including atazanavir. He completed the treatment and achieved SVR. CONCLUSION Direct-acting antiviral treatment for patients coinfected with HCV/HIV is as effective as in patients infected only with HCV. It was generally well tolerated, except in one patient who discontinued the treatment due to severe headache.
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Affiliation(s)
- Hisashi Ishida
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Akio Ishihara
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Satoshi Tanaka
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Tetsuya Iwasaki
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Hiroko Hasegawa
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Tomofumi Akasaka
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Yuko Sakakibara
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Shoichi Nakazuru
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Tomoko Uehira
- Department of Infectious Diseases, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Takuma Shirasaka
- Department of Infectious Diseases, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Eiji Mita
- Department of Gastroenterology and Hepatology, National Hospital Organization Osaka National Hospital, Osaka, Japan
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Han B, Martin R, Xu S, Parvangada A, Svarovskaia ES, Mo H, Dvory-Sobol H. Sofosbuvir susceptibility of genotype 1 to 6 HCV from DAA-naïve subjects. Antiviral Res 2019; 170:104574. [PMID: 31394118 DOI: 10.1016/j.antiviral.2019.104574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
High sequence diversity of HCV may lead to variation in susceptibility to antiviral agents amongst different genotypes and subtypes of the virus. We assessed the susceptibility to sofosbuvir of chimeric replicons carrying the full length NS5B coding region from 479 HCV infected, treatment-naïve patients, including 15 subtypes in 6 genotypes. NS5B replicon vectors with subtype 1b, subtype 4a and subtype 6a backbone were modified to support testing of patient samples. We also evaluated sofosbuvir susceptibility in a panel of 331 replicons containing engineered NS5B inhibitor resistance-associated substitutions. The mean 50% effective sofosbuvir concentration (EC50) amongst different genotypes ranged from 32 (subtype 2a) to 130 nM (genotype 4); while some variation in susceptibility amongst patient isolates was observed, the 95th percentile for any genotype did not exceed 189 nM. Levels of resistance to sofosbuvir in replicons containing S282T were between 2.4 and 18 fold-change in EC50; no other single NS5B resistance-associated substitution demonstrated reduced sofosbuvir susceptibility. These data suggest that S282T is the only known substitution that confers detectable resistance to sofosbuvir in vitro. Sofosbuvir displayed potent antiviral activity across a diverse range of NS5B mutants and HCV clinical isolates in multiple subtypes of genotypes 1 to 6.
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Affiliation(s)
- Bin Han
- Gilead Sciences, Foster City, CA, USA
| | | | - Simin Xu
- Gilead Sciences, Foster City, CA, USA
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46
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Fukasawa M. [Anti-hepatitis C Virus Strategy Targeting the Entry Steps]. YAKUGAKU ZASSHI 2019; 139:89-95. [PMID: 30606936 DOI: 10.1248/yakushi.18-00164-5] [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: 11/22/2022]
Abstract
Hepatitis C virus (HCV) infection is a major leading cause of chronic severe liver diseases such as cirrhosis and hepatocellular carcinoma. The recent direct-acting antivirals (DAAs) for the treatment of HCV infection offer very high cure rates, but DAAs are vulnerable to drug resistance because HCV is an RNA virus, which generally has very high mutation rates. DAA resistance-associated variants of HCV could reduce the effectiveness of DAAs in the future. Thus, the continuous development of new anti-HCV drugs against different target molecules is needed. We have been studying the host factors involved in HCV entry into cells. From those studies, we obtained novel candidates for host-targeting anti-HCV entry inhibitors, such as monoclonal antibodies against HCV receptors, which can be used together with DAAs. In this symposium review, we present and discuss our recent work on anti-HCV strategies targeting HCV entry steps.
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Affiliation(s)
- Masayoshi Fukasawa
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases
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47
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Akahane T, Kurosaki M, Itakura J, Tsuji K, Joko K, Kimura H, Nasu A, Ogawa C, Kojima Y, Hasebe C, Wada S, Uchida Y, Sohda T, Suzuki H, Yoshida H, Kusakabe A, Tamada T, Kobashi H, Mitsuda A, Kondo M, Shigeno M, Ide Y, Morita A, Kitamura T, Abe T, Izumi N. Real-world efficacy and safety of sofosbuvir + ribavirin for hepatitis C genotype 2: A nationwide multicenter study by the Japanese Red Cross Liver Study Group. Hepatol Res 2019; 49:264-270. [PMID: 30171740 DOI: 10.1111/hepr.13246] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/15/2022]
Abstract
AIM This study aimed to describe the real-world efficacy and safety of sofosbuvir (SOF) + ribavirin (RBV) for chronic hepatitis C, genotype 2. METHODS This was a retrospective analysis of a nationwide, multicenter registry including 914 hepatitis C genotype 2 Japanese patients treated with SOF + RBV for 12 weeks. The rate of sustained virologic response at 12 weeks after treatment (SVR12), incidence of adverse events, and changes in serological parameters were analyzed. RESULTS Treatment was completed in 98.9% of patients. Ribavirin dose reduction was required in 29.7% of patients. The SVR12 rate was 96.8% in the intention-to-treat population and 97.6% in the per-protocol population. Factors associated with SVR12 were absence of advanced fibrosis (odds ratio, 5.76, P = 0.003) and interferon-treatment-naïve status (odds ratio, 4.79, P = 0.017). Dose reduction or total adherence of RBV was not associated with SVR. The resistance-associated substitution S282 T in NS5B was not detected in any patient at virologic failure. Serum albumin levels significantly increased, and the degree of increase was greater in patients with advanced fibrosis than in those without (0.21 ± 0.32 vs. 0.05 ± 0.29, P < 0.0001). Alpha-fetoprotein decreased significantly at end of treatment (P < 0.0001), and the degree of decrease was greater in patients with advanced fibrosis than in those without (21.7 ± 60.8 vs. 2.5 ± 15.5, P < 0.001). The most commonly reported adverse event was anemia (13.7%). CONCLUSIONS Treatment with SOF + RBV was highly effective and safe in Japanese patients with HCV genotype 2 infection.
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Affiliation(s)
- Takehiro Akahane
- Department of Gastroenterology, Japanese Red Cross Ishinomaki Hospital, Ishinomaki, Japan
| | - Masayuki Kurosaki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino, Japan
| | - Jun Itakura
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino, Japan
| | - Keiji Tsuji
- Department of Gastroenterology, Hiroshima Red Cross Hospital and Atomic-bomb Survivors Hospital, Hiroshima, Japan
| | - Kouji Joko
- Center for Liver-Biliary-Pancreatic Diseases, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Hiroyuki Kimura
- Department of Gastroenterology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Akihiro Nasu
- Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan
| | - Chikara Ogawa
- Department of Gastroenterology, Takamatsu Red Cross Hospital, Takamatsu, Japan
| | - Yuji Kojima
- Department of Hepatology, Japanese Red Cross Ise Hospital, Ise, Japan
| | - Chitomi Hasebe
- Department of Gastroenterology, Japanese Red Cross Asahikawa Hospital, Asahikawa, Japan
| | - Shuichi Wada
- Department of Gastroenterology, Nagano Red Cross Hospital, Nagano, Japan
| | - Yasushi Uchida
- Department of Gastroenterology, Matsue Red Cross Hospital, Matsue, Japan
| | - Tetsuro Sohda
- Department of Hepatology, Japanese Red Cross Fukuoka Hospital, Fukuoka, Japan
| | - Hideyuki Suzuki
- Department of Internal Medicine, Japanese Red Cross Haramachi Hospital, Haramachi, Japan
| | - Hideo Yoshida
- Department of Gastroenterology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Atsunori Kusakabe
- Department of Gastroenterology, Japanese Red Cross Nagoya Daini Hospital, Nagoya, Japan
| | - Takashi Tamada
- Department of Gastroenterology, Takatsuki Red Cross Hospital, Takatsuki, Osaka, Japan
| | - Haruhiko Kobashi
- Department of Hepatology, Japanese Red Cross Okayama Hospital, Okayama, Japan
| | - Akeri Mitsuda
- Department of Internal Medicine, Tottori Red Cross Hospital, Tottori, Japan
| | - Masahiko Kondo
- Department of Gastroenterology, Japanese Red Cross Otsu Hospital, Otsu, Japan
| | - Masaya Shigeno
- Department of Gastroenterology, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Yasushi Ide
- Department of Internal Medicine, Karatsu Red Cross Hospital, Karatsu, Japan
| | - Atsuhiro Morita
- Department of Gastroenterology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Tadashi Kitamura
- Department of Gastroenterology, Shizuoka Red Cross Hospital, Shizuoka, Japan
| | - Takehiko Abe
- Department of Gastroenterology, Japanese Red Cross Maebashi Hospital, Maebashi, Japan
| | - Namiki Izumi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino, Japan
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48
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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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Baumert TF, Berg T, Lim JK, Nelson DR. Status of Direct-Acting Antiviral Therapy for Hepatitis C Virus Infection and Remaining Challenges. Gastroenterology 2019; 156:431-445. [PMID: 30342035 PMCID: PMC6446912 DOI: 10.1053/j.gastro.2018.10.024] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Chronic infection with hepatitis C virus is a major cause of liver disease and hepatocellular carcinoma worldwide. After the discovery of hepatitis C virus 3 decades ago, the identification of the structure of the viral proteins, combined with high-throughput replicon models, enabled the discovery and development of direct-acting antivirals. These agents have revolutionized patient care, with cure rates of more than 90%. We review the status of direct-acting antiviral therapies for hepatitis C virus infection and discuss remaining challenges. We highlight licensed compounds, discuss the potential to shorten therapy even further, and review different options for treatment failure and resistance. We also provide an overview of clinical experience with generic agents and evidence for their efficacy. Finally, we discuss the need for new drugs and outline promising targets for future therapies.
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Affiliation(s)
- Thomas F Baumert
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France; Pôle Hépato-digestif, Institut Hospitalo-Universitaire, Nouvel Hôpital Civil, Strasbourg, France.
| | - Thomas Berg
- Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Joseph K Lim
- Section of Digestive Diseases and Yale Liver Center, Yale University School of Medicine, New Haven, Connecticut
| | - David R Nelson
- Department of Medicine, University of Florida, Gainesville, Florida.
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Abstract
The advent of direct-acting antivirals (DAAs) has brought about a sudden renaissance in the treatment of chronic hepatitis C virus (HCV) infection with SVR rates now routinely >90%. However, due to the error-prone nature of the HCV RNA polymerase, resistance-associated substitutions (RASs) to DAAs may be present at baseline and can result in a significant effect on treatment outcomes and hamper the achievement of sustained virologic response. By further understanding the patterns and nature of these RASs, it is anticipated that the incidence of treatment failure will continue to decrease in frequency with the development of drug regimens with increasing potency, barrier to resistance, and genotypic efficacy. This review summarizes our current knowledge of RASs associated with HCV infection as well as the clinical effect of RASs on treatment with currently available DAA regimens.
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Affiliation(s)
- Darrick K Li
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Raymond T Chung
- Liver Center and Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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