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Haga Y, Coates S, Ray R. Hepatitis C virus chronicity and oncogenic potential: Vaccine development progress. Mol Aspects Med 2024; 99:101305. [PMID: 39167987 DOI: 10.1016/j.mam.2024.101305] [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: 06/07/2024] [Revised: 08/01/2024] [Accepted: 08/15/2024] [Indexed: 08/23/2024]
Abstract
Hepatitis C virus (HCV) infection is a major health problem worldwide. It can cause liver cirrhosis and hepatocellular carcinoma (HCC), making it a cause of morbidity from liver disease. Thus, there is an urgent need for a prophylactic HCV vaccine. Fortunately, modern medicine has transformed the therapy for HCV infection through development of direct-acting antiviral agents (DAAs), achieving high rates of sustained virologic response and giving significant relief from HCC and associated mortality, but unfortunately it fails to eradicate the risk of HCC, especially in HCV-cleared patients with already advanced liver disease. Additionally, DAA-cured patients do not develop sufficient antiviral immunity and are susceptible to reinfection. A comprehensive strategy to control HCV infection must include a vaccine development approach in which the host can develop humoral and cellular immunity to eradicate HCV successfully; however, this remains a challenge as HCV has developed systems to evade immune attacks from its host. This review highlights the current understanding of HCV's effect on liver disease and cancer progression, the nature of immune responses from cell populations interacting with HCV, and the current strategies for vaccine development. The information in this review will advance prophylactic intervention strategies for HCV infection, with the end goal being to prevent chronicity and subsequent liver disease leading to HCC.
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Affiliation(s)
- Yuki Haga
- Department of Internal Medicine, Saint Louis University, Missouri, MO, 63104, USA
| | - Sydney Coates
- Department of Internal Medicine, Saint Louis University, Missouri, MO, 63104, USA
| | - Ranjit Ray
- Department of Internal Medicine, Saint Louis University, Missouri, MO, 63104, USA; Department Molecular Microbiology & Immunology, Saint Louis University, Missouri, MO, 63104, USA.
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2
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Han D, Zhao F, Chen Y, Xue Y, Bao K, Chang Y, Lu J, Wang M, Liu T, Gao Q, Cui W, Xu Y. Distinct Characteristic Binding Modes of Benzofuran Core Inhibitors to Diverse Genotypes of Hepatitis C Virus NS5B Polymerase: A Molecular Simulation Study. Int J Mol Sci 2024; 25:8028. [PMID: 39125602 PMCID: PMC11311972 DOI: 10.3390/ijms25158028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
The benzofuran core inhibitors HCV-796, BMS-929075, MK-8876, compound 2, and compound 9B exhibit good pan-genotypic activity against various genotypes of NS5B polymerase. To elucidate their mechanism of action, multiple molecular simulation methods were used to investigate the complex systems of these inhibitors binding to GT1a, 1b, 2a, and 2b NS5B polymerases. The calculation results indicated that these five inhibitors can not only interact with the residues in the palm II subdomain of NS5B polymerase, but also with the residues in the palm I subdomain or the palm I/III overlap region. Interestingly, the binding of inhibitors with longer substituents at the C5 position (BMS-929075, MK-8876, compound 2, and compound 9B) to the GT1a and 2b NS5B polymerases exhibits different binding patterns compared to the binding to the GT1b and 2a NS5B polymerases. The interactions between the para-fluorophenyl groups at the C2 positions of the inhibitors and the residues at the binding pockets, together with the interactions between the substituents at the C5 positions and the residues at the reverse β-fold (residues 441-456), play a key role in recognition and the induction of the binding. The relevant studies could provide valuable information for further research and development of novel anti-HCV benzofuran core pan-genotypic inhibitors.
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Affiliation(s)
- Di Han
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Fang Zhao
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yifan Chen
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yiwei Xue
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Ke Bao
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yuxiao Chang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Jiarui Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Meiting Wang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Taigang Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China;
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China;
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
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3
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Noskov S, Arefeva A, Radaeva K, Makarenko I, Gefen M, Drai R. Bioequivalence Study of Velpatasvir/Sofosbuvir Oral Coated Tablets in Healthy Volunteers Under Fasting Conditions. Clin Pharmacol Drug Dev 2024. [PMID: 38881205 DOI: 10.1002/cpdd.1435] [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: 03/19/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024]
Abstract
This study was conducted as a single-site, open-label, randomized, replicated crossover trial with 4 treatment periods. The aim was to evaluate the bioequivalence of a generic test drug containing velpatasvir and sofosbuvir compared to an established brand-name medication in healthy White subjects under fasting conditions. Blood samples were collected at specified intervals up to 72 hours after dosing to measure the concentrations of velpatasvir and sofosbuvir using a certified high-performance liquid chromatography with tandem mass spectrometry method. The bioequivalence of the 2 formulations was confirmed when statistical analysis showed that confidence intervals for the log-transformed peak concentration and area under the concentration-time curve from time 0 to the last quantifiable sample were within an acceptable range from 80% to 125%. Criteria for bioequivalence were met for both area under the concentration-time curve from time 0 until the last quantifiable sample and peak concentration parameters. No adverse effects were reported during this trial in both groups.
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Affiliation(s)
| | | | | | | | - Maria Gefen
- R&D Center, GEROPHARM, Saint-Petersburg, Russia
| | - Roman Drai
- R&D Center, GEROPHARM, Saint-Petersburg, Russia
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Jaitpal S, Ng KW, San Juan AM, Martinez C, Phillips C, Tripathy S, Mabbott S. DNA-directed formation of plasmonic core-satellite nanostructures for quantification of hepatitis C viral RNA. Chem Sci 2024; 15:8112-8126. [PMID: 38817589 PMCID: PMC11134388 DOI: 10.1039/d4sc00891j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/19/2024] [Indexed: 06/01/2024] Open
Abstract
Hepatitis C virus (HCV) continues to be a significant public health challenge, affecting an estimated 71 million people globally and posing risks of severe liver diseases. Despite advancements in treatments, diagnostic limitations hinder the global elimination efforts targeted by 2030. This study introduces an innovative diagnostic approach, integrating catalytic hairpin assembly (CHA) with plasmonic core-satellite gold nanoparticle (AuNP) assemblies, to enable sensitive and specific detection of HCV RNA. We optimized the stoichiometry of DNA hairpins to form highly stable three-way junctions (3WJs), minimizing non-specific reactions in an enzyme-free, isothermal amplification process. The resulting dual-transduction biosensor combines colorimetric and surface-enhanced Raman spectroscopy (SERS) techniques, utilizing the Raman reporter malachite green isothiocyanate (MGITC) for signal generation. Our system targets a conserved 23-nucleotide sequence within the HCV 5'-UTR, essential for RNA replication, facilitating pan-genotypic HCV detection that complements direct-acting antiviral strategies. We evaluated the biosensor's efficacy using fluorescence spectroscopy, native PAGE, AFM, and TEM. Findings indicate that the 60 nm core AuNPs surrounded by 20 nm satellite AuNPs achieved a ten-fold increase in sensitivity over the 10 nm satellites, detecting HCV RNA concentrations as low as 1.706 fM. This sensitivity is crucial, given the extremely low viral loads present during early infection stages. Our research demonstrates the promise of enzyme-free molecular biosensors for HCV, with the potential to provide cost-efficient, rapid, point-of-care testing, although further sensitivity enhancements are needed to address the challenges of early-stage detection.
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Affiliation(s)
- Siddhant Jaitpal
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
- Center for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station 600 Discovery Drive College Station TX 77840-3006 USA
| | - Ka Wai Ng
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
- Center for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station 600 Discovery Drive College Station TX 77840-3006 USA
| | - Angela Michelle San Juan
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
- Center for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station 600 Discovery Drive College Station TX 77840-3006 USA
| | - Cecilia Martinez
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
| | - Christian Phillips
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
| | - Sayantan Tripathy
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
- Center for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station 600 Discovery Drive College Station TX 77840-3006 USA
| | - Samuel Mabbott
- Department of Biomedical Engineering, Texas A&M University 600 Discovery Drive College Station TX 77840-3006 USA
- Center for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station 600 Discovery Drive College Station TX 77840-3006 USA
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5
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Sallam M, Khalil R. Contemporary Insights into Hepatitis C Virus: A Comprehensive Review. Microorganisms 2024; 12:1035. [PMID: 38930417 PMCID: PMC11205832 DOI: 10.3390/microorganisms12061035] [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: 04/30/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting antiviral (DAA) regimens significantly improved HCV treatment, offering potentially high rates of cure for chronic hepatitis C. However, the promising aim of eventual HCV eradication remains challenging. Key challenges include the variability in DAA access across different regions, slightly variable response rates to DAAs across diverse patient populations and HCV genotypes/subtypes, and the emergence of resistance-associated substitutions (RASs), potentially conferring resistance to DAAs. Therefore, periodic reassessment of current HCV knowledge is needed. An up-to-date review on HCV is also necessitated based on the observed shifts in HCV epidemiological trends, continuous development and approval of therapeutic strategies, and changes in public health policies. Thus, the current comprehensive review aimed to integrate the latest knowledge on the epidemiology, pathophysiology, diagnostic approaches, treatment options and preventive strategies for HCV, with a particular focus on the current challenges associated with RASs and ongoing efforts in vaccine development. This review sought to provide healthcare professionals, researchers, and policymakers with the necessary insights to address the HCV burden more effectively. We aimed to highlight the progress made in managing and preventing HCV infection and to highlight the persistent barriers challenging the prevention of HCV infection. The overarching goal was to align with global health objectives towards reducing the burden of chronic hepatitis, aiming for its eventual elimination as a public health threat by 2030.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Roaa Khalil
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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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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7
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Farooq S, Faiz S, Wahab AT, Choudhary MI. Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis. Sci Rep 2024; 14:11159. [PMID: 38750152 PMCID: PMC11096182 DOI: 10.1038/s41598-024-59342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
Hepatitis is a major public health issue, affecting 10-17 million people worldwide, with its prevalence continuously increasing. The Hepatitis C virus (HCV) is responsible for liver related diseases, which include liver cirrhosis, hepatocellular carcinoma, and chronic hepatitis. Pakistan is experiencing a serious rise in HCV cases. This study aimed to assess the prevalence and distribution of HCV genotypes in Sindh, Pakistan. Serum samples from HCV-positive patients were collected from various local hospitals in Sindh. These samples were first screened for HCV antibodies using ELISA. Samples that tested positive for HCV RNA underwent further genotyping through sequencing using the standard Sanger method. The genotypes were identified by comparing the sequences with those available in the National Center for Biotechnology Information (NCBI) database, and a phylogenetic tree was constructed. The phylogenetic analysis showed that all isolates in this study were clustered with genotypes 3a and 3b, except for one sequence that was clustered with genotype 1a. No isolates were found to be clustered with reference genomes of genotypes 2, 4, 5, 6, and 7 suggesting that genotype 3a is endemic in this region. The analyzed sequences demonstrated a 98% similarity with reference and isolated sequences. In summary, sequencing of the HCV 5' UTR essential for identifying the predominant genotype of HCV RNA in the Sindh region Further research on the distribution of HCV genotypes in other regions of Pakistan could aid in improving screening processes, identifying more effective treatment options, and developing suitable prevention strategies.
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Affiliation(s)
- Saba Farooq
- Mediagnost Gesellschaft Für Forschung Und Herstellung Von Diagnostika, Reutlingen, Germany.
- National Institute of Virology, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Sirmast Faiz
- National Institute of Virology, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Atia-Tul Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21412, Jeddah, Saudi Arabia
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8
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Rananaware SR, Meister KS, Shoemaker GM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Karalkar VN, Lange IH, Pizzano BLM, Chang M, Ahmadimashhadi MR, Flannery SJ, Nguyen LT, Wang GP, Jain PK. PAM-free diagnostics with diverse type V CRISPR-Cas systems. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306194. [PMID: 38746294 PMCID: PMC11092703 DOI: 10.1101/2024.05.02.24306194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.
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9
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Li H, Huang H, Huang W, Du M, Long D, Xu G, Mei W, Huang K. Hepatitis C virus subtype diversity and transmission clusters characteristics among drug users in Zhuhai, South China. BMC Infect Dis 2024; 24:451. [PMID: 38685009 PMCID: PMC11057121 DOI: 10.1186/s12879-024-09323-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) infection poses a major public health challenge globally, especially among injecting drug users. China has the world's largest burden of HCV infections. However, little is known about the characteristics of transmission networks among drug user populations. This study aims to investigate the molecular epidemiology and transmission characteristics of HCV infections among drug users in Zhuhai, a bustling port city connecting Mainland China and its Special Administrative Regions. METHODS Participants enrolled in this study were drug users incarcerated at Zhuhai's drug rehabilitation center in 2015. Their sociodemographic and behavioral information, including gender, promiscuity, drug use method, and so forth, was collected using a standardized questionnaire. Plasmas separated from venous blood were analyzed for HCV infection through ELISA and RT-PCR methods to detect anti-HCV antibodies and HCV RNA. The 5'UTR fragment of the HCV genome was amplified and further sequenced for subtype identifications and phylogenetic analysis. The phylogenetic tree was inferred using the Maximum Likelihood method based on the Tamura-Nei model, and the transmission cluster network was constructed using Cytoscape3.8.0 software with a threshold of 0.015. Binary logistic regression models were employed to assess the factors associated with HCV infection. RESULTS The overall prevalence of HCV infection among drug users was 44.37%, with approximately 19.69% appearing to clear the HCV virus successfully. Binary logistic regression analysis revealed that those aged over 40, engaging in injecting drug use, and being native residents were at heightened risk for HCV infection among drug user cohorts. The predominant HCV subtypes circulating among those drug users were 6a (60.26%), followed by 3b (16.7%), 3a (12.8%), 1b (6.41%) and 1a (3.85%), respectively. Molecular transmission network analysis unveiled the presence of six transmission clusters, with the largest propagation cluster consisting of 41 individuals infected with HCV subtype 6a. Furthermore, distinct transmission clusters involved eight individuals infected with subtype 3b and seven with subtype 3a were also observed. CONCLUSION The genetic transmission networks revealed a complex transmission pattern among drug users in Zhuhai, emphasizing the imperative for a targeted and effective intervention strategy to mitigate HCV dissemination. These insights are pivotal for shaping future national policies on HCV screening, treatment, and prevention in port cities.
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Affiliation(s)
- Hongxia Li
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
- School of Public Health, Jinan University, Guangzhou, Guangdong, China
| | - Huitao Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
| | - Wenyan Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
| | - Man Du
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
| | - Dongling Long
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
| | - Guangxian Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China.
| | - Wenhua Mei
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China.
- School of Public Health, Jinan University, Guangzhou, Guangdong, China.
| | - Kaisong Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China.
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Yang TH, Gao WC, Ma X, Liu Q, Pang PP, Zheng YT, Jia Y, Zheng CB. A Review on The Pathogenesis of Cardiovascular Disease of Flaviviridea Viruses Infection. Viruses 2024; 16:365. [PMID: 38543730 PMCID: PMC10974792 DOI: 10.3390/v16030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/23/2024] Open
Abstract
Members of the Flaviviridae family, encompassing the Flavivirus and Hepacivirus genera, are implicated in a spectrum of severe human pathologies. These diseases span a diverse spectrum, including hepatitis, vascular shock syndrome, encephalitis, acute flaccid paralysis, and adverse fetal outcomes, such as congenital heart defects and increased mortality rates. Notably, infections by Flaviviridae viruses have been associated with substantial cardiovascular compromise, yet the exploration into the attendant cardiovascular sequelae and underlying mechanisms remains relatively underexplored. This review aims to explore the epidemiology of Flaviviridae virus infections and synthesize their cardiovascular morbidities. Leveraging current research trajectories and our investigative contributions, we aspire to construct a cogent theoretical framework elucidating the pathogenesis of Flaviviridae-induced cardiovascular injury and illuminate prospective therapeutic avenues.
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Affiliation(s)
- Tie-Hua Yang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China; (T.-H.Y.); (P.-P.P.)
- Key Laboratory of Animal Models and Human Diseases Mechanisms of Chinese Academy of Sciences, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; (X.M.); (Y.-T.Z.)
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen-Cong Gao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China;
| | - Xin Ma
- Key Laboratory of Animal Models and Human Diseases Mechanisms of Chinese Academy of Sciences, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; (X.M.); (Y.-T.Z.)
- College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
| | - Qian Liu
- School of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Pan-Pan Pang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China; (T.-H.Y.); (P.-P.P.)
- Key Laboratory of Animal Models and Human Diseases Mechanisms of Chinese Academy of Sciences, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; (X.M.); (Y.-T.Z.)
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Diseases Mechanisms of Chinese Academy of Sciences, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; (X.M.); (Y.-T.Z.)
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yinnong Jia
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China;
| | - Chang-Bo Zheng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China;
- College of Modern Biomedical Industry, Kunming Medical University, Kunming 650500, China
- Yunnan Vaccine Laboratory, Kunming 650500, China
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11
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Wang N, Liu Q, Che F, Sun Q, Wang Y, Yang C, Dai Y, Cheng J. Establishment and methodological evaluation of a chemiluminescence assay for detection of anti-envelope protein (E1, E2) antibodies in the serum of hepatitis C virus-infected patients. J Clin Lab Anal 2024; 38:e25011. [PMID: 38491776 PMCID: PMC10943255 DOI: 10.1002/jcla.25011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/01/2024] [Accepted: 01/13/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND To establish a chemiluminescence method for detecting anti-E1 and anti-E2 antibodies in the serum of patients with hepatitis C virus (HCV) infection. METHODS The microplate was coated with recombinant envelope proteins E1 and E2 by indirect method, respectively, and the kits for detecting anti-E1 and anti-E2 antibodies were prepared. The methodological indexes were evaluated. RESULTS The methodological indexes of the kits were as follows: precision test (the variation coefficient of anti-E1 antibody 6.71%-8.95% for within run and 9.91%-12.16% for between run, the variation coefficient of anti-E2 antibody 6.06%-8.44% for within run and 10.77%-13.98% for between run, respectively). The blank limit and detection limit were 1.18 RLIR and 3.16 RLIR for the anti-E1 antibody, and 1.26 RLIR and 3.32 RLIR for the anti-E2 antibody, respectively. The correlation coefficients (r) of anti-E1 and anti-E2 were 0.9963 and 0.9828, the analysis and measurement ranges (AMR) were 1.66-41.28 RLIR and 1.55-19.46 RLIR, and the average recovery was 96.4% and 93.7%, respectively. The rheumatoid factor and other positive serum samples had no interference or cross-reaction to the test, and the kits were stable within 15 months. The positive rates of anti-E1 and anti-E2 antibodies in 45 patients with HCV infection were 35.6% (16/45) and 44.4% (20/45), respectively. CONCLUSIONS The kits for detecting anti-E1 and anti-E2 meet the requirements of methodology, and can be used in screening diagnosis, disease monitoring, prognosis evaluation, disease mechanism, and epidemiological studies of HCV infection. The HCV envelope proteins E1 and E2 have an immune response in HCV-infected patients.
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Affiliation(s)
- Ningning Wang
- School of Laboratory MedicineBengbu Medical CollegeBengbuChina
| | - Qingqing Liu
- School of Laboratory MedicineBengbu Medical CollegeBengbuChina
| | - Feihu Che
- Department of Clinical ResearchThe 903rd Hospital of PLAHangzhouChina
| | - Qingyang Sun
- Department of Clinical ResearchThe 903rd Hospital of PLAHangzhouChina
| | - Yue Wang
- Department of Clinical ResearchThe 903rd Hospital of PLAHangzhouChina
| | - Chunli Yang
- Department of Clinical ResearchThe 903rd Hospital of PLAHangzhouChina
| | - Yuzhu Dai
- Department of Clinical ResearchThe 903rd Hospital of PLAHangzhouChina
| | - Jun Cheng
- Department of Clinical ResearchThe 903rd Hospital of PLAHangzhouChina
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12
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Ghebremeskel GG, Berhe Solomon M, Achila OO, Mengistu ST, Asmelash RF, Berhane Mesfin A, Hamida ME. Real-world treatment outcome of direct-acting antivirals and patient survival rates in chronic hepatitis C virus infection in Eritrea. Sci Rep 2023; 13:20792. [PMID: 38012181 PMCID: PMC10682448 DOI: 10.1038/s41598-023-47258-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/10/2023] [Indexed: 11/29/2023] Open
Abstract
Reliable real-world data on direct acting anti-retroviral (DAA) uptake and treatment outcomes are lacking for patients with hepatitis C virus (HCV) in sub-Saharan Africa. This study provides data on HCV DAA-based treatment outcomes, mortality, loss-to-follow up, and associated factors among patients in Eritrea. A multicenter retrospective observational cohort study was conducted in two tertiary hospitals in Asmara, Eritrea. A structured checklist was used to collect data from patient's cards. Descriptive and inferential statistics used included means (± Standard deviation (SD), medians (Interquartile range (IQR), chi-squire (χ2), Kaplan-Meier estimates, and multivariate Cox proportional hazard models. A total of 238 patients with median age of 59 years (IQR 50-69 years) were enrolled in the study. Out of the 227 patients initiated on treatment, 125 patients had viral load measurements at 12 weeks after end of treatment (EOT) whereas 102 patients had no viral load measurements at 12 weeks EOT. Among the patients with HCV RNA data post-EOT 12, 116 (92.8%) had sustained viral response (SVR). The prevalence of death and loss-to-follow up (LTFU) were (7.5%, 95% CI 1.7-4.1) and 67 (28.1%, 95% CI 22.3-33.9) translating into an incidence of 1.1 (95% CI 0.8-1.5) per 10,000 person days. Independent predictors of LTFU included the enrollment year (2020: aHR = 2.2, 95% CI 1-4.7; p value = 0.04); Hospital (Hospital B: aHR = 2.2, 95% CI 1-4.7; p value = 0.03) and the FIB-4 score (FIB-Score < 1.45: aHR = 3.7, 95% CI 1.2-11.5; p value = 0.02). The SVR rates achieved in this cohort were high. However, high LTFU and high mortality driven largely by late presentation and suboptimal population screening/case finding, were uncovered. These challenges can be addressed by test-and-treat programs that simultaneously prioritize programmatic screening, decentralization of care, and better patient tracking in the HCV care cascade.
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Affiliation(s)
| | | | - Oliver Okoth Achila
- Unit of Clinical Laboratory Science, Orotta College of Medicine and Health Sciences (OCMHS), Asmara, Eritrea
| | | | | | - Araia Berhane Mesfin
- National Communicable Disease Control Division, Ministry of Health, Asmara, Eritrea
| | - Mohammed Elfatih Hamida
- Department of Medical Microbiology, Orotta College of Medicine and Health Sciences (OCMHS), Asmara, Eritrea
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13
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Zhang Z, Guo W, Lu Y, Kang Q, Sui L, Liu H, Zhao Y, Zou X, Li Q. Hypovirulence-associated mycovirus epidemics cause pathogenicity degeneration of Beauveria bassiana in the field. Virol J 2023; 20:255. [PMID: 37924080 PMCID: PMC10623766 DOI: 10.1186/s12985-023-02217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The entomogenous fungus Beauveria bassiana is used as a biological insecticide worldwide, wild B. bassiana strains with high pathogenicity in the field play an important role in controlling insect pests via not only screening of highly virulent strains but also natural infection, but the pathogenicity degeneration of wild strains severely affected aforementioned effects. Previous studies have showed that multiple factors contributed to this phenomenon. It has been extensively proved that the mycovirus infection caused hypovirulence of phytopathogenic fungi, which has been used for plant disease biocontrol. However, it remains unknown whether the mycovirus epidemics is a key factor causing hypovirulence of B. bassiana naturally in the field. METHODS Wild strains of B. bassiana were collected from different geographic locations in Jilin Province, China, to clarify the epidemic and diversity of the mycoviruses. A mycovirus Beauveria bassiana chrysovirus 2 (BbCV2) we have previously identified was employed to clarify its impact on the pathogenicity of host fungi B. bassiana against the larvae of insect pest Ostrinia furnacalis. The serological analysis was conducted by preparing polyclonal antibody against a BbCV2 coat protein, to determine whether it can dissociate outside the host fungal cells and subsequently infect new hosts. Transcriptome analysis was used to reveal the interactions between viruses and hosts. RESULTS We surprisingly found that the mycovirus BbCV2 was prevalent in the field as a core virus in wild B. bassiana strains, without obvious genetic differentiation, this virus possessed efficient and stable horizontal and vertical transmission capabilities. The serological results showed that the virus could not only replicate within but also dissociate outside the host cells, and the purified virions could infect B. bassiana by co-incubation. The virus infection causes B. bassiana hypovirulence. Transcriptome analysis revealed decreased expression of genes related to insect epidermis penetration, hypha growth and toxin metabolism in B. bassiana caused by mycovirus infection. CONCLUSION Beauveria bassiana infected by hypovirulence-associated mycovirus can spread the virus to new host strains after infecting insects, and cause the virus epidemics in the field. The findings confirmed that mycovirus infection may be an important factor affecting the pathogenicity degradation of B. bassiana in the field.
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Affiliation(s)
- Zhengkun Zhang
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Wenbo Guo
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Yang Lu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Qin Kang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 101408, People's Republic of China
| | - Li Sui
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Hongyu Liu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Yu Zhao
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Xiaowei Zou
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Qiyun Li
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China.
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, People's Republic of China.
- Jilin Agricultural Science and Technology University, Jilin, 132109, People's Republic of China.
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14
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Abe H, Ushijima Y, Bikangui R, Ondo GN, Pemba CM, Zadeh VR, Mpingabo PI, Ueda H, Agnandji ST, Lell B, Yasuda J. Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa. Microorganisms 2023; 11:2046. [PMID: 37630606 PMCID: PMC10458803 DOI: 10.3390/microorganisms11082046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Viral hepatitis remains one of the largest public health concerns worldwide. Especially in Central Africa, information on hepatitis virus infections has been limited, although the prevalence in this region has been reported to be higher than the global average. To reveal the current status of hepatitis B and C virus (HBV and HCV) infections and the genetic diversity of the viruses, we conducted longitudinal surveillance in Gabon. We detected 22 HBV and 9 HCV infections in 2047 patients with febrile illness. Genetic analyses of HBV identified subgenotype A1 for the first time in Gabon and an insertion generating a frameshift to create an X-preC/C fusion protein. We also revealed that most of the detected HCVs belonged to the "Gabon-specific" HCV subtype 4e (HCV-4e), and the entire nucleotide sequence of the HCV-4e polyprotein was determined to establish the first reference sequence. The HCV-4e strains possessed resistance-associated substitutions similar to those of other HCV-4 strains, indicating that the use of direct-acting antiviral therapy may be complex. These results provide a better understanding of the current situation of hepatitis B and C virus infections in Central Africa and will help public health organizations develop effective countermeasures to eliminate chronic viral hepatitis in this region.
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Affiliation(s)
- Haruka Abe
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (H.A.); (C.M.P.); (V.R.Z.); (P.I.M.); (H.U.)
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan;
- Vietnam Research Station, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Yuri Ushijima
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan;
- Division of Biomedical Science, Institute of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Rodrigue Bikangui
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP. 242, Gabon; (R.B.); (G.N.O.); (S.T.A.); (B.L.)
| | - Georgelin Nguema Ondo
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP. 242, Gabon; (R.B.); (G.N.O.); (S.T.A.); (B.L.)
| | - Christelle M. Pemba
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (H.A.); (C.M.P.); (V.R.Z.); (P.I.M.); (H.U.)
| | - Vahid R. Zadeh
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (H.A.); (C.M.P.); (V.R.Z.); (P.I.M.); (H.U.)
| | - Patrick I. Mpingabo
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (H.A.); (C.M.P.); (V.R.Z.); (P.I.M.); (H.U.)
| | - Hayato Ueda
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (H.A.); (C.M.P.); (V.R.Z.); (P.I.M.); (H.U.)
| | - Selidji T. Agnandji
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP. 242, Gabon; (R.B.); (G.N.O.); (S.T.A.); (B.L.)
- Institute for Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP. 242, Gabon; (R.B.); (G.N.O.); (S.T.A.); (B.L.)
- Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (H.A.); (C.M.P.); (V.R.Z.); (P.I.M.); (H.U.)
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan;
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
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15
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Brown MG, Lindo JF, Vickers IE, Nelson K, Phillips Y, Wilson-Clarke C, Gavi S, Morse GD, Talal AH. Seroprevalence and Genotype Diversity of Hepatitis C Virus in the Caribbean-A Review. Trop Med Infect Dis 2023; 8:370. [PMID: 37505666 PMCID: PMC10385806 DOI: 10.3390/tropicalmed8070370] [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: 04/21/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023] Open
Abstract
Hepatitis C (HCV) continues to present a global public health challenge, with no vaccine available for prevention. Despite the availability of direct-acting antivirals (DAAs) to cure HCV, it remains prevalent in many regions including the Caribbean. As efforts are made to eliminate HCV from the region, existing barriers, such as the high cost of DAAs and lack of an established database of HCV cases within the Caribbean, must be addressed. This review seeks to assess epidemiologic trends (seroprevalence and genotypic diversity) of HCV in the Caribbean and identify gaps in surveillance of the disease. The literature for the period 1 January 2005 to October 2022 was reviewed to gather country-specific data on HCV across the Caribbean. References were identified through indexed journals accessed through established databases using the following keywords: Caribbean, genotype distribution, and general epidemiologic characteristics. The usage pattern of HCV drugs was determined from information obtained from pharmacists across the Caribbean including Jamaica. The prevalence of HCV in the Caribbean was 1.5%; the region should therefore be considered an area of moderate HCV prevalence. The prevalence of HCV among intravenous drug users (21.9-58.8%), persons living with HIV/AIDS (0.8 to 58.5%), prisoners (32.8-64%), and men who have sex with men (MSM) (0.8-6.9%) was generally higher than in the general population (0.8-2.3%). Genotype 1 (83%) was most prevalent followed by genotypes 2 (7.2%) and 3 (2.1%), respectively. Less than 50% of countries in the Caribbean have reliable or well-curated surveillance data on HCV. Drugs currently being used for treatment of HCV infections across the Caribbean include Epclusa (sofosbuvir/velpatasvir) and Harvoni (ledipasvir/sofosbuvir). Some of these drugs are only available in the private sector and are sourced externally whenever needed. While trends point to a potentially higher prevalence of HCV, it will require well-designed random surveys to obtain better estimates of the infection seroprevalence, supported by strong public health laboratory systems. DAAs that are pan-genotypic should translate into treatments that are affordable, accessible, and available to improve cure rates and reduce the HCV burden in the population.
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Affiliation(s)
- Michelle G Brown
- Department of Microbiology, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - John F Lindo
- Department of Microbiology, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Ivan E Vickers
- Department of Microbiology, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Kereann Nelson
- Department of Microbiology, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Yakima Phillips
- Department of Microbiology, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Cameil Wilson-Clarke
- Department of Basic Medical Sciences, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Samuel Gavi
- Translational Pharmacology Research Core, Center for Integrated Global Biomedical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, NY 14203, USA
| | - Gene D Morse
- Translational Pharmacology Research Core, Center for Integrated Global Biomedical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, NY 14203, USA
| | - Andrew H Talal
- Division of Gastroenterology, Hepatology, and Nutrition, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 875 Ellicott Street, Suite 6089, Buffalo, NY 14203, USA
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16
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Mosa A, Campo D, Khudyakov Y, AbouHaidar M, Gehring A, Zahoor A, Ball J, Urbanowicz R, Feld J. Polyvalent immunization elicits a synergistic broadly neutralizing immune response to hypervariable region 1 variants of hepatitis C virus. Proc Natl Acad Sci U S A 2023; 120:e2220294120. [PMID: 37276424 PMCID: PMC10268328 DOI: 10.1073/pnas.2220294120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/29/2023] [Indexed: 06/07/2023] Open
Abstract
A hepatitis C virus (HCV) vaccine is urgently needed. Vaccine development has been hindered by HCV's genetic diversity, particularly within the immunodominant hypervariable region 1 (HVR1). Here, we developed a strategy to elicit broadly neutralizing antibodies to HVR1, which had previously been considered infeasible. We first applied a unique information theory-based measure of genetic distance to evaluate phenotypic relatedness between HVR1 variants. These distances were used to model the structure of HVR1's sequence space, which was found to have five major clusters. Variants from each cluster were used to immunize mice individually, and as a pentavalent mixture. Sera obtained following immunization neutralized every variant in a diverse HCVpp panel (n = 10), including those resistant to monovalent immunization, and at higher mean titers (1/ID50 = 435) than a glycoprotein E2 (1/ID50 = 205) vaccine. This synergistic immune response offers a unique approach to overcoming antigenic variability and may be applicable to other highly mutable viruses.
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Affiliation(s)
- Alexander I. Mosa
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, M5G 2C4ON, Canada
| | - David S. Campo
- Molecular Epidemiology and Bioinformatics, Centers for Disease Control and Prevention, Atlanta30333, Georgia
| | - Yury Khudyakov
- Molecular Epidemiology and Bioinformatics, Centers for Disease Control and Prevention, Atlanta30333, Georgia
| | - Mounir G. AbouHaidar
- Department of Cell and Systems Biology, University of Toronto, Toronto, M5S 3G5ON, Canada
| | - Adam J. Gehring
- Department of Immunology, University of Toronto, Toronto, M5S 1A8ON, Canada
| | - Atif Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, M5G 2C4ON, Canada
| | - Jonathan K. Ball
- Wolfson Centre for Global Virus Infections, University of Nottingham, NottinghamNG8 1BB, United Kingdom
| | - Richard A. Urbanowicz
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolCH64 7TE, United Kingdom
| | - Jordan J. Feld
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, M5G 2C4ON, Canada
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17
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Ramos D, Pinto M, Sousa Coutinho R, Silva C, Quina M, Gomes JP, Pádua E. Looking at the Molecular Target of NS5A Inhibitors throughout a Population Highly Affected with Hepatitis C Virus. Pathogens 2023; 12:754. [PMID: 37375444 DOI: 10.3390/pathogens12060754] [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: 04/20/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Hepatitis C virus (HCV) is associated with liver damage and an increased progression rate to cirrhosis and hepatocellular carcinoma. In Portugal, it is prevalent in vulnerable populations such as injection drug users (IDU). HCV is characterized by a high intra-host variability, and the selecting driving forces could select variants containing resistance-associated substitutions (RAS) that reduce treatment effectiveness. The main goal of this study was to analyze the sequence variation of NS5A in treatment-naïve IDU. The epidemiological and clinical status of hepatitis C were analyzed, and samples were sequenced by Sanger and Next-Generation sequencing (NGS) to assess RAS and confirm HCV subtypes. Phylogenetic classification was concordant: 1a, 52.4%; 1b, 10.7%; 3a, 20.2%; 4a, 8.3%; 4d, 7.1%; and one 2k/1b recombinant. A 1a/3a mixed infection was detected by NGS. RAS were found in 34.5% (29/84) of samples using Sanger sequencing, while in 42.9% (36/84) using NGS. In sequences from subtypes 1a and 1b, RAS K24R, M28V, Q30H/R, H58D/P/Q/R, and RAS L31M and P58S were detected, respectively. In subtype 3a, RAS A30S/T, Y93H and polymorphisms in position 62 were identified. Additionally, RAS P58L was detected in genotype 4. The strategy used for the molecular survey of baseline HCV resistance is of particular importance to achieve treatment effectiveness and contribute to the elimination of hepatitis C.
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Affiliation(s)
- Diogo Ramos
- Reference Laboratory of HIV and Hepatitis B and C, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal
| | - Rodrigo Sousa Coutinho
- Association Ares do Pinhal, Association for the Rehabilitation of Drug Addicts, Low-Threshold Methadone Substitution Program, R. José Inácio Andrade, Loja 2-A6-10B Quinta do Lavrado, P-1900-418 Lisbon, Portugal
| | - Carolina Silva
- Reference Laboratory of HIV and Hepatitis B and C, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal
| | - Miriam Quina
- Reference Laboratory of HIV and Hepatitis B and C, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal
| | - Elizabeth Pádua
- Reference Laboratory of HIV and Hepatitis B and C, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal
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18
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Nonyong P, Ekalaksananan T, Phanthanawiboon S, Overgaard HJ, Alexander N, Thaewnongiew K, Sawaswong V, Nimsamer P, Payungporn S, Phadungsombat J, Nakayama EE, Shioda T, Pientong C. Intrahost Genetic Diversity of Dengue Virus in Human Hosts and Mosquito Vectors under Natural Conditions Which Impact Replicative Fitness In Vitro. Viruses 2023; 15:982. [PMID: 37112962 PMCID: PMC10143933 DOI: 10.3390/v15040982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/08/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Dengue virus (DENV) is an arbovirus whose transmission cycle involves disparate hosts: humans and mosquitoes. The error-prone nature of viral RNA replication drives the high mutation rates, and the consequently high genetic diversity affects viral fitness over this transmission cycle. A few studies have been performed to investigate the intrahost genetic diversity between hosts, although their mosquito infections were performed artificially in the laboratory setting. Here, we performed whole-genome deep sequencing of DENV-1 (n = 11) and DENV-4 (n = 13) derived from clinical samples and field-caught mosquitoes from the houses of naturally infected patients, in order to analyze the intrahost genetic diversity of DENV between host types. Prominent differences in DENV intrahost diversity were observed in the viral population structure between DENV-1 and DENV-4, which appear to be associated with differing selection pressures. Interestingly, three single amino acid substitutions in the NS2A (K81R), NS3 (K107R), and NS5 (I563V) proteins in DENV-4 appear to be specifically acquired during infection in Ae. aegypti mosquitoes. Our in vitro study shows that the NS2A (K81R) mutant replicates similarly to the wild-type infectious clone-derived virus, while the NS3 (K107R), and NS5 (I563V) mutants have prolonged replication kinetics in the early phase in both Vero and C6/36 cells. These findings suggest that DENV is subjected to selection pressure in both mosquito and human hosts. The NS3 and NS5 genes may be specific targets of diversifying selection that play essential roles in early processing, RNA replication, and infectious particle production, and they are potentially adaptive at the population level during host switching.
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Affiliation(s)
- Patcharaporn Nonyong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Supranee Phanthanawiboon
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
| | - Hans J. Overgaard
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway;
| | - Neal Alexander
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Kesorn Thaewnongiew
- Department of Disease Control, Office of Disease Prevention and Control, Region 7 Khon Kaen, Ministry of Public Health, Khon Kaen 40000, Thailand;
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
| | - Pattaraporn Nimsamer
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
| | - Sunchai Payungporn
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen 40002, Thailand
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19
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Geng X, Li L, Luo Y, Yang W, Hu J, Zhao Z, Cheng C, Zhang T, Zhang Y, Liu L, Xie Y, Li G, Liu D, Bai R, Bai X, Wang G, Chen H, Wang Y, Chen H, Sun B. Tumor Cell Derived Lnc-FSD2-31:1 Contributes to Cancer-Associated Fibroblasts Activation in Pancreatic Ductal Adenocarcinoma Progression through Extracellular Vesicles Cargo MiR-4736. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203324. [PMID: 36727832 PMCID: PMC10074102 DOI: 10.1002/advs.202203324] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/10/2023] [Indexed: 05/11/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) presents with high mortality and short overall survival. Cancer-associated fibroblasts (CAFs) act as refuge for cancer cells in PDAC. Mechanisms of intracelluar communication between CAFs and cancer cells need to be explored. Long noncoding RNAs (lncRNAs) are involved in the modulation of oncogenesis and tumor progression of PDAC; however, specific lncRNAs and their mechanism of action have not been clarified clearly in tumoral microenvironment. This work aims to identify novel lncRNAs involved in cellular interaction between cancer cells and CAFs in PDAC. To this end, differentially expressed lncRNAs between long-term and short-term survival PDAC patients are screened. Lnc-FSD2-31:1 is found to be significantly increased in long-term survival patients. This work then discovers that tumor-derived lnc-FSD2-31:1 restrains CAFs activation via miR-4736 transported by extracellular vesicles (EVs) in vitro and in vivo. Mechanistically, EVs-derived miR-4736 suppresses autophagy and contributes to CAFs activation by targeting ATG7. Furthermore, blocking miR-4736 suppresses tumor growth in genetically engineered KPC (LSL-KrasG12D/+, LSL-Trp53R172H/+, and Pdx-1-Cre) mouse model of PDAC. This study demonstrates that intratumoral lnc-FSD2-31:1 modulates autophagy in CAFs resulting in their activation through EVs-derived miR-4736. Targeting miR-4736 may be a potential biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Xinglong Geng
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Le Li
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yan Luo
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Wenbo Yang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Jisheng Hu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Zhongjie Zhao
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Chundong Cheng
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Tao Zhang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yangyang Zhang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Liwei Liu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yu Xie
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Guanqun Li
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Danxi Liu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Rui Bai
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Xuewei Bai
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Gang Wang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Hua Chen
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yongwei Wang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Hongze Chen
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Bei Sun
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
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20
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Sasi VM, Ullrich S, Ton J, Fry SE, Johansen-Leete J, Payne RJ, Nitsche C, Jackson CJ. Predicting Antiviral Resistance Mutations in SARS-CoV-2 Main Protease with Computational and Experimental Screening. Biochemistry 2022; 61:2495-2505. [DOI: 10.1021/acs.biochem.2c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vishnu M. Sasi
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Jennifer Ton
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Sarah E. Fry
- School of Chemistry, The University of Sydney, Sydney NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney NSW 2006, Australia
| | - Jason Johansen-Leete
- School of Chemistry, The University of Sydney, Sydney NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney NSW 2006, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra ACT 2601, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Australian National University, Canberra ACT 2601, Australia
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21
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Wang AE, Hsieh E, Turner BJ, Terrault N. Integrating Management of Hepatitis C Infection into Primary Care: the Key to Hepatitis C Elimination Efforts. J Gen Intern Med 2022; 37:3435-3443. [PMID: 35484367 PMCID: PMC9551010 DOI: 10.1007/s11606-022-07628-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/18/2022] [Indexed: 11/24/2022]
Abstract
Elimination of hepatitis C virus (HCV), a leading cause of liver disease in the USA and globally, has been made possible with the advent of highly efficacious direct acting antivirals (DAAs). DAA regimens offer cure of HCV with 8-12 weeks of a well-tolerated once daily therapy. With increasingly straightforward diagnostic and treatment algorithms, HCV infection can be managed not only by specialists, but also by primary care providers. Engaging primary care providers greatly increases capacity to diagnose and treat chronic HCV and ultimately make HCV elimination a reality. However, barriers remain at each step in the HCV cascade of care from screening to evaluation and treatment. Since primary care is at the forefront of patient contact, it represents the ideal place to concentrate efforts to identify barriers and implement solutions to achieve universal HCV screening and increase curative treatment.
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Affiliation(s)
- Allison E Wang
- Department of Internal Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eric Hsieh
- Department of Internal Medicine, University of Southern California, Los Angeles, CA, USA
| | - Barbara J Turner
- Department of Internal Medicine, University of Southern California, Los Angeles, CA, USA
| | - Norah Terrault
- Department of Internal Medicine, University of Southern California, Los Angeles, CA, USA.
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, University of Southern California, Los Angeles, CA, USA.
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22
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Gao CC, Bai J, Han H, Qin HY. The versatility of macrophage heterogeneity in liver fibrosis. Front Immunol 2022; 13:968879. [PMID: 35990625 PMCID: PMC9389038 DOI: 10.3389/fimmu.2022.968879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Liver fibrosis is a highly conserved wound healing response to liver injury, characterized by excessive deposition of extracellular matrix (ECM) in the liver which might lead to loss of normal functions. In most cases, many types of insult could damage hepatic parenchymal cells like hepatocytes and/or cholangiocytes, and persistent injury might lead to initiation of fibrosis. This process is accompanied by amplified inflammatory responses, with immune cells especially macrophages recruited to the site of injury and activated, in order to orchestrate the process of wound healing and tissue repair. In the liver, both resident macrophages and recruited macrophages could activate interstitial cells which are responsible for ECM synthesis by producing a variety of cytokines and chemokines, modulate local microenvironment, and participate in the regulation of fibrosis. In this review, we will focus on the main pathological characteristics of liver fibrosis, as well as the heterogeneity on origin, polarization and functions of hepatic macrophages in the setting of liver fibrosis and their underlying mechanisms, which opens new perspectives for the treatment of liver fibrosis.
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Affiliation(s)
- Chun-Chen Gao
- State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi’an, China
| | - Jian Bai
- State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi’an, China
| | - Hua Han
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, China
| | - Hong-Yan Qin
- State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi’an, China
- *Correspondence: Hong-Yan Qin,
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23
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Hayes CN, Imamura M, Tanaka J, Chayama K. Road to elimination of HCV: Clinical challenges in HCV management. Liver Int 2022; 42:1935-1944. [PMID: 34967486 DOI: 10.1111/liv.15150] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022]
Abstract
Since its discovery in 1989, the road to a cure for hepatitis C virus (HCV) has been slow, but most patients can now expect to achieve a sustained virological response (SVR). With direct-acting antiviral (DAA) combination therapies such as glecaprevir/pibrentasvir and velpatasvir/sofosbuvir, 98% of patients successfully eradicate the virus, even if previous treatments failed or if resistance-associated substitutions (RASs) are present. Adverse events are rare or mild, and patients with compensated cirrhosis and other co-morbidities are often eligible for treatment. However, a small number of patients fail to eradicate the virus even after retreatment. The cause of failure is mainly due to emergence of NS5A P32 deletion mutants after initial DAA therapy in genotype 1b patients, although the reason is unknown for some patients. Alternative therapies that do not rely on NS5A inhibitors, such as sofosbuvir plus ribavirin, can be attempted in these patients. While scaled-up treatment efforts present a challenge, another problem is that many carriers are unaware of their infection. Long-term damage to the liver becomes irreversible, and patients who are not diagnosed in time can develop liver cancer or liver failure even after eliminating the virus. The long-term costs of treatment of advanced liver disease in undiagnosed patients relative to the immediate costs of DAA therapy should be considered. As no vaccine is yet available, eventual elimination of the virus requires identifying and treating undiagnosed cases and screening of high-risk populations such as injection drug users and men who have sex with men and female sex workers.
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Affiliation(s)
- C Nelson Hayes
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Junko Tanaka
- Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan.,Department of Epidemiology, Infectious Disease Control and Prevention, Graduate school of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Chayama
- Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan.,Collaborative Research Laboratory of Medical Innovation, Hiroshima University, Hiroshima, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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24
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Sahibzada KI, Ganova-Raeva L, Dimitrova Z, Ramachandran S, Lin Y, Longmire G, Arthur L, Xia GL, Khudyakov Y, Khan I, Sadaf S. Hepatitis C virus transmission cluster among injection drug users in Pakistan. PLoS One 2022; 17:e0270910. [PMID: 35839216 PMCID: PMC9286280 DOI: 10.1371/journal.pone.0270910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Hepatitis C virus (HCV) infections are public health problem across the globe, particularly in developing countries. Pakistan has the second highest prevalence of HCV infection worldwide. Limited data exist from Pakistan about persons who inject drugs (PWID) and are at significant risk of exposure to HCV infection and transmission. Serum specimens (n = 110) collected from PWID residing in four provinces were tested for molecular markers of HCV infection. Next generation sequencing (NGS) of the hypervariable region (HVR1) of HCV and Global Hepatitis Outbreak and Surveillance Technology (GHOST) were used to determine HCV genotype, genetic heterogeneity, and construct transmission networks. Among tested specimens, 47.3% were found anti-HCV positive and 34.6% were HCV RNA-positive and belonged to four genotypes, with 3a most prevalent followed by 1a, 1b and 4a. Variants sampled from five cases formed phylogenetic cluster and a transmission network. One case harbored infection with two different genotypes. High prevalence of infections and presence of various genotypes indicate frequent introduction and transmission of HCV among PWID in Pakistan. Identification of a transmission cluster across three provinces, involving 20% of all cases, suggests the existence of a countrywide transmission network among PWIDs. Understanding the structure of this network should assist in devising effective public health strategies to eliminate HCV infection in Pakistan.
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Affiliation(s)
- Kashif Iqbal Sahibzada
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Lilia Ganova-Raeva
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Zoya Dimitrova
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Sumathi Ramachandran
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Yulin Lin
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Garrett Longmire
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Leonard Arthur
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Guo-liang Xia
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Yury Khudyakov
- Division of Viral Hepatitis, Center of Disease Control and Prevention, Molecular Epidemiology and Bioinformatics, Atlanta, GA, United States of America
| | - Idrees Khan
- University of Peshawar, Peshawar, KPK, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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25
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Circulating MicroRNAs as a Tool for Diagnosis of Liver Disease Progression in People Living with HIV-1. Viruses 2022; 14:v14061118. [PMID: 35746590 PMCID: PMC9227922 DOI: 10.3390/v14061118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/20/2022] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that post-transcriptionally regulate gene expression by binding specific cell mRNA targets, preventing their translation. miRNAs are implicated in the regulation of important physiological and pathological pathways. Liver disease, including injury, fibrosis, metabolism dysregulation, and tumor development disrupts liver-associated miRNAs. In addition to their effect in the originating tissue, miRNAs can also circulate in body fluids. miRNA release is an important form of intercellular communication that plays a role in the physiological and pathological processes underlying multiple diseases. Circulating plasma levels of miRNAs have been identified as potential disease biomarkers. One of the main challenges clinics face is the lack of available noninvasive biomarkers for diagnosing and predicting the different stages of liver disease (e.g., nonalcoholic fatty liver disease and nonalcoholic steatohepatitis), particularly among individuals infected with human immunodeficiency virus type 1 (HIV-1). Liver disease is a leading cause of death unrelated to acquired immunodeficiency syndrome (AIDS) among people living with HIV-1 (PLWH). Here, we review and discuss the utility of circulating miRNAs as biomarkers for early diagnosis, prognosis, and assessment of liver disease in PLWH. Remarkably, the identification of dysregulated miRNA expression may also identify targets for new therapeutics.
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26
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Kubota N, Fujiwara N, Hoshida Y. Liver cancer risk-predictive molecular biomarkers specific to clinico-epidemiological contexts. Adv Cancer Res 2022; 156:1-37. [PMID: 35961696 PMCID: PMC7616039 DOI: 10.1016/bs.acr.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hepatocellular carcinoma (HCC) risk prediction is increasingly important because of the low annual HCC incidence in patients with the rapidly emerging non-alcoholic fatty liver disease or cured HCV infection. To date, numerous clinical HCC risk biomarkers and scores have been reported in literature. However, heterogeneity in clinico-epidemiological context, e.g., liver disease etiology, patient race/ethnicity, regional environmental exposure, and lifestyle-related factors, obscure their real clinical utility and applicability. Proper characterization of these factors will help refine HCC risk prediction according to certain clinical context/scenarios and contribute to improved early HCC detection. Molecular factors underlying the clinical heterogeneity encompass various features in host genetics, hepatic and systemic molecular dysregulations, and cross-organ interactions, which may serve as clinical-context-specific biomarkers and/or therapeutic targets. Toward the goal to enable individual-risk-based HCC screening by incorporating the HCC risk biomarkers/scores, their assessment in patient with well-defined clinical context/scenario is critical to gauge their real value and to maximize benefit of the tailored patient management for substantial improvement of the poor HCC prognosis.
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Affiliation(s)
- Naoto Kubota
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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27
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Gomez-Quiroz LE, Roman S. Influence of genetic and environmental risk factors in the development of hepatocellular carcinoma in Mexico. Ann Hepatol 2022; 27 Suppl 1:100649. [PMID: 34902602 DOI: 10.1016/j.aohep.2021.100649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 02/06/2023]
Abstract
The latest studies on the epidemiology of diverse types of cancers have located in the scene the relevance of liver tumors, particularly hepatocellular carcinoma (HCC). HCC is a life-threatening malignancy triggered by chronic exposure to hepatitis B and C viruses, excessive alcohol intake, hepatic lipid droplet accumulation, and aflatoxins that lead to persistent liver damage. The occurrence of such etiological risk factors deeply marks the variability in the incidence of HCC worldwide reflected by geography, ethnicity, age, and lifestyle factors influenced by cultural aspects. New perspectives on the primary risk factors and their potential gene-environment interactions (GxE) have been well-addressed in some cancers; however, it continues to be a partially characterized issue in liver malignancies. In this review, the epidemiology of the risk factors for HCC are described enhancing the GxE interactions identified in Mexico, which could mark the risk of this liver malignancy among the population and the measures needed to revert them. Updated healthcare policies focusing on preventive care should be tailored based on the genetic and environmental risk factors, which may influence the effect of the etiological agents of HCC. Robust regional investigations related to epidemiological, clinical, and basic studies are warranted to understand this health problem complying with the rules of ethnic, genetic, environmental, and social diversity.
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Affiliation(s)
- Luis E Gomez-Quiroz
- Área de Medicina Experimental y Traslacional, Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Jalisco, Mexico; Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico.
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28
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Single nucleotide polymorphisms in PNPLA3, ADAR-1 and IFIH1 are associated with advanced liver fibrosis in patients co-infected with HIV-1//hepatitis C virus. AIDS 2021; 35:2497-2502. [PMID: 34482352 DOI: 10.1097/qad.0000000000003066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Nonalcoholic fatty liver disease (NAFLD), insulin resistance and liver fibrosis are prevalent in individuals co-infected with HIV type 1 (HIV-1)/hepatitis C virus (HCV), even after HCV eradication. Our aim was to evaluate single nucleotide polymorphisms (SNPs) associated with advanced liver fibrosis in HIV-1/HCV co-infected patients. DESIGN/METHODS In a cohort of 102 participants, we genotyped 16 SNPs in 10 genes previously associated with NAFLD and the innate immune response and correlated the genotypes with liver fibrosis and fat accumulation. RESULTS Multinomial logistic regression analysis identified three metabolic parameters that were significantly associated with advanced liver fibrosis (stage F3-F4): albumin [odds ratio (OR) 0.80, 95% confidence interval (CI) 0.69-0.91, P = 0.001], percentage of visceral fat area (PVFA) (OR 1.06, 95% CI 1.01-1.12, P = 0.03) and BMI (OR 1.47, 95% CI 1.22-1.77, P < 0.0001). After adjustment for sex, albumin, PVFA and BMI, we found that three SNPs were significantly associated with advanced fibrosis, one each in PNPLA3/rs738409 (P = 0.016), ADAR-1/rs1127313 (P = 0.029) and IFIH1/rs1990760 (P = 0.033). CONCLUSION Our results indicate that genotyping for these SNPs can be a useful predictive tool for liver fibrosis progression and liver fat accumulation in patients co-infected with HIV-1/HCV.
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29
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Mohammed AS, Balapure A, Khan AA, Khaja MN, Ganesan R, Dutta JR. Genotyping simplified: rationally designed antisense oligonucleotide-mediated PCR amplification-free colorimetric sensing of viral RNA in HCV genotypes 1 and 3. Analyst 2021; 146:4767-4774. [PMID: 34231566 DOI: 10.1039/d1an00590a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular diagnosis of viral genotyping devoid of polymerase chain reaction (PCR) amplification in clinical cohorts has hitherto been challenging. Here we present a simplified molecular diagnostic strategy for direct genotyping of hepatitis C virus (HCV) 1 and 3 (prevalent worldwide) using a combination of rationally designed genotype-specific antisense oligonucleotides (ASOs) and plasmonic gold nanoparticles. The ASOs specific to genotypes 1 and 3 have been designed from the nonstructural region 5A (NS5A) of the viral genome using the ClustalW multiple sequence alignment tool. A total of 79 clinical samples including 18 HCV genotype 1, 18 HCV genotype 3, one HIV positive, one HBV positive, and 41 healthy controls have been tested against both the designed ASOs. The study reveals 100% specificity and sensitivity with the employed samples and thereby opens up new avenues for PCR-free direct genotyping of other viruses as well, through the rational design of ASOs.
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Affiliation(s)
- Almas Shamaila Mohammed
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India.
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30
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Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus. Viruses 2021; 13:v13040616. [PMID: 33916702 PMCID: PMC8067247 DOI: 10.3390/v13040616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Replication of RNA viruses is characterized by exploration of sequence space which facilitates their adaptation to changing environments. It is generally accepted that such exploration takes place mainly in response to positive selection, and that further diversification is boosted by modifications of virus population size, particularly bottleneck events. Our recent results with hepatitis C virus (HCV) have shown that the expansion in sequence space of a viral clone continues despite prolonged replication in a stable cell culture environment. Diagnosis of the expansion was based on the quantification of diversity indices, the occurrence of intra-population mutational waves (variations in mutant frequencies), and greater individual residue variations in mutant spectra than those anticipated from sequence alignments in data banks. In the present report, we review our previous results, and show additionally that mutational waves in amplicons from the NS5A-NS5B-coding region are equally prominent during HCV passage in the absence or presence of the mutagenic nucleotide analogues favipiravir or ribavirin. In addition, by extending our previous analysis to amplicons of the NS3- and NS5A-coding region, we provide further evidence of the incongruence between amino acid conservation scores in mutant spectra from infected patients and in the Los Alamos National Laboratory HCV data banks. We hypothesize that these observations have as a common origin a permanent state of HCV population disequilibrium even upon extensive viral replication in the absence of external selective constraints or changes in population size. Such a persistent disequilibrium—revealed by the changing composition of the mutant spectrum—may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed.
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