1
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Ali AA, Tabll AA. Unlocking potential: Virus-like particles as a promising strategy for effective HCV vaccine development. Virology 2025; 602:110307. [PMID: 39580887 DOI: 10.1016/j.virol.2024.110307] [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: 10/01/2024] [Revised: 11/01/2024] [Accepted: 11/14/2024] [Indexed: 11/26/2024]
Abstract
Hepatitis C virus (HCV) is a leading cause of liver disease worldwide. The development of prophylactic vaccine is essential for HCV global eradication. Despite over three decades of research, no effective vaccine for HCV has been developed, primarily due to the virus's genetic diversity, immune evasion mechanisms, and incomplete understanding of protective immunity. However, Virus-Like Particles (VLPs) offer a promising approach to overcoming these challenges. VLPs mimic the structure of native virus but without the infectious genome, making them safe and non-infectious vaccines candidates. The capability of VLPs to incorporate neutralizing and conformational epitopes, and engage humoral and cellular immune responses, positions them as a promising tool for overcoming challenges associated with the HCV vaccine development. This review examines the challenges and immunological considerations for HCV vaccine development and provides an overview of the VLPs-based vaccines development. It also discusses future directions and public health implications of HCV vaccine development.
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Affiliation(s)
- Ahmed A Ali
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, (NRC), 12622, Cairo, Egypt.
| | - Ashraf A Tabll
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, 12622, Cairo, Egypt; Egyptian Centre for Research and Regenerative Medicine (ECRRM), 11517, Cairo, Egypt.
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2
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Lee JK, Choi JW, Park I, Kim NE, Kwon HC, Kwon J, Song YJ. Roseoside Is a Bioactive Compound in Kirengeshoma koreana Nakai Extract with Potent In Vitro Antiviral Activity Against Hepatitis C Virus. Molecules 2024; 29:5130. [PMID: 39519772 PMCID: PMC11547465 DOI: 10.3390/molecules29215130] [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: 09/20/2024] [Revised: 10/16/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
Hepatitis C virus (HCV) is a pathogen that causes cirrhosis and hepatocellular carcinoma through chronic hepatitis C. This study focused on the anti-HCV activity of a 70% ethanol extract of Kirengeshoma koreana Nakai (KKE) and its bioactive chemical constituent(s). The KKE and its n-butanol (n-BuOH) fraction induced a significant reduction in HCV RNA levels without inducing cytotoxicity. A high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis revealed the presence of roseoside in the n-butanol fraction of the KKE, which inhibited HCV RNA replication in a concentration- and time-dependent manner without exerting cytotoxicity. Consistent with in silico molecular docking analysis data, roseoside targets and inhibits HCV NS5A/B replicase. Collectively, our findings demonstrate that roseoside is a chemical constituent in KKE that interferes with HCV replication by targeting NS5A/B replicase.
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Affiliation(s)
- Jun-Kyu Lee
- Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea; (J.-K.L.); (J.-W.C.); (N.-E.K.)
| | - Ji-Wan Choi
- Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea; (J.-K.L.); (J.-W.C.); (N.-E.K.)
| | - InWha Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea; (I.P.); (H.C.K.)
| | - Na-Eun Kim
- Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea; (J.-K.L.); (J.-W.C.); (N.-E.K.)
| | - Hak Cheol Kwon
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea; (I.P.); (H.C.K.)
| | - Jaeyoung Kwon
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea; (I.P.); (H.C.K.)
| | - Yoon-Jae Song
- Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea; (J.-K.L.); (J.-W.C.); (N.-E.K.)
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3
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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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4
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Echeverría N, Gámbaro F, Beaucourt S, Soñora M, Hernández N, Cristina J, Moratorio G, Moreno P. Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region. Viruses 2024; 16:560. [PMID: 38675902 PMCID: PMC11053413 DOI: 10.3390/v16040560] [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: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatitis C virus (HCV) remains a significant global health challenge, affecting millions of people worldwide, with chronic infection a persistent threat. Despite the advent of direct-acting antivirals (DAAs), challenges in diagnosis and treatment remain, compounded by the lack of an effective vaccine. The HCV genome, characterized by high genetic variability, consists of eight distinct genotypes and over ninety subtypes, underscoring the complex dynamics of the virus within infected individuals. This study delves into the intriguing realm of HCV genetic diversity, specifically exploring the phenomenon of mixed infections and the subsequent detection of recombinant forms within the conserved internal ribosome entry site (IRES) region. Previous studies have identified recombination as a rare event in HCV. However, our findings challenge this notion by providing the first evidence of 1a/3a (and vice versa) inter-genotypic recombination within the conserved IRES region. Utilizing advanced sequencing methods, such as deep sequencing and molecular cloning, our study reveals mixed infections involving genotypes 1a and 3a. This comprehensive approach not only confirmed the presence of mixed infections, but also identified the existence of recombinant forms not previously seen in the IRES region. The recombinant sequences, although present as low-frequency variants, open new avenues for understanding HCV evolution and adaptation.
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Affiliation(s)
- Natalia Echeverría
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Fabiana Gámbaro
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
| | - Stéphanie Beaucourt
- Viral Populations and Pathogenesis Laboratory, Institut Pasteur, 75015 Paris, France;
| | - Martín Soñora
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Nelia Hernández
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay;
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
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5
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Poddar S, Roy R, Kar P. The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations. J Biomol Struct Dyn 2024:1-16. [PMID: 38393644 DOI: 10.1080/07391102.2024.2319679] [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: 12/02/2023] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
The Hepatitis C Virus (HCV), responsible for causing hepatitis and a significant contributor to liver disorders, presents a challenge for treatment due to its high genetic variability. Despite efforts, there is still no effective medication available for this virus. One of the promising targets for drug development involves targeting glycoprotein E2. However, our understanding of the dynamic behavior of E2 and its associated glycans remains limited. In this study, we investigated the dynamic characteristics of E2 with varying degrees of glycosylation using all-atom molecular dynamics simulations. We also explored glycan's interactions with the protein and among themselves. An overall increase in correlation between the vital protein regions was observed with an increase in glycan number. The protein dynamics is followed by the analysis of glycan dynamics, where the flexibility of the individual glycans was analyzed in their free and bound state, which revealed a decrease in their fluctuation in some cases. Furthermore, we generated the free energy landscape of individual N-glycan linkages in both free and bound states and observed both increases and decreases in flexibility, which can be attributed to the formation and breakage of hydrogen bonds with amino acids. Finally, we found that for a high glycosylation system, glycans interact with glycoprotein and form hydrogen bonds among themselves. Moreover, the hydrogen bond profiles of a given glycan can vary when influenced by other glycans. In summary, our study provides valuable insights into the dynamics of the core region of HCV E2 glycoprotein and its associated glycans.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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6
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Kalyanasundaram G, Feng JE, Congiusta F, Iorio R, DiCaprio M, Anoushiravani AA. Treating Hepatitis C Before Total Knee Arthroplasty is Cost-Effective: A Markov Analysis. J Arthroplasty 2024; 39:307-312. [PMID: 37604270 DOI: 10.1016/j.arth.2023.08.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Patients who have the hepatitis C virus (HCV) have increased mortality and complication rates following total knee arthroplasty (TKA). Recent advances in HCV therapy have enabled clinicians to eradicate the disease using direct-acting antivirals (DAAs); however, its cost-effectiveness before TKA remains to be demonstrated. The aim of this study was to perform a cost-effectiveness analysis comparing no therapy to DAAs before TKA. METHODS A Markov model using input values from the published literature was performed to evaluate the cost-effectiveness of DAA treatment before TKA. Input values included event probabilities, mortality, cost, and health state quality-adjusted life-year (QALY) values for patients who have and do not have HCV. Patients who have HCV were modeled to have an increased rate of periprosthetic joint infection (PJI) infection (9.9 to 0.7%). The incremental cost-effectiveness ratio (ICER) of no therapy versus DAA was compared to a willingness-to-pay threshold of $100,000/QALY. Sensitivity analyses were performed to investigate the effects of uncertainty associated with input variables. RESULTS Total knee arthroplasty in the setting of no therapy and DAA added 8.1 and 13.5 QALYs at a cost of $25,000 and $114,900. The ICER associated with DAA in comparison to no therapy was $16,800/QALY, below the willingness-to-pay threshold of $100,000/QALY. Sensitivity analyses demonstrated that the ICER was affected by patient age, inflation rate, DAA cost and effectiveness, HCV-associated mortality, and DAA-induced reduction in PJI rate. CONCLUSION Direct-acting antiviral treatment before TKA reduces risk of PJI and is cost-effective. Strong consideration should be given to treating patients who have HCV before elective TKA. LEVEL OF EVIDENCE Cost-effectiveness Analysis; Level III.
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Affiliation(s)
| | - James E Feng
- Department of Orthopaedic Surgery, Beaumont Health, Royal Oak, Michigan
| | | | - Richard Iorio
- Department of Surgery, Brigham Women's Health, Boston, Massachusetts
| | - Matthew DiCaprio
- Department of Orthopaedic Surgery, Albany Medical Center, Albany, New York
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7
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Medina C, García AH, Crespo FI, Toro FI, Mayora SJ, De Sanctis JB. A Synopsis of Hepatitis C Virus Treatments and Future Perspectives. Curr Issues Mol Biol 2023; 45:8255-8276. [PMID: 37886964 PMCID: PMC10605161 DOI: 10.3390/cimb45100521] [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: 09/28/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Hepatitis C virus (HCV) infection is a worldwide public health problem. Chronic infection with HCV can lead to liver cirrhosis or cancer. Although some immune-competent individuals can clear the virus, others develop chronic HCV disease due to viral mutations or an impaired immune response. IFNs type I and III and the signal transduction induced by them are essential for a proper antiviral effect. Research on the viral cycle and immune escape mechanisms has formed the basis of therapeutic strategies to achieve a sustained virological response (SVR). The first therapies were based on IFNα; then, IFNα plus ribavirin (IFN-RBV); and then, pegylated-IFNα-RBV (PEGIFNα-RIV) to improve cytokine pharmacokinetics. However, the maximum SVR was 60%, and several significant side effects were observed, decreasing patients' treatment adherence. The development of direct-acting antivirals (DAAs) significantly enhanced the SVR (>90%), and the compounds were able to inhibit HCV replication without significant side effects, even in paediatric populations. The management of coinfected HBV-HCV and HCV-HIV patients has also improved based on DAA and PEG-IFNα-RBV (HBV-HCV). CD4 cells are crucial for an effective antiviral response. The IFNλ3, IL28B, TNF-α, IL-10, TLR-3, and TLR-9 gene polymorphisms are involved in viral clearance, therapeutic responses, and hepatic pathologies. Future research should focus on searching for strategies to circumvent resistance-associated substitution (RAS) to DAAs, develop new therapeutic schemes for different medical conditions, including organ transplant, and develop vaccines for long-lasting cellular and humoral responses with cross-protection against different HCV genotypes. The goal is to minimise the probability of HCV infection, HCV chronicity and hepatic carcinoma.
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Affiliation(s)
- Christian Medina
- Institute of Immunology Dr. Nicolás E. Bianco C., Faculty of Medicine, Universidad Central de Venezuela, Caracas 1040, Venezuela; (C.M.); (F.I.C.); (F.I.T.); (S.J.M.)
| | - Alexis Hipólito García
- Institute of Immunology Dr. Nicolás E. Bianco C., Faculty of Medicine, Universidad Central de Venezuela, Caracas 1040, Venezuela; (C.M.); (F.I.C.); (F.I.T.); (S.J.M.)
| | - Francis Isamarg Crespo
- Institute of Immunology Dr. Nicolás E. Bianco C., Faculty of Medicine, Universidad Central de Venezuela, Caracas 1040, Venezuela; (C.M.); (F.I.C.); (F.I.T.); (S.J.M.)
| | - Félix Isidro Toro
- Institute of Immunology Dr. Nicolás E. Bianco C., Faculty of Medicine, Universidad Central de Venezuela, Caracas 1040, Venezuela; (C.M.); (F.I.C.); (F.I.T.); (S.J.M.)
| | - Soriuska José Mayora
- Institute of Immunology Dr. Nicolás E. Bianco C., Faculty of Medicine, Universidad Central de Venezuela, Caracas 1040, Venezuela; (C.M.); (F.I.C.); (F.I.T.); (S.J.M.)
| | - Juan Bautista De Sanctis
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, 779 00 Olomouc, Czech Republic
- The Czech Advanced Technology and Research Institute (Catrin), Palacky University, 779 00 Olomouc, Czech Republic
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8
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Chowdhary S, Deka R, Panda K, Kumar R, Solomon AD, Das J, Kanoujiya S, Gupta AK, Sinha S, Ruokolainen J, Kesari KK, Gupta PK. Recent Updates on Viral Oncogenesis: Available Preventive and Therapeutic Entities. Mol Pharm 2023; 20:3698-3740. [PMID: 37486263 PMCID: PMC10410670 DOI: 10.1021/acs.molpharmaceut.2c01080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
Human viral oncogenesis is a complex phenomenon and a major contributor to the global cancer burden. Several recent findings revealed cellular and molecular pathways that promote the development and initiation of malignancy when viruses cause an infection. Even, antiviral treatment has become an approach to eliminate the viral infections and prevent the activation of oncogenesis. Therefore, for a better understanding, the molecular pathogenesis of various oncogenic viruses like, hepatitis virus, human immunodeficiency viral (HIV), human papillomavirus (HPV), herpes simplex virus (HSV), and Epstein-Barr virus (EBV), could be explored, especially, to expand many potent antivirals that may escalate the apoptosis of infected malignant cells while sparing normal and healthy ones. Moreover, contemporary therapies, such as engineered antibodies antiviral agents targeting signaling pathways and cell biomarkers, could inhibit viral oncogenesis. This review elaborates the recent advancements in both natural and synthetic antivirals to control viral oncogenesis. The study also highlights the challenges and future perspectives of using antivirals in viral oncogenesis.
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Affiliation(s)
- Shivam Chowdhary
- Department
of Industrial Microbiology, Sam Higginbottom
University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh India
| | - Rahul Deka
- Department
of Bioengineering and Biotechnology, Birla
Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Kingshuk Panda
- Department
of Applied Microbiology, Vellore Institute
of Technology, Vellore 632014, Tamil Nadu, India
| | - Rohit Kumar
- Department
of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida 201310, Uttar Pradesh, India
| | - Abhishikt David Solomon
- Department
of Molecular & Cellular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India
| | - Jimli Das
- Centre
for
Biotechnology and Bioinformatics, Dibrugarh
University, Assam 786004, India
| | - Supriya Kanoujiya
- School
of
Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashish Kumar Gupta
- Department
of Biophysics, All India Institute of Medical
Sciences, New Delhi 110029, India
| | - Somya Sinha
- Department
of Biotechnology, Graphic Era Deemed to
Be University, Dehradun 248002, Uttarakhand, India
| | - Janne Ruokolainen
- Department
of Applied Physics, School of Science, Aalto
University, 02150 Espoo, Finland
| | - Kavindra Kumar Kesari
- Department
of Applied Physics, School of Science, Aalto
University, 02150 Espoo, Finland
- Division
of Research and Development, Lovely Professional
University, Phagwara 144411, Punjab, India
| | - Piyush Kumar Gupta
- Department
of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida 201310, Uttar Pradesh, India
- Department
of Biotechnology, Graphic Era Deemed to
Be University, Dehradun 248002, Uttarakhand, India
- Faculty
of Health and Life Sciences, INTI International
University, Nilai 71800, Malaysia
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9
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Moussaoui A, Volpert V. The influence of immune cells on the existence of virus quasi-species. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:15942-15961. [PMID: 37919996 DOI: 10.3934/mbe.2023710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
This article investigate a nonlocal reaction-diffusion system of equations modeling virus distribution with respect to their genotypes in the interaction with the immune response. This study demonstrates the existence of pulse solutions corresponding to virus quasi-species. The proof is based on the Leray-Schauder method, which relies on the topological degree for elliptic operators in unbounded domains and a priori estimates of solutions. Furthermore, linear stability analysis of a spatially homogeneous stationary solution identifies the critical conditions for the emergence of spatial and spatiotemporal structures. Finally, numerical simulations are used to illustrate nonlinear dynamics and pattern formation in the nonlocal model.
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Affiliation(s)
- Ali Moussaoui
- Laboratoire d'Analyse Non linéaire et Mathématiques Appliquées, Department of Mathematics, Faculty of Sciences, University of Tlemcen, Algeria
| | - Vitaly Volpert
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, Villeurbanne 69622, France
- Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian Federation
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10
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Zhao J, Zhao Y, Zhang G. Key Aspects of Coronavirus Avian Infectious Bronchitis Virus. Pathogens 2023; 12:pathogens12050698. [PMID: 37242368 DOI: 10.3390/pathogens12050698] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an enveloped and positive-sense single-stranded RNA virus. IBV was the first coronavirus to be discovered and predominantly causes respiratory disease in commercial poultry worldwide. This review summarizes several important aspects of IBV, including epidemiology, genetic diversity, antigenic diversity, and multiple system disease caused by IBV as well as vaccination and antiviral strategies. Understanding these areas will provide insight into the mechanism of pathogenicity and immunoprotection of IBV and may improve prevention and control strategies for the disease.
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Affiliation(s)
- Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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11
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Athamneh RY, Abudalo R, Sallam M, Alqudah A, Alquran H, Amawi KF, Abu-Harirah HA. Sub-genotypes of hepatitis C virus in the Middle East and North Africa: Patterns of distribution and temporal changes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105412. [PMID: 36791585 DOI: 10.1016/j.meegid.2023.105412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Infection with the hepatitis C virus (HCV) remains a considerable public health concern in the Middle East and North Africa (MENA). The objectives of this study were to analyze the HCV genotype (GT) and sub-genotype (SGT) distribution in the MENA region and to assess the temporal change in the number of sequences within the MENA region. All HCV molecular sequences collected in the MENA region had been retrieved from GenBank as of 1 August 2022. The number of HCV sequences retrieved was 6740 representing sequences from a total of 17 MENA countries with a majority from Iran (n = 1969, 29.2%), Egypt (n = 1591, 23.6%), Tunisia (n = 1305, 19.4%) and Saudi Arabia (n = 1085, 16.1%). The determination of GT/SGT was based on the NCBI genotyping and Blast tool. Genotype 1 (GT1) dominated infections in the MENA (n = 2777, 41.2%), followed by GT4 (n = 2566, 39.0%). Additionally, SGT4a (1515/6393, 23.7%) was the most common SGT in the MENA, and SGT4a was dominant in Egypt and Saudi Arabia, followed by SGT1b (n = 1308, 20.5%), which was dominant in Morocco and Tunisia, while SGT1a (n = 1275, 19.9%) was common in Iran, Iraq and Palestine. Furthermore, significant temporal increase in the number of HCV MENA sequences was observed. On the SGT level, specific patterns of HCV genetic diversity were seen in the MENA region, with the most common SGT being 4a, in addition to increasing the availability of HCV sequences in the MENA region.
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Affiliation(s)
- Rabaa Y Athamneh
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan.
| | - Rawan Abudalo
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan; Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Abdelrahim Alqudah
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Hasan Alquran
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Kawther Faisal Amawi
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Hashem A Abu-Harirah
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
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12
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Anoushiravani AA, Kalyanasundaram G, Feng JE, Congiusta F, Iorio R, DiCaprio M. Treating Hepatitis C Prior to Total Hip Arthroplasty is Cost Effective: A Markov Analysis. J Arthroplasty 2023:S0883-5403(23)00198-5. [PMID: 36878438 DOI: 10.1016/j.arth.2023.02.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 03/08/2023] Open
Abstract
INTRODUCTION Patients infected with the hepatitis C virus (HCV) have high complication rates following total hip arthroplasty (THA). Advances in HCV therapy now enable clinicians to eradicate the disease, however, its cost effectiveness from an orthopaedic perspective remains to be demonstrated. We sought to conduct a cost effectiveness analysis comparing no therapy to direct acting antiviral therapy (DAA) prior to THA among HCV positive patients. METHODS A Markov model was utilized to evaluate the cost-effectiveness of treating HCV with DAA prior to THA. The model was powered with event probabilities, mortality, cost and quality adjusted life-year values for patients with and without HCV that were obtained from the published literature. This included treatment costs, successes of HCV eradication, incidences of superficial or periprosthetic joint infection (PJI), probabilities of utilizing various PJI treatment modalities, PJI treatment success/failures, and mortality rates. The incremental cost-effectiveness ratio (ICER) was compared to a willingness-to-pay threshold of $50,000/QALY. RESULTS Our Markov model indicates that in comparison to no therapy, DAA prior to THA is cost-effective for HCV positive patients. THA in the setting of no therapy and DAA added 8.06 and 14.39 QALYs at a mean cost of $28,800 and $115,800. The ICER associated with HCV DAA in comparison to no therapy was $13,800/QALY, below the willingness-to-pay threshold of $50,000/QALY. CONCLUSION Hepatitis-C treatment with DAA prior to THA is cost-effective at all current drug list prices. Given these findings, strong consideration should be given to treating patients for HCV prior to elective THA.
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Affiliation(s)
| | | | - James E Feng
- Department of Orthopaedic Surgery, Corewell Health William Beaumont University Hospital, Royal Oak, Michigan
| | | | - Richard Iorio
- Department of Orthopaedic Surgery, Brigham Women's Health, Boston, Massachusetts
| | - Matthew DiCaprio
- Department of Orthopaedic Surgery, Albany Medical Center, Albany, New York
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13
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Elbahrawy A, Atalla H, Alboraie M, Alwassief A, Madian A, El Fayoumie M, Tabll AA, Aly HH. Recent Advances in Protective Vaccines against Hepatitis Viruses: A Narrative Review. Viruses 2023; 15:214. [PMID: 36680254 PMCID: PMC9862019 DOI: 10.3390/v15010214] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Vaccination has been confirmed to be the safest and, sometimes, the only tool of defense against threats from infectious diseases. The successful history of vaccination is evident in the control of serious viral infections, such as smallpox and polio. Viruses that infect human livers are known as hepatitis viruses and are classified into five major types from A to E, alphabetically. Although infection with hepatitis A virus (HAV) is known to be self-resolving after rest and symptomatic treatment, there were 7134 deaths from HAV worldwide in 2016. In 2019, hepatitis B virus (HBV) and hepatitis C virus (HCV) resulted in an estimated 820,000 and 290,000 deaths, respectively. Hepatitis delta virus (HDV) is a satellite virus that depends on HBV for producing its infectious particles in order to spread. The combination of HDV and HBV infection is considered the most severe form of chronic viral hepatitis. Hepatitis E virus (HEV) is another orally transmitted virus, common in low- and middle-income countries. In 2015, it caused 44,000 deaths worldwide. Safe and effective vaccines are already available to prevent hepatitis A and B. Here, we review the recent advances in protective vaccines against the five major hepatitis viruses.
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Affiliation(s)
- Ashraf Elbahrawy
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Hassan Atalla
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed Alboraie
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed Alwassief
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Al-Azhar University, Cairo 11884, Egypt
- Gastroenterology Unit, Department of Internal Medicine, Sultan Qaboos University Hospital, P.O. Box 50, Muscat 123, Oman
| | - Ali Madian
- Department of Internal Medicine, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt
| | - Mohammed El Fayoumie
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Ashraf A. Tabll
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Center, Giza 12622, Egypt
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo 11517, Egypt
| | - Hussein H. Aly
- Department of Virology II, National Institute of Infectious Diseases, Toyama1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
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14
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Mechanisms and Consequences of Genetic Variation in Hepatitis C Virus (HCV). Curr Top Microbiol Immunol 2023; 439:237-264. [PMID: 36592248 DOI: 10.1007/978-3-031-15640-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) is an important contributor to the global incidence of liver diseases, including liver cirrhosis and hepatocellular carcinoma. Although common for single-stranded RNA viruses, HCV displays a remarkable high level of genetic diversity, produced primarily by the error-prone viral polymerase and host immune pressure. The high genetic heterogeneity of HCV has led to the evolution of several distinct genotypes and subtypes, with important consequences for pathogenesis, and clinical outcomes. Genetic variability constitutes an evasion mechanism against immune suppression, allowing the virus to evolve epitope escape mutants that avoid immune recognition. Thus, heterogeneity and variability of the HCV genome represent a great hindrance for the development of vaccines against HCV. In addition, the high genetic plasticity of HCV allows the virus to rapidly develop antiviral resistance mutations, leading to treatment failure and potentially representing a major hindrance for the cure of chronic HCV patients. In this chapter, we will present the central role that genetic diversity has in the viral life cycle and epidemiology of HCV. Incorporation errors and recombination, both the result of HCV polymerase activity, represent the main mechanisms of HCV evolution. The molecular details of both mechanisms have been only partially clarified and will be presented in the following sections. Finally, we will discuss the major consequences of HCV genetic diversity, namely its capacity to rapidly evolve antiviral and immunological escape variants that represent an important limitation for clearance of acute HCV, for treatment of chronic hepatitis C and for broadly protective vaccines.
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15
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Selective Depletion of ZAP-Binding CpG Motifs in HCV Evolution. Pathogens 2022; 12:pathogens12010043. [PMID: 36678391 PMCID: PMC9866289 DOI: 10.3390/pathogens12010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Hepatitis C virus (HCV) is a bloodborne pathogen that can cause chronic liver disease and hepatocellular carcinoma. The loss of CpGs from virus genomes allows escape from restriction by the host zinc-finger antiviral protein (ZAP). The evolution of HCV in the human host has not been explored in the context of CpG depletion. We analysed 2616 full-length HCV genomes from 1977 to 2021. During the four decades of evolution in humans, we found that HCV genomes have become significantly depleted in (a) CpG numbers, (b) CpG O/E ratios (i.e., relative abundance of CpGs), and (c) the number of ZAP-binding motifs. Interestingly, our data suggests that the loss of CpGs in HCV genomes over time is primarily driven by the loss of ZAP-binding motifs; thus suggesting a yet unknown role for ZAP-mediated selection pressures in HCV evolution. The HCV core gene is significantly enriched for the number of CpGs and ZAP-binding motifs. In contrast to the rest of the HCV genome, the loss of CpGs from the core gene does not appear to be driven by ZAP-mediated selection. This work highlights CpG depletion in HCV genomes during their evolution in humans and the role of ZAP-mediated selection in HCV evolution.
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16
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Tisthammer KH, Solis C, Orcales F, Nzerem M, Winstead R, Dong W, Joy JB, Pennings PS. Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus. PLoS Genet 2022; 18:e1010179. [PMID: 35500034 PMCID: PMC9113599 DOI: 10.1371/journal.pgen.1010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/17/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Like many viruses, Hepatitis C Virus (HCV) has a high mutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be site and virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes.
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Affiliation(s)
- Kaho H. Tisthammer
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
- * E-mail:
| | - Caroline Solis
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Faye Orcales
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Madu Nzerem
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ryan Winstead
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Colombia, Canada
| | - Jeffrey B. Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Colombia, Canada
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, British Colombia, Canada
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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17
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Marascio N, Rotundo S, Quirino A, Matera G, Liberto MC, Costa C, Russo A, Trecarichi EM, Torti C. Similarities, differences, and possible interactions between hepatitis E and hepatitis C viruses: Relevance for research and clinical practice. World J Gastroenterol 2022; 28:1226-1238. [PMID: 35431515 PMCID: PMC8968488 DOI: 10.3748/wjg.v28.i12.1226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/06/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Hepatitis E virus (HEV) and hepatitis C virus (HCV) are both RNA viruses with a tropism for liver parenchyma but are also capable of extrahepatic manifestations. Hepatitis E is usually a viral acute fecal-oral transmitted and self-limiting disease presenting with malaise, jaundice, nausea and vomiting. Rarely, HEV causes a chronic infection in immunocompromised persons and severe fulminant hepatitis in pregnant women. Parenteral HCV infection is typically asymptomatic for decades until chronic complications, such as cirrhosis and cancer, occur. Despite being two very different viruses in terms of phylogenetic and clinical presentations, HEV and HCV show many similarities regarding possible transmission through organ transplantation and blood transfusion, pathogenesis (production of antinuclear antibodies and cryoglobulins) and response to treatment with some direct-acting antiviral drugs. Although both HEV and HCV are well studied individually, there is a lack of knowledge about coinfection and its consequences. The aim of this review is to analyze current literature by evaluating original articles and case reports and to hypothesize some interactions that can be useful for research and clinical practice.
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Affiliation(s)
- Nadia Marascio
- Department of Health Sciences, Unit of Microbiology, University “Magna Graecia” of Catanzaro, Catanzaro 88100, Italy
| | - Salvatore Rotundo
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, "Magna Graecia" University of Catanzaro, Catanzaro 88100, Italy
| | - Angela Quirino
- Department of Health Sciences, Unit of Microbiology, University “Magna Graecia” of Catanzaro, Catanzaro 88100, Italy
| | - Giovanni Matera
- Department of Health Sciences, Unit of Microbiology, University “Magna Graecia” of Catanzaro, Catanzaro 88100, Italy
| | - Maria Carla Liberto
- Department of Health Sciences, Unit of Microbiology, University “Magna Graecia” of Catanzaro, Catanzaro 88100, Italy
| | - Chiara Costa
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, "Magna Graecia" University of Catanzaro, Catanzaro 88100, Italy
| | - Alessandro Russo
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, "Magna Graecia" University of Catanzaro, Catanzaro 88100, Italy
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, "Magna Graecia" University of Catanzaro, Catanzaro 88100, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, "Magna Graecia" University of Catanzaro, Catanzaro 88100, Italy
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18
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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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19
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Echeverría N, Comas V, Aldunate F, Perbolianachis P, Moreno P, Cristina J. In the era of rapid mRNA-based vaccines: Why is there no effective hepatitis C virus vaccine yet? World J Hepatol 2021; 13:1234-1268. [PMID: 34786164 PMCID: PMC8568586 DOI: 10.4254/wjh.v13.i10.1234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/14/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is responsible for no less than 71 million people chronically infected and is one of the most frequent indications for liver transplantation worldwide. Despite direct-acting antiviral therapies fuel optimism in controlling HCV infections, there are several obstacles regarding treatment accessibility and reinfection continues to remain a possibility. Indeed, the majority of new HCV infections in developed countries occur in people who inject drugs and are more plausible to get reinfected. To achieve global epidemic control of this virus the development of an effective prophylactic or therapeutic vaccine becomes a must. The coronavirus disease 19 (COVID-19) pandemic led to auspicious vaccine development against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus, which has renewed interest on fighting HCV epidemic with vaccination. The aim of this review is to highlight the current situation of HCV vaccine candidates designed to prevent and/or to reduce HCV infectious cases and their complications. We will emphasize on some of the crossroads encountered during vaccine development against this insidious virus, together with some key aspects of HCV immunology which have, so far, hampered the progress in this area. The main focus will be on nucleic acid-based as well as recombinant viral vector-based vaccine candidates as the most novel vaccine approaches, some of which have been recently and successfully employed for SARS-CoV-2 vaccines. Finally, some ideas will be presented on which methods to explore for the design of live-attenuated vaccines against HCV.
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Affiliation(s)
- Natalia Echeverría
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Victoria Comas
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay
| | - Fabián Aldunate
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Paula Perbolianachis
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
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20
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Ali ME, Halby HM, Ali MY, Hassan EA, El-Mokhtar MA, Sayed IM, Thabet MM, Fouad M, El-Ashmawy AM, Mahran ZG. Role of Serum Vitamin D, Interleukin 13, and microRNA-135a in Hepatocellular Carcinoma and Treatment Failure in Egyptian HCV-Infected Patients Receiving Direct Antiviral Agents. Viruses 2021; 13:2008. [PMID: 34696438 PMCID: PMC8539757 DOI: 10.3390/v13102008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/12/2022] Open
Abstract
Direct-acting antivirals (DAAs) are used for hepatitis C virus (HCV) treatment. However, treatment failure and hepatocellular carcinoma (HCC) development following treatment was reported. In this study, we assessed the role of serum vitamin D, interleukin 13 (IL-13), and microRNA-135a in the prediction of treatment failure with DAA and HCC development among Egyptian HCV-infected patients. A total of 950 patients with HCV-related chronic liver disease underwent DAA treatment. Before DAAs, serum vitamin D and IL-13 were determined by ELISA, and gene expression of miRNA-135a was assessed in serum by real-time PCR. The predictive abilities of these markers were determined using the receiver operating characteristic (ROC) curve. Sustained virological response (SVR) was achieved in 92.6% of HCV-infected patients (responders). High viral load, IL-13, miRNA-135a, and low vitamin D levels were associated with treatment failure and HCC development. HCC development was recorded in non-responders, but not in the responders (35.7% vs. 0% p < 0.001). In conclusion: serum IL-13, Vitamin D, and miRNA-135a could be potential biomarkers in monitoring DAA treatment and HCC prediction. DAAs-induced SVR may decrease the incidence of HCC.
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Affiliation(s)
- Mohamed E. Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt; (M.E.A.); (H.M.H.); (M.Y.A.)
| | - Hamada M. Halby
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt; (M.E.A.); (H.M.H.); (M.Y.A.)
| | - Mamdouh Yones Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt; (M.E.A.); (H.M.H.); (M.Y.A.)
| | - Elham Ahmed Hassan
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Mohamed A. El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt; (M.A.E.-M.); (I.M.S.)
| | - Ibrahim M. Sayed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt; (M.A.E.-M.); (I.M.S.)
| | - Marwa M. Thabet
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Magdy Fouad
- Hepato-Gastroenterology Unit, Tropical Medicine Department, Faculty of Medicine, El-Minia University, Minya 61519, Egypt;
| | - Ahmed M. El-Ashmawy
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Zainab Gaber Mahran
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
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21
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Characterization of linear epitope specificity of antibodies potentially contributing to spontaneous clearance of hepatitis C virus. PLoS One 2021; 16:e0256816. [PMID: 34449828 PMCID: PMC8396737 DOI: 10.1371/journal.pone.0256816] [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: 03/11/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022] Open
Abstract
Background Around 30% of the HCV infected patients can spontaneously clear the virus. Cumulative evidence suggests the role of neutralizing antibodies in such spontaneous resolution. Understanding the epitope specificity of such antibodies will inform the rational vaccine design as such information is limited to date. In addition to conformational epitope targeted antibodies, linear epitope specific antibodies have been identified that are broadly cross reactive against diverse HCV strains. In this study, we have characterized the potential role of three conserved linear epitopes in the spontaneous clearance of HCV. Methods We tested the reactivity of sera from chronic patients (CP) and spontaneous resolvers (SR) with linear peptides corresponding to three conserved regions of HCV envelope protein E2 spanning amino acids 412–423, 523–532 and 432–443 using ELISA. Subsequently, we characterized the dependency of HCV neutralization by the reactive serum samples on the antibodies specific for these epitopes using pseudoparticle-based neutralization assay. In ELISA most of the CP sera showed reactivity to multiple peptides while most of the SR samples were reactive to a single peptide suggesting presence of more specific antibodies in the SR sera. In most of the HCVpp neutralizing sera of particular peptide reactivity the neutralization was significantly affected by the presence of respective peptide. HCV neutralization by CP sera was affected by multiple peptides while 75% of the HCVpp neutralizing SR sera were competed by the 432 epitope. Conclusions These findings suggest that individuals who spontaneously resolve HCV infection at the acute phase, can produce antibodies specific for conserved linear epitopes, and those antibodies can potentially play a role in the spontaneous viral clearance. The epitope present in the 432–443 region of E2 was identified as the primary neutralizing epitope with potential role in spontaneous viral clearance and this epitope potentiates for the design of immunogen for prophylactic vaccine.
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22
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N6-methyladenosine modification of HCV RNA genome regulates cap-independent IRES-mediated translation via YTHDC2 recognition. Proc Natl Acad Sci U S A 2021; 118:2022024118. [PMID: 33649237 DOI: 10.1073/pnas.2022024118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) infections are associated with the risk of progression to fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV RNA genome is translated by an internal ribosome entry site (IRES)-dependent mechanism. The structure and function of the HCV IRES have been investigated by both biological and biophysical criteria. Recently, the role of N6-methyladenosine (m6A) in cellular RNA and viral transcripts has been intensely investigated. The HCV RNA genome is m6A-methylated, and this modification regulates the viral life cycle. In this study, we investigated the role of m6A modification of the HCV genome in the IRES-dependent translation function by mutating m6A consensus motifs (DRACH) within the IRES element in stem-loop III and IV regions and studied their effect on translation initiation. There are several DRACH motifs within the IRES element. Of these, the DRACH motif at nucleotide (nt) 329-333, located about 7 nt upstream of initiator AUG (iAUG) codon, regulates IRES-mediated translation initiation. Mutational analysis showed that m6A methylation of the adenosine at nt 331 is essential for the IRES-dependent translation. m6A reader protein YTHDC2, containing the RNA helicase domain, recognizes m6A-methylated adenosine at nt 331 and, in concert with the cellular La antigen, supports HCV IRES-dependent translation. The RNA helicase dead YTHDC2 (E332Q) mutant failed to stimulate HCV translation initiation. This report highlights the functional roles of m6A modification and YTHDC2 in the HCV IRES-dependent translation initiation, thus offering alternative therapeutic avenues to interfere with the infectious process.
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23
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Santana MS, Lopes R, Peron IH, Cruz CR, Gaspar AM, Costa PI. Natural Bioactive Compounds as Adjuvant Therapy for Hepatitis C Infection. CURRENT NUTRITION & FOOD SCIENCE 2021. [DOI: 10.2174/1573401316999201009152726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background:
Hepatitis C virus infection is a significant global health burden, which
causes acute or chronic hepatitis. Acute hepatitis C is generally asymptomatic and progresses to
cure, while persistent infection can progress to chronic liver disease and extrahepatic manifestations.
Standard treatment is expensive, poorly tolerated, and has variable sustained virologic responses
amongst the different viral genotypes. New therapies involve direct acting antivirals; however,
it is also very expensive and may not be accessible for all patients worldwide. In order to provide
a complementary approach to the already existing therapies, natural bioactive compounds are
investigated as to their several biologic activities, such as direct antiviral properties against hepatitis
C, and effects on mitigating chronic progression of the disease, which include hepatoprotective,
antioxidant, anticarcinogenic and anti-inflammatory activities; additionally, these compounds present
advantages, as chemical diversity, low cost of production and milder or inexistent side effects.
Objective:
To present a broad perspective on hepatitis C infection, the chronic disease, and natural
compounds with promising anti-HCV activity. Methods: This review consists of a systematic review
study about the natural bioactive compounds as a potential therapy for hepatitis C infection.
Results:
The quest for natural products has yielded compounds with biologic activity, including viral
replication inhibition in vitro, demonstrating antiviral activity against hepatitis C.
Conclusion:
One of the greatest advantages of using natural molecules from plant extracts is the
low cost of production, not requiring chemical synthesis, which can lead to less expensive therapies
available to low and middle-income countries.
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Affiliation(s)
- Moema S. Santana
- Food and Nutrition Department, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara-SP, Brazil
| | - Rute Lopes
- Department of Biotechnology, Institute of Chemistry, Sao Paulo State University (UNESP), Araraquara-SP, Brazil
| | - Isabela H. Peron
- Food and Nutrition Department, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara-SP, Brazil
| | - Carla R. Cruz
- Food and Nutrition Department, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara-SP, Brazil
| | - Ana M.M. Gaspar
- Department of Biotechnology, Institute of Chemistry, São Paulo State University (UNESP), Araraquara-SP, Brazil
| | - Paulo I. Costa
- Food and Nutrition Department, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara-SP, Brazil
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24
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Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs. Sci Rep 2021; 11:9986. [PMID: 33976241 PMCID: PMC8113533 DOI: 10.1038/s41598-021-88132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Most individuals chronically infected with hepatitis C virus (HCV) are asymptomatic during the initial stages of infection and therefore the precise timing of infection is often unknown. Retrospective estimation of infection duration would improve existing surveillance data and help guide treatment. While intra-host viral diversity quantifications such as Shannon entropy have previously been utilized for estimating duration of infection, these studies characterize the viral population from only a relatively short segment of the HCV genome. In this study intra-host diversities were examined across the HCV genome in order to identify the region most reflective of time and the degree to which these estimates are influenced by high-risk activities including those associated with HCV acquisition. Shannon diversities were calculated for all regions of HCV from 78 longitudinally sampled individuals with known seroconversion timeframes. While the region of the HCV genome most accurately reflecting time resided within the NS3 gene, the gene region with the highest capacity to differentiate acute from chronic infections was identified within the NS5b region. Multivariate models predicting duration of infection from viral diversity significantly improved upon incorporation of variables associated with recent public, unsupervised drug use. These results could assist the development of strategic population treatment guidelines for high-risk individuals infected with HCV and offer insights into variables associated with a likelihood of transmission.
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25
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Zhan W, Muhuri M, Tai PWL, Gao G. Vectored Immunotherapeutics for Infectious Diseases: Can rAAVs Be The Game Changers for Fighting Transmissible Pathogens? Front Immunol 2021; 12:673699. [PMID: 34046041 PMCID: PMC8144494 DOI: 10.3389/fimmu.2021.673699] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Conventional vaccinations and immunotherapies have encountered major roadblocks in preventing infectious diseases like HIV, influenza, and malaria. These challenges are due to the high genomic variation and immunomodulatory mechanisms inherent to these diseases. Passive transfer of broadly neutralizing antibodies may offer partial protection, but these treatments require repeated dosing. Some recombinant viral vectors, such as those based on lentiviruses and adeno-associated viruses (AAVs), can confer long-term transgene expression in the host after a single dose. Particularly, recombinant (r)AAVs have emerged as favorable vectors, given their high in vivo transduction efficiency, proven clinical efficacy, and low immunogenicity profiles. Hence, rAAVs are being explored to deliver recombinant antibodies to confer immunity against infections or to diminish the severity of disease. When used as a vaccination vector for the delivery of antigens, rAAVs enable de novo synthesis of foreign proteins with the conformation and topology that resemble those of natural pathogens. However, technical hurdles like pre-existing immunity to the rAAV capsid and production of anti-drug antibodies can reduce the efficacy of rAAV-vectored immunotherapies. This review summarizes rAAV-based prophylactic and therapeutic strategies developed against infectious diseases that are currently being tested in pre-clinical and clinical studies. Technical challenges and potential solutions will also be discussed.
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Affiliation(s)
- Wei Zhan
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
| | - Manish Muhuri
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Phillip W. L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, United States
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, United States
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26
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Tisthammer KH, Dong W, Joy JB, Pennings PS. Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a. Viruses 2021; 13:511. [PMID: 33808782 PMCID: PMC8003410 DOI: 10.3390/v13030511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Understanding within-host evolution is critical for predicting viral evolutionary outcomes, yet such studies are currently lacking due to difficulty involving human subjects. Hepatitis C virus (HCV) is an RNA virus with high mutation rates. Its complex evolutionary dynamics and extensive genetic diversity are demonstrated in over 67 known subtypes. In this study, we analyzed within-host mutation frequency patterns of three HCV subtypes, using a large number of samples obtained from treatment-naïve participants by next-generation sequencing. We report that overall mutation frequency patterns are similar among subtypes, yet subtype 3a consistently had lower mutation frequencies and nucleotide diversity, while subtype 1a had the highest. We found that about 50% of genomic sites are highly conserved across subtypes, which are likely under strong purifying selection. We also compared within-host and between-host selective pressures, which revealed that Hyper Variable Region 1 within hosts was under positive selection, but was under slightly negative selection between hosts, which indicates that many mutations created within hosts are removed during the transmission bottleneck. Examining the natural prevalence of known resistance-associated variants showed their consistent existence in the treatment-naïve participants. These results provide insights into the differences and similarities among HCV subtypes that may be used to develop and improve HCV therapies.
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Affiliation(s)
- Kaho H. Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (J.B.J.)
| | - Jeffrey B. Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (J.B.J.)
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC V5Z 3J5, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
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27
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Qi M, Yang M, Xu L, Ma C, Huang P, Sun J, Shi J, Hu Y. Complete genome analysis identifies recombinant events and positive selection sites of hepatitis C virus from mainland China during 2010-2019. Virus Res 2021; 296:198354. [PMID: 33639223 DOI: 10.1016/j.virusres.2021.198354] [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: 01/13/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 11/18/2022]
Abstract
Identification of new recombinant HCV strains and positive selection sites are crucially important for the formulation of virus intervention measures. However, little is known about the recombinant variant information and positive selection sites of circulating HCV strains in mainland China. In this study, we systematically identified recombinant variants and positive selection sites of HCV in mainland China during the 2010-2019. Phylogenetic analysis results indicated that HCV-6 was one of the dominant genotypes in mainland China during 2010-2019, whereas genotypes 7 and 8 were not detected. Recombinant analysis based on 102 full-length genome sequences of Chinese epidemic strains of HCV identified four intra-genotypic recombinants (strains WYHCV286, GB28, GZ2983, and HCV156) and one inter-genotypic recombinant (strain HH075). Specifically, two breakpoints in the 5' UTR of two recombinants, the strains HH075 and WYHCV286, are rather unusual and has not been described before. Further, selection pressure analyses revealed five positive selective sites, which were located in the core, E2, and NS5B protein. Notably, positive selective sites in NS5B and core protein may be partially responsible for the drug resistance and immune evasion. To the best of our knowledge, this study firstly reported five specific intertypic and intratypic recombinants of Chinese epidemic strains of HCV, which highlight their significance for anti-HCV treatment and vaccine development.
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Affiliation(s)
- Mengdi Qi
- Kunming Medical University, Kunming, Yunnan, China; Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Mengmei Yang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Liangzi Xu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Chunli Ma
- Kunming Medical University, Kunming, Yunnan, China; Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Pu Huang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
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28
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El-Mesery M, El-Mowafy M, Youssef LF, El-Mesery A, Abed SY, Elgaml A. Serum Soluble Fibrinogen-Like Protein 2 Represents a Novel Biomarker for Differentiation Between Acute and Chronic Egyptian Hepatitis B Virus-Infected Patients. J Interferon Cytokine Res 2021; 41:52-59. [DOI: 10.1089/jir.2020.0118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Mohamed El-Mesery
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Laila F. Youssef
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Ahmed El-Mesery
- Department of Tropical Medicine, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Sally Yussef Abed
- Department of Respiratory Care, College of Applied Medical Science in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Horus University, New Damietta, Egypt
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29
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Changes of Gut-Microbiota-Liver Axis in Hepatitis C Virus Infection. BIOLOGY 2021; 10:biology10010055. [PMID: 33451143 PMCID: PMC7828638 DOI: 10.3390/biology10010055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/02/2021] [Accepted: 01/08/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary Gut microbiota alteration is linked to many health disorders including hepatitis C virus (HCV) infection. This dysbiosis in turn impacts the coordination between the gut and the liver that is known as the gut–liver-axis. Here, we discuss the latest findings regarding the changes in gut microbiota structure and functionality post HCV infection and its treatment regimens. In addition, we underline the contribution of the microbiota alterations to HCV associated liver complications. Abstract The gut–liver-axis is a bidirectional coordination between the gut, including microbial residents, the gut microbiota, from one side and the liver on the other side. Any disturbance in this crosstalk may lead to a disease status that impacts the functionality of both the gut and the liver. A major cause of liver disorders is hepatitis C virus (HCV) infection that has been illustrated to be associated with gut microbiota dysbiosis at different stages of the disease progression. This dysbiosis may start a cycle of inflammation and metabolic disturbance that impacts the gut and liver health and contributes to the disease progression. This review discusses the latest literature addressing this interplay between the gut microbiota and the liver in HCV infection from both directions. Additionally, we highlight the contribution of gut microbiota to the metabolism of antivirals used in HCV treatment regimens and the impact of these medications on the microbiota composition. This review sheds light on the potential of the gut microbiota manipulation as an alternative therapeutic approach to control the liver complications post HCV infection.
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30
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Martinez MA, Franco S. Discovery and Development of Antiviral Therapies for Chronic Hepatitis C Virus Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:139-157. [PMID: 34258740 DOI: 10.1007/978-981-16-0267-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
At the beginning of this decade, an estimated 71 million people were living with chronic hepatitis C virus (HCV) infection worldwide. After the acute stage of HCV infection, 18-34% of individuals exhibit spontaneous clearance. However, the remaining 66-82% of infected individuals progress to chronic HCV infection and are at subsequent risk of progression to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Chronic hepatitis C progression is generally slow during the first two decades of infection, but can be accelerated during this time in association with advancing age and cofactors, such as heavy alcohol intake and human immunodeficiency virus (HIV) co-infection. Since acute HCV infection is generally asymptomatic, HCV goes undiagnosed in a significant percentage of infected individuals. In 2014, direct-acting antiviral (DAA) therapy for chronic HCV was developed, which has increased the cure rates to nearly 100%. DAA therapy is among the best examples of success in the fight against viral infections. DAAs have transformed HCV management and have opened the door for the global eradication of HCV.
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Affiliation(s)
- Miguel Angel Martinez
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Sandra Franco
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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31
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Elkhalifa D, Al-Hashimi I, Al Moustafa AE, Khalil A. A comprehensive review on the antiviral activities of chalcones. J Drug Target 2020; 29:403-419. [PMID: 33232192 DOI: 10.1080/1061186x.2020.1853759] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Some viral outbreaks have plagued the world since antiquity, including the most recent COVID-19 pandemic. The continuous spread and emergence of new viral diseases have urged the discovery of novel treatment options that can overcome the limitations of currently marketed antiviral drugs. Chalcones are natural open chain flavonoids that are found in various plants and can be synthesised in labs. Several studies have shown that these small organic molecules exert a number of pharmacological activities, including antiviral, anti-inflammatory, antimicrobial and anticancer. The purpose of this review is to provide a summary of the antiviral activities of chalcones and their derivatives on a set of human viral infections and their potential for targeting the most recent COVID-19 disease. Accordingly, we herein review chalcones activities on the following human viruses: Middle East respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus, human immunodeficiency, influenza, human rhinovirus, herpes simplex, dengue, human cytomegalovirus, hepatitis B and C, Rift Valley fever and Venezuelan equine encephalitis. We hope that this review will pave the way for the design and development of potentially potent and broad-spectrum chalcone based antiviral drugs.
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Affiliation(s)
- Dana Elkhalifa
- College of Pharmacy, QU Health, Qatar University, Doha, Qatar.,Department of Pharmacy, Aspetar Orthopedic and Sports Medicine Hospital, Doha, Qatar
| | | | - Ala-Eddin Al Moustafa
- College of Medicine, QU Health, Qatar University, Doha, Qatar.,Biomedical Research Centre, Qatar University, Doha, Qatar.,Oncology Department, McGill University, Montreal, Quebec, Canada.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Ashraf Khalil
- College of Pharmacy, QU Health, Qatar University, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
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32
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Rowell CER, Dobrovolny HM. Energy Requirements for Loss of Viral Infectivity. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:281-294. [PMID: 32757142 PMCID: PMC7405386 DOI: 10.1007/s12560-020-09439-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Outside the host, viruses will eventually lose their ability to infect cells due to conformational changes that occur to proteins on the viral capsid. In order to undergo a conformational change, these proteins require energy to activate the chemical reaction that leads to the conformational change. In this study, data from the literature is used to calculate the energy required for viral inactivation for a variety of different viruses by means of the Arrhenius equation. We find that some viruses (rhinovirus, poliovirus, human immunodeficiency virus, Alkhumra hemorrhagic fever virus, and hepatitis A virus) have high inactivation energies, indicative of breaking of a chemical double bond. We also find that several viruses (respiratory syncytial virus, poliovirus, and norovirus) have nonlinear Arrhenius plots, suggesting that there is more than a single pathway for inactivation of these viruses.
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Affiliation(s)
- Caroline E R Rowell
- Department of Chemistry, Wingate University, Hendersonville, NC, USA
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, USA
| | - Hana M Dobrovolny
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, USA.
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33
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Chan CP, Uemura H, Kwan TH, Wong NS, Oka S, Chan DPC, Lee SS. Review on the molecular epidemiology of sexually acquired hepatitis C virus infection in the Asia-Pacific region. J Int AIDS Soc 2020; 23:e25618. [PMID: 32969173 PMCID: PMC7511596 DOI: 10.1002/jia2.25618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/29/2020] [Accepted: 08/26/2020] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION Sexual acquisition has emerged as a transmission route for hepatitis C virus (HCV) of growing importance among human immunodeficiency virus (HIV)-positive populations. In Western countries, HCV epidemics have been increasingly detected among men who have sex with men (MSM). This review describes the molecular epidemiology of sexually acquired HCV infection in the Asia-Pacific region. METHODS A systematic search was performed on PubMed in March 2019. Either abstract or full-text of each publication in the search results was screened for eligibility. Studies from different countries/cities involving eligible cases, who acquired HCV sexually with identified subtype, were synthesized for the evaluation of molecular epidemiology in the Asia-Pacific region. Two large-scale systematic reviews on the genotype distribution of HCV at a population level and among PWID were used as references for comparison. RESULTS AND DISCUSSION Overall, 13 full-text articles with 549 subjects originating from nine countries/cities were reviewed. A total of five genotypes and 14 subtypes were identified, dominated by subtypes 1b (23.0%), 2a (19.1%) and 3a (29.5%). A majority of the infected cases occurred in HIV-positive MSM. In some places, notably Hong Kong, India and Indonesia, the predominant subtype in sexually acquired HCV infection in MSM was different from that circulating in the general population. Shared transmission networks between people who inject drugs (PWID) and MSM were shown in Australia and New Zealand, whereas overlapping risk elicited from a small number of subjects existed in Tokyo, Taipei and Guangxi. MSM-specific clusters were identified in Hong Kong, Taipei and Hubei. CONCLUSIONS The distribution of sexually acquired HCV was sparsely scattered across countries/cities in the Asia-Pacific region. The threat of overlapping risk differed by locations, whereas transnational outbreaks remained uncommon. The paucity of information has hindered progress with comprehensive assessment in the Asia-Pacific region, where seroprevalence of HCV among HIV-positive MSM was relatively high.
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Affiliation(s)
- Chin Pok Chan
- Stanley Ho Centre for Emerging Infectious DiseasesThe Chinese University of Hong KongShatinHong Kong
| | - Haruka Uemura
- AIDS Clinical CenterNational Center for Global Health and MedicineTokyoJapan
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious DiseasesThe Chinese University of Hong KongShatinHong Kong
| | - Ngai Sze Wong
- Stanley Ho Centre for Emerging Infectious DiseasesThe Chinese University of Hong KongShatinHong Kong
| | - Shinichi Oka
- AIDS Clinical CenterNational Center for Global Health and MedicineTokyoJapan
| | - Denise Pui Chung Chan
- Stanley Ho Centre for Emerging Infectious DiseasesThe Chinese University of Hong KongShatinHong Kong
| | - Shui Shan Lee
- Stanley Ho Centre for Emerging Infectious DiseasesThe Chinese University of Hong KongShatinHong Kong
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34
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Eliseev A, Gibson KM, Avdeyev P, Novik D, Bendall ML, Pérez-Losada M, Alexeev N, Crandall KA. Evaluation of haplotype callers for next-generation sequencing of viruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 82:104277. [PMID: 32151775 PMCID: PMC7293574 DOI: 10.1016/j.meegid.2020.104277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023]
Abstract
Currently, the standard practice for assembling next-generation sequencing (NGS) reads of viral genomes is to summarize thousands of individual short reads into a single consensus sequence, thus confounding useful intra-host diversity information for molecular phylodynamic inference. It is hypothesized that a few viral strains may dominate the intra-host genetic diversity with a variety of lower frequency strains comprising the rest of the population. Several software tools currently exist to convert NGS sequence variants into haplotypes. Previous benchmarks of viral haplotype reconstruction programs used simulation scenarios that are useful from a mathematical perspective but do not reflect viral evolution and epidemiology. Here, we tested twelve NGS haplotype reconstruction methods using viral populations simulated under realistic evolutionary dynamics. We simulated coalescent-based populations that spanned known levels of viral genetic diversity, including mutation rates, sample size and effective population size, to test the limits of the haplotype reconstruction methods and to ensure coverage of predicted intra-host viral diversity levels (especially HIV-1). All twelve investigated haplotype callers showed variable performance and produced drastically different results that were mainly driven by differences in mutation rate and, to a lesser extent, in effective population size. Most methods were able to accurately reconstruct haplotypes when genetic diversity was low. However, under higher levels of diversity (e.g., those seen intra-host HIV-1 infections), haplotype reconstruction quality was highly variable and, on average, poor. All haplotype reconstruction tools, except QuasiRecomb and ShoRAH, greatly underestimated intra-host diversity and the true number of haplotypes. PredictHaplo outperformed, in regard to highest precision, recall, and lowest UniFrac distance values, the other haplotype reconstruction tools followed by CliqueSNV, which, given more computational time, may have outperformed PredictHaplo. Here, we present an extensive comparison of available viral haplotype reconstruction tools and provide insights for future improvements in haplotype reconstruction tools using both short-read and long-read technologies.
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Affiliation(s)
- Anton Eliseev
- Computer Technologies Laboratory, ITMO University, Saint-Petersburg, Russia
| | - Keylie M Gibson
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
| | - Pavel Avdeyev
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; Department of Mathematics, George Washington University, Washington, DC, USA
| | - Dmitry Novik
- Computer Technologies Laboratory, ITMO University, Saint-Petersburg, Russia
| | - Matthew L Bendall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Saint-Petersburg, Russia
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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35
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Fadl N, Salem TZ. Hepatitis C genotype 4: A report on resistance-associated substitutions in NS3, NS5A, and NS5B genes. Rev Med Virol 2020; 30:e2120. [PMID: 32478480 DOI: 10.1002/rmv.2120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022]
Abstract
AUTHOR CONTRIBUTION FN performed the literature review and wrote the manuscript; STZ coauthored, edited, and reviewed the manuscript. ABSTRACT Treatment response in Hepatitis C virus (HCV) has generated varied effects in patients. Recently, nonresponsive and relapse patients related to host and genotype variabilities have been reported in clinical trials. However, these trials included minimal sample sizes of patients with genotype 4, the most prevalent genotype in Egypt and the Middle East, compared with genotypes 1 and 2. The genetic variabilities that have been detected within the HCV genes, especially the ones associated with genotype 4, and are linked to treatment response, will be the focus of this review with emphasis on direct acting antiviral agents. In addition, the major studies and clinical trials performed globally and their inclusivity of genotype 4 are reported. This review also delineates future study areas and missing data that need further investigation when it comes to genotype 4.
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Affiliation(s)
- Nahla Fadl
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Tamer Z Salem
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Department of Microbial Genetics, AGERI, ARC, Giza, Egypt
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36
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Positional Correlation Natural Vector: A Novel Method for Genome Comparison. Int J Mol Sci 2020; 21:ijms21113859. [PMID: 32485813 PMCID: PMC7312176 DOI: 10.3390/ijms21113859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Advances in sequencing technology have made large amounts of biological data available. Evolutionary analysis of data such as DNA sequences is highly important in biological studies. As alignment methods are ineffective for analyzing large-scale data due to their inherently high costs, alignment-free methods have recently attracted attention in the field of bioinformatics. In this paper, we introduce a new positional correlation natural vector (PCNV) method that involves converting a DNA sequence into an 18-dimensional numerical feature vector. Using frequency and position correlation to represent the nucleotide distribution, it is possible to obtain a PCNV for a DNA sequence. This new numerical vector design uses six suitable features to characterize the correlation among nucleotide positions in sequences. PCNV is also very easy to compute and can be used for rapid genome comparison. To test our novel method, we performed phylogenetic analysis with several viral and bacterial genome datasets with PCNV. For comparison, an alignment-based method, Bayesian inference, and two alignment-free methods, feature frequency profile and natural vector, were performed using the same datasets. We found that the PCNV technique is fast and accurate when used for phylogenetic analysis and classification of viruses and bacteria.
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Duncan JD, Urbanowicz RA, Tarr AW, Ball JK. Hepatitis C Virus Vaccine: Challenges and Prospects. Vaccines (Basel) 2020; 8:vaccines8010090. [PMID: 32079254 PMCID: PMC7157504 DOI: 10.3390/vaccines8010090] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/25/2020] [Accepted: 02/04/2020] [Indexed: 02/07/2023] Open
Abstract
The hepatitis C virus (HCV) causes both acute and chronic infection and continues to be a global problem despite advances in antiviral therapeutics. Current treatments fail to prevent reinfection and remain expensive, limiting their use to developed countries, and the asymptomatic nature of acute infection can result in individuals not receiving treatment and unknowingly spreading HCV. A prophylactic vaccine is therefore needed to control this virus. Thirty years since the discovery of HCV, there have been major gains in understanding the molecular biology and elucidating the immunological mechanisms that underpin spontaneous viral clearance, aiding rational vaccine design. This review discusses the challenges facing HCV vaccine design and the most recent and promising candidates being investigated.
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Affiliation(s)
- Joshua D. Duncan
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (R.A.U.); (A.W.T.); (J.K.B.)
- NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
- Correspondence:
| | - Richard A. Urbanowicz
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (R.A.U.); (A.W.T.); (J.K.B.)
- NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Alexander W. Tarr
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (R.A.U.); (A.W.T.); (J.K.B.)
- NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Jonathan K. Ball
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (R.A.U.); (A.W.T.); (J.K.B.)
- NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
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Single-molecular real-time deep sequencing reveals the dynamics of multi-drug resistant haplotypes and structural variations in the hepatitis C virus genome. Sci Rep 2020; 10:2651. [PMID: 32060395 PMCID: PMC7021670 DOI: 10.1038/s41598-020-59397-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/24/2020] [Indexed: 12/25/2022] Open
Abstract
While direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have dramatically progressed, patients still suffer from treatment failures. For the radical eradication of HCV, a deeper understanding of multiple resistance-associated substitutions (RASs) at the single-clone level is essential. To understand HCV quasispecies and their dynamics during DAA treatment, we applied single-molecule real-time (SMRT) deep sequencing on sera from 12 patients with genotype-1b HCV infections with DAA treatment failures, both pre- and post-treatment. We identified >3.2 kbp sequences between NS3 and NS5A genes of 187,539 clones in total, classifying into haplotype codes based on the linkage of seven RAS loci. The number of haplotype codes during the treatment, per sample, significantly decreased from 14.67 ± 9.12 to 6.58 ± 7.1, while the number of nonsynonymous codons on the seven RAS loci, per clone, significantly increased from 1.50 ± 0.92 to 3.64 ± 0.75. In five cases, the minority multi-drug resistant haplotypes at pre-treatment were identical to the major haplotypes at relapse. Moreover, various structural variations (SVs) were detected and their dynamics analysed. These results suggest that SMRT deep sequencing is useful for detecting minority haplotypes and SVs, and to evaluate the dynamics of viral genomes at the single-clone level.
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Sallam M, Batarseh R, Natsheh A, Abbadi J, Al-Fraihat E, Yaseen A, Kaddomi D, Khamees N, Mahafzah A, Şahin GÖ. An update on hepatitis C virus genotype distribution in Jordan: a 12-year retrospective study from a tertiary care teaching hospital in Amman. BMC Infect Dis 2019; 20:3. [PMID: 31892307 PMCID: PMC6938611 DOI: 10.1186/s12879-019-4735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
Background Nucleic acid hybridization (NAH) of hepatitis C virus (HCV) is a practical and reliable tool for virus genotyping. Genotype assignment is an important factor in the prediction of treatment success in chronic hepatitis C patients. The aim of this study was to determine the genotype distribution among HCV clinical isolates in Jordan between 2007 and 2018. Methods Electronic and paper-based clinical data registry records from 2007 to 2018 at the Jordan University Hospital (JUH) were retrospectively examined for individuals with HCV genotype, HCV viral load, and alanine aminotransferase (ALT) testing results. Genotype determination was based on NAH technique using the HCV 5′ untranslated region (5′ UTR) with 386 requests available from 342 unique individuals. Results A total of 263 out of 342 unique individuals (76.9%) had genotyping results available for final analysis with 259 individuals each having a single genotyping result. The most common HCV genotypes in the study were: genotype 4 (n = 142, 54.0%), genotype 1 (n = 87, 33.1%), genotype 3 (n = 16, 6.1%), genotype 2 (n = 9, 3.4%), other undetermined genotypes (n = 5, 1.9%) and mixed infections (n = 4, 1.5%). Sub-genotyping results were available for 46 individuals as follows: sub-genotype 4c/d (n = 13, 28.3%), sub-genotype 1a (n = 11, 23.9%), sub-genotype 1b (n = 10, 21.7%), sub-genotype 4a (n = 8, 17.4%), sub-genotype 3a (n = 2, 4.3%), sub-genotypes 2a/c and 4 h (n = 1, 2.2% for both). Individuals infected with genotype 1 showed higher viral load when compared to those infected with genotype 4 (p = 0.048, t-test). Younger HCV-infected individuals (< 52 years) had higher ALT levels compared to older individuals (p = 0.036, t-test). Self-reported risk factors for HCV acquisition included: history of previous surgery, invasive dental procedures, and blood transfusion, delivery at home, circumcision at home and wet cupping therapy (hijama). Conclusions High genetic diversity of HCV was found in Jordan, with genotypes 4 and 1 as the most prevalent genotypes co-circulating in the country. Potential impact of virus genotype on disease markers (viral load, ALT) was detected and needs further assessment. The study can be helpful to plan for future prevention and management of HCV infection in Jordan.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.
| | - Rawan Batarseh
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Anas Natsheh
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Jumana Abbadi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Esraa Al-Fraihat
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Alaa' Yaseen
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Doaa Kaddomi
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Nadia Khamees
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Gülşen Özkaya Şahin
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.,Department of Clinical Microbiology, Laboratory Medicine, Skåne University Hospital, 22100, Lund, Sweden
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40
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Watanabe N, Suzuki T, Date T, Hussan HA, Hmwe SS, Aizaki H, Sugiyama M, Mizokami M, Delaney Iv W, Cheng G, Muramatsu M, Wakita T. Establishment of infectious genotype 4 cell culture-derived hepatitis C virus. J Gen Virol 2019; 101:188-197. [PMID: 31859613 DOI: 10.1099/jgv.0.001378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To establish infectious genotype 4a (GT4a) cell culture-derived hepatitis C virus (HCVcc), we constructed full-length ED43 and 12 mutants possessing single or double mutations that increase ED43 replicon replication, and performed cell culture after RNA transfection. Sequential long-term culture of full-length ED43 RNA-transfected cells showed increased viral production in two ED43 mutants named ED43 QK/SI and TR/SI among the tested clones. These ED43 mutants possessed a common mutation, R1405G, in the NS3 helicase region and another mutation, D2413G or V2414A, in the NS5a-NS5b cleavage site. Furthermore, serial reinfection of naïve Huh7.5.1 cells accelerated peak HCV production at an earlier time point after every infection. After the fourth infection, we found a common mutation, R1405G, and six additional mutations in both ED43 QK/SI and TR/SI mutants. All seven mutations supported continuous viral production for more than 40 days in both ED43 QS-7M (QK/SI with seven mutations) and ED43 TS-7M (TR/SI with seven mutations). In addition, ED43 TS-7M did not require additional mutations for continuous virus culture up to 124 days. Both ED43 QS-7M and TS-7M were sensitive to the neutralizing E2 antibodies HCV1 and AR3A and the direct-acting antivirals, simeprevir, ledipasvir and sofosbuvir. In conclusion, we established an infectious ED43 strain containing adaptive mutations, which is important for the analysis of HCV genotype-specific pathogenesis, development of pan-genotypic agents and analysis of drug resistance.
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Affiliation(s)
- Noriyuki Watanabe
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaya Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoko Date
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hussein Aly Hussan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Su Su Hmwe
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | | | | | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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41
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Kamelian K, Montoya V, Olmstead A, Dong W, Harrigan R, Morshed M, Joy JB. Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods. Sci Rep 2019; 9:16433. [PMID: 31712570 PMCID: PMC6848190 DOI: 10.1038/s41598-019-52613-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenetic analysis. WGS and phylogenetic analysis were performed to investigate geographic clustering of samples from five Canadians with travel-acquired ZIKV infections and to assess the limitations of phylogenetic analysis of ZIKV sequences using a phylogenetic cluster approach. Genomic variability of ZIKV samples was assessed and for context, compared with hepatitis C virus (HCV) samples. Phylogenetic analysis confirmed the suspected region of ZIKV infection for one of five samples and one sample failed to cluster with sequences from its suspected country of infection. Travel-acquired ZIKV samples depicted low genomic variability relative to HCV samples. A floating patristic distance threshold classified all pre-2000 ZIKV sequences into separate clusters, while only Cambodian, Peruvian, Malaysian, and South Korean sequences were similarly classifiable. While phylogenetic analysis of ZIKV data can identify the broad geographical region of ZIKV infection, ZIKV’s low genomic variability is likely to limit precise interpretations of phylogenetic analysis of the origins of travel-related cases.
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Affiliation(s)
- Kimia Kamelian
- University of British Columbia, Division of AIDS, Department of Medicine, Vancouver, BC, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard Harrigan
- University of British Columbia, Division of AIDS, Department of Medicine, Vancouver, BC, Canada
| | - Muhammad Morshed
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.,University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,University of British Columbia, Division of Infectious Diseases, Department of Medicine, Vancouver, BC, Canada.
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Boyd A, Duchesne L, Lacombe K. Research gaps in viral hepatitis. J Int AIDS Soc 2019; 21 Suppl 2:e25054. [PMID: 29633564 PMCID: PMC5978714 DOI: 10.1002/jia2.25054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/20/2017] [Indexed: 12/21/2022] Open
Abstract
Introduction The World Health Organization has aimed for global elimination of both hepatitis B virus (HBV) and hepatitis C virus (HCV) by 2030. Treatments available to cure HCV and control HBV, as well as vaccination to prevent HBV infection, have certainly allowed for such bold goals, yet the final steps to usher in elimination require further evidence. Discussion We broadly discuss the needs for three major public health approaches. First, an effective vaccine exists for HBV and mass‐vaccination campaigns have resulted in decreases in hepatitis B surface antigen seroprevalence and overall rates of liver‐related morality. Still, HBV vaccination coverage is poor in certain regions of the world, while the reasons for such low coverage require further study. A prophylactic vaccine is probably needed to eliminate HCV, but is not being readily developed. Second, identifying HBV/HCV infected individuals remains a priority to increase awareness of disease status, particularly for key populations. Research evaluating large‐scale implementation of novel, rapid and mobile point‐of‐care tests would be helpful to determine whether increased awareness is achievable in these settings. Third, antiviral therapy allows for strong HBV suppression and HCV cure, while its access depends on financial factors among many others. Although there is strong evidence to treat key populations and specific groups with progressed disease, as stated in current guidelines, the advantages of extending treatment eligibility to decrease onward spread of HBV/HCV infection and prevent further burden of disease are lacking “real world” evidence. Novel anti‐HBV treatments are being developed to target intrahepatocellular HBV replication, but are still in the early phases of clinical development. Each of the strategies mentioned above has specific implications for HIV infection. Conclusions There are certainly effective tools to combat the spread of viral hepatitis and treat infected individuals – yet how they are able to reach key populations, and the infrastructure required to do so, continue to represent the largest research gap when evaluating the progress towards elimination. Continuously adapted and informed research is required to establish the priorities in achieving elimination goals.
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Affiliation(s)
- Anders Boyd
- INSERM, UMR_S1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,Department of Infectious Diseases, Research and Prevention, Public Health Service of Amsterdam, Amsterdam, Netherlands
| | - Léa Duchesne
- INSERM, UMR_S1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Karine Lacombe
- Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, AP-HP, Paris, France.,Sorbonne Universités, INSERM, UPMC Univ Paris 06, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
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43
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Uribe-Noguez LA, Mata-Marín JA, Ocaña-Mondragón A, Pompa-Mera EN, Ribas-Aparicio RM, Arroyo-Anduiza CI, Gomez-Torres ME, Chaparro-Sánchez A, Gaytán-Martínez J, Mauss S. Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico. J Infect Chemother 2019; 26:205-210. [PMID: 31537472 DOI: 10.1016/j.jiac.2019.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.
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Affiliation(s)
- Luis Antonio Uribe-Noguez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico; Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico; Centro de Simulación Médica, Facultad Mexicana de Medicina, Universidad La Salle, Mexico City, Mexico.
| | - José Antonio Mata-Marín
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alicia Ocaña-Mondragón
- Laboratorio Central de Epidemiología, División de Laboratorios de Vigilancia e Investigación Epidemiológica, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Ericka Nelly Pompa-Mera
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico
| | - Carla Ileana Arroyo-Anduiza
- Departamento de Patología Clínica, Banco Central de Sangre, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - María Elena Gomez-Torres
- Laboratorio de Urgencias, Hospital de Infectología, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alberto Chaparro-Sánchez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Jesus Gaytán-Martínez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Stefan Mauss
- Center for HIV and Hepatogastroenterology, Duesseldorf, Germany
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44
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Dvory-Sobol H, Han B, Lu J, Yu M, Beran RK, Cheng G, Martin R, Svarovskaia E, Mo H. In vitro resistance profile of hepatitis C virus NS5A inhibitor velpatasvir in genotypes 1 to 6. J Viral Hepat 2019; 26:991-1001. [PMID: 31009123 DOI: 10.1111/jvh.13116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/29/2022]
Abstract
Velpatasvir is a pan-genotypic hepatitis C virus (HCV) NS5A inhibitor, which is used with sofosbuvir for treatment of infection with HCV genotypes 1-6. In vitro resistance studies were performed to characterize NS5A changes that might confer reduced velpatasvir susceptibility in vivo. Resistance selection studies using HCV replicon cells for subtypes 1a, 1b, 2a, 2b, 3a, 4a, 5a and 6a identified NS5A resistance-associated substitutions (RASs) at nine positions, most often 28M/S/T, 31F/I/M/P/V and 93D/H/N/S. In subtype 1a, RASs were selected at positions 31 and/or 93, while in subtype 1b, replicons with two or more RASs at positions 31, 54 or 93 were selected. Y93H was selected in subtypes 1a, 1b, 2a, 3a and 4a. In subtype 5a or 6a, L31P or P32L/Q was selected, respectively. Velpatasvir susceptibility of 358 replicons from genotypes 1 to 6 containing one or more NS5A RASs was also evaluated. The majority (63%) of subtypes 1a and 1b single RAS-containing replicons retained susceptibility to velpatasvir (<2.5-fold change in EC50 ). High levels of resistance to velpatasvir were observed for six single mutants in subtype 1a, including M28G, A92K, Y93H/N/R/W and for one mutant, A92K, in subtype 1b. Most single mutants in subtypes 2a, 2b, 3a, 4a and 5a displayed low levels of reduced velpatasvir susceptibility. High-level resistance was observed for C92T and Y93H/N in subtype 2b, Y93H/S in 3a, and L31V and P32A/L/Q/R in 6a, and several double mutants in these subtypes. Overall, velpatasvir maintained activity against most common RASs that are known to confer resistance to first-generation NS5A inhibitors.
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Affiliation(s)
| | - Bin Han
- Gilead Sciences, Foster City, California
| | - Julia Lu
- Gilead Sciences, Foster City, California
| | - Mei Yu
- Gilead Sciences, Foster City, California
| | | | | | | | | | - Hongmei Mo
- Gilead Sciences, Foster City, California
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Ortiz GA, Trivedi HD, Nader C. Pharmacokinetics and drug interactions of medications used to treat hepatitis C virus infection in the setting of chronic kidney disease and kidney transplantation. Hemodial Int 2019; 22 Suppl 1:S22-S35. [PMID: 29694720 DOI: 10.1111/hdi.12648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hepatitis C infection in patients with chronic kidney disease or kidney transplant carries higher morbidity and mortality compared to noninfected patients. Historically, patients with advanced kidney disease and kidney transplant recipients were undertreated given the multiple adverse effects and limited efficacy of interferon-based therapies for chronic hepatitis C. The development of direct-acting antivirals in the past few years has opened an unprecedented opportunity for treating these populations. However, the impaired renal clearance of some of these medications in patients with kidney disease, and the potential interactions of antiviral therapies with immunosuppressants after kidney transplantation, present some challenges in choosing the proper regimen. This review provides an overview of the essential pharmacokinetics and drug interactions of relevant antiviral therapies in the treatment of chronic hepatitis C in patients with advanced kidney disease and after kidney transplantation.
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Affiliation(s)
- Guillermo A Ortiz
- Department of Medicine, St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Hirsh D Trivedi
- Liver Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Claudia Nader
- Division of Infectious Diseases, Department of Medicine, St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
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Hepatitis C Virus Genetic Variability, Human Immune Response, and Genome Polymorphisms: Which Is the Interplay? Cells 2019; 8:cells8040305. [PMID: 30987134 PMCID: PMC6523096 DOI: 10.3390/cells8040305] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/26/2019] [Accepted: 03/30/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the main cause of chronic hepatitis, affecting an estimated 150 million people worldwide. Initial exposure to HCV is most often followed by chronic hepatitis, with only a minority of individuals spontaneously clearing the virus. The induction of sustained and broadly directed HCV-specific CD4+ and CD8+ T cell responses, together with neutralizing antibodies (nAb), and specific genetic polymorphism have been associated with spontaneous resolution of the infection. However, due to its high variability, HCV is able to overwhelm the host immune response through the rapid acquisition of mutations in the epitopes targeted by T cells and neutralizing antibodies. In this context, immune-mediated pressure represents the main force in driving HCV evolution. This review summarizes the data on HCV diversity and the current state of knowledge about the contributions of antibodies, T cells, and host genetic polymorphism in driving HCV evolution in vivo.
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47
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Abstract
The advent of direct-acting antivirals (DAAs) has brought about a sudden renaissance in the treatment of chronic hepatitis C virus (HCV) infection with SVR rates now routinely >90%. However, due to the error-prone nature of the HCV RNA polymerase, resistance-associated substitutions (RASs) to DAAs may be present at baseline and can result in a significant effect on treatment outcomes and hamper the achievement of sustained virologic response. By further understanding the patterns and nature of these RASs, it is anticipated that the incidence of treatment failure will continue to decrease in frequency with the development of drug regimens with increasing potency, barrier to resistance, and genotypic efficacy. This review summarizes our current knowledge of RASs associated with HCV infection as well as the clinical effect of RASs on treatment with currently available DAA regimens.
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Affiliation(s)
- Darrick K Li
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Raymond T Chung
- Liver Center and Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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Shunmugam L, Soliman MES. Targeting HCV polymerase: a structural and dynamic perspective into the mechanism of selective covalent inhibition. RSC Adv 2018; 8:42210-42222. [PMID: 35558797 PMCID: PMC9092151 DOI: 10.1039/c8ra07346e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022] Open
Abstract
Background: Concerns have been raised over the emerging pandemic status of hepatitis C virus (HCV). Current available drugs lack specificity, stability and potency. The HCV NS5B RNA-dependent RNA polymerase (RdRp) is a vital component in viral replication and is often targeted in antiviral therapies. Recent experimental procedures have led to the discovery of a novel covalent RdRp inhibitor, compound 47, which selectively targets cysteine 366 of the HCV RdRp and exhibits promising pharmacokinetic outcomes. Selective covalent inhibition of HCV is, however, a highly neglected subject in the literature, that is reinforced by the lack of efficient structure-based drug design protocols. In this paper, an atomistic insight into a novel selective approach to inhibit HCV RdRp is provided. Methodology/Results: Covalent molecular dynamic analyses revealed the inhibitory mechanism of compound 47 on the RdRp. Inhibitor binding induced distinctive internal movements resulting in the disruption of normal physiological interdomain interactions. Conclusion: Compound 47 stimulates reorganization of key protein elements required for RNA transcription, thus hampering viral replication as well as disrupting the overall conformation of HCV. This study will open new lines of approach for the design of novel selective inhibitors against HCV as well as other viral families.
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Affiliation(s)
- Letitia Shunmugam
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
- School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa +27 (0) 31 260 7872 +27 (0) 31 260 8048
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Kassela K, Karakasiliotis I, Kokkiou E, Souvalidou F, Mimidis P, Veletza S, Panopoulou M, Koskinas J, Mimidis K, Mavromara P. Intergenotypic 2k/1b hepatitis C virus recombinants in the East Macedonia and Thrace region of Greece. Ann Gastroenterol 2018; 32:88-92. [PMID: 30598597 PMCID: PMC6302191 DOI: 10.20524/aog.2018.0322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023] Open
Abstract
Background Intergenotypic recombinant hepatitis C virus (HCV) strains emerge rarely during coinfection of the same individual with two HCV genotypes. Few recombinant HCV strains have been identified to date and only one, CRF01 2k/1b, has become a worldwide concern. This study reevaluated the genotyping of three HCV genotype 2 strains from a group of patients with an unusually low rate of sustained virological response after pegylated interferon/ribavirin treatment. In addition, genetic determinants of host interferon resistance were evaluated. Methods The HCV type 2 strains from the patients’ serum were subjected to partial sequencing of the core-E1, NS2, NS5A and NS5B regions by reverse transcription polymerase chain reaction. Furthermore, the IFNL3 rs12979860 and the IFNL4 rs368234815 single nucleotide polymorphisms were defined in two of the three patients. Results All three strains were phylogenetically related to the Russia-derived CRF01 2k/1b while they encompassed the exact same 2k/1b junction site within NS2. Conclusion This is the first report of HCV 2k/1b recombinants in Greece and the greater area of the Balkans.
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Affiliation(s)
- Katerina Kassela
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara).,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Ioannis Karakasiliotis, Penelope Mavromara)
| | - Ioannis Karakasiliotis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Ioannis Karakasiliotis, Penelope Mavromara).,Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Ioannis Karakasiliotis, Stavroula Veletza)
| | - Eleni Kokkiou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara)
| | - Fani Souvalidou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara)
| | - Panayotis Mimidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara)
| | - Stavroula Veletza
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Ioannis Karakasiliotis, Stavroula Veletza)
| | - Maria Panopoulou
- Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Maria Panopoulou)
| | - John Koskinas
- Department of Internal Medicine, Medical School of Athens, Hippokration Hospital Athens (John Koskinas)
| | - Konstantinos Mimidis
- 1 Department of Internal Medicine, Democritus University of Thrace Medical School, Alexandroupolis (Konstantinos Mimidis), Greece
| | - Penelope Mavromara
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara).,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Ioannis Karakasiliotis, Penelope Mavromara)
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50
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Prakash S, Shukla S, Ramakrishna V, Jain A. Distribution of hepatitis C genotypes in Uttar Pradesh, India; rare genotype 4 detected. J Med Virol 2018; 90:1875-1881. [PMID: 30085356 DOI: 10.1002/jmv.25277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/07/2018] [Indexed: 12/29/2022]
Abstract
AIM The worldwide prevalence of hepatitis C virus infection (HCV) is nearly 150 to 170 million cases. The prevalence of HCV infection in India is estimated to be around 1%. In India HCV genotype (GT)3 is the predominant GT followed by GT1. Our study aims to establish the prevalent GTs/subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. METHODS The study was a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital from September 2014 to April 2017, and was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried out on a stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger's sequencing of the core region. The phylogenetic analysis of 179 HCV strains with a high-quality sequencing data was performed. RESULTS The distributions of prevalent GTs/subtypes as noted in the current study were ( n [%]): GT1a, 101 (25%); GT1b, 12 (2.9%); GT1c, 1 (0.25%); GT3a, 275 (68.07%); GT3b, 9 (2.2%); GT3g, 2 (0.49%); GT3i, 3 (0.74%); and GT4a, 1 (0.24%). HCV GTs GT2, GT5, and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. CONCLUSIONS HCV GTs 3a and 1a are the commonest circulating GTs in Uttar Pradesh, India.
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Affiliation(s)
- Shantanu Prakash
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Suruchi Shukla
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Vangala Ramakrishna
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Amita Jain
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
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