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Álvarez ÁL, Arboleya A, Abade dos Santos FA, García-Manso A, Nicieza I, Dalton KP, Parra F, Martín-Alonso JM. Highs and Lows in Calicivirus Reverse Genetics. Viruses 2024; 16:866. [PMID: 38932159 PMCID: PMC11209508 DOI: 10.3390/v16060866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an "infectious clone". This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones.
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Affiliation(s)
- Ángel L. Álvarez
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Aroa Arboleya
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Fábio A. Abade dos Santos
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Nacional de Investigação Agrária e Veterinária, 2780-157 Oeiras, Portugal
| | - Alberto García-Manso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Inés Nicieza
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Kevin P. Dalton
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José M. Martín-Alonso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
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Song J, Hong J, Yang C, Zhang Y, Li Z, He P, Ding Q. Recapitulation of the Powassan virus life cycle in cell culture. mBio 2024; 15:e0346823. [PMID: 38411112 PMCID: PMC11005349 DOI: 10.1128/mbio.03468-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 01/31/2024] [Indexed: 02/28/2024] Open
Abstract
Powassan virus (POWV) is a tick-borne flavivirus known for causing fatal neuroinvasive diseases in humans. Recently, there has been a noticeable increase in POWV infections, emphasizing the urgency of understanding viral replication, pathogenesis, and developing interventions. Notably, there are no approved vaccines or therapeutics for POWV, and its classification as a biosafety level-3 (BSL-3) agent hampers research. To overcome these obstacles, we developed a replicon system, a self-replicating RNA lacking structural proteins, making it safe to operate in a BSL-2 environment. We constructed a POWV replicon carrying the Gaussia luciferase (Gluc) reporter gene and blasticidin (BSD) selectable marker. Continuous BSD selection led to obtain a stable POWV replicon-carrying Huh7 cell lines. We identified cell culture adaptive mutations G4079A, G4944T and G6256A, resulting in NS2AR195K, NS3G122G, and NS3V560M, enhancing RNA replication. We demonstrated the utility of the POWV replicon system for high-throughput screening (HTS) assay to identify promising antivirals against POWV replication. We further explored the applications of the POWV replicon system, generating single-round infectious particles (SRIPs) by transfecting Huh7-POWV replicon cells with plasmids encoding viral capsid (C), premembrane (prM), and envelope (E) proteins, and revealed the distinct antigenic profiles of POWV with ZIKV. In summary, the POWV replicon and SRIP systems represent crucial platforms for genetic and functional analysis of the POWV life cycle and facilitating the discovery of antiviral drugs.IMPORTANCEIn light of the recent surge in human infections caused by POWV, a biosafety level-3 (BSL-3) classified virus, there is a pressing need to understand the viral life cycle and the development of effective countermeasures. To address this, we have pioneered the establishment of a POWV RNA replicon system and a replicon-based POWV SRIP system. Importantly, these systems are operable in BSL-2 laboratories, enabling comprehensive investigations into the viral life cycle and facilitating antiviral screening. In summary, these useful tools are poised to advance our understanding of the POWV life cycle and expedite the development of antiviral interventions.
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Affiliation(s)
- Jingwei Song
- School of Medicine, Tsinghua University, Beijing, China
| | - Jiayao Hong
- School of Medicine, Tsinghua University, Beijing, China
| | - Chen Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Yu Zhang
- School of Medicine, Tsinghua University, Beijing, China
| | - Zhuoyang Li
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Tsinghua University, Beijing, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Peifeng He
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Tsinghua University, Beijing, China
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van der Meulen K, Smets G, Rüdelsheim P. Viral Replicon Systems and Their Biosafety Aspects. APPLIED BIOSAFETY 2023; 28:102-122. [PMID: 37342518 PMCID: PMC10278005 DOI: 10.1089/apb.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Introduction Viral RNA replicons are self-amplifying RNA molecules generated by deleting genetic information of one or multiple structural proteins of wild-type viruses. Remaining viral RNA is used as such (naked replicon) or packaged into a viral replicon particle (VRP), whereby missing genes or proteins are supplied via production cells. Since replicons mostly originate from pathogenic wild-type viruses, careful risk consideration is crucial. Methods A literature review was performed compiling information on potential biosafety risks of replicons originating from positive- and negative-sense single-stranded RNA viruses (except retroviruses). Results For naked replicons, risk considerations included genome integration, persistence in host cells, generation of virus-like vesicles, and off-target effects. For VRP, the main risk consideration was formation of primary replication competent virus (RCV) as a result of recombination or complementation. To limit the risks, mostly measures aiming at reducing the likelihood of RCV formation have been described. Also, modifying viral proteins in such a way that they do not exhibit hazardous characteristics in the unlikely event of RCV formation has been reported. Discussion and Conclusion Despite multiple approaches developed to reduce the likelihood of RCV formation, scientific uncertainty remains on the actual contribution of the measures and on limitations to test their effectiveness. In contrast, even though effectiveness of each individual measure is unclear, using multiple measures on different aspects of the system may create a solid barrier. Risk considerations identified in the current study can also be used to support risk group assignment of replicon constructs based on a purely synthetic design.
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Kurhade C, Xie X, Shi PY. Reverse genetic systems of SARS-CoV-2 for antiviral research. Antiviral Res 2023; 210:105486. [PMID: 36657881 PMCID: PMC9776485 DOI: 10.1016/j.antiviral.2022.105486] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Reverse genetic systems are widely used to engineer recombinant viruses with desired mutations. In response to the COVID-19 pandemic, four types of reverse genetic systems have been developed for SARS-CoV-2: (i) a full-length infectious clone that can be used to prepare recombinant SARS-CoV-2 at biosafety level 3 (BSL3), (ii) a trans-complementation system that can be used to produce single-round infectious SARS-CoV-2 at BSL2, (iii) an attenuated SARS-CoV-2 vaccine candidate (with deletions of viral accessory genes) that may be developed for veterinary use as well as for antiviral screening at BSL2, and (iv) replicon systems with deletions of viral structural genes that can be used at BSL2. Each of these genetic systems has its advantages and disadvantages that can be used to address different questions for basic and translational research. Due to the long genomic size and bacteria-toxic sequences of SARS-CoV-2, several experimental approaches have been established to rescue recombinant viruses and replicons, including (i) in vitro DNA ligation, (ii) bacterial artificial chromosome (BAC) system, (iii) yeast artificial chromosome (YAC) system, and (iv) circular polymerase extension reaction (CPER). This review summarizes the current status of SARS-CoV-2 genetic systems and their applications for studying viral replication, pathogenesis, vaccines, and therapeutics.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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5
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Upstone L, Colley R, Harris M, Goonawardane N. Functional characterization of 5' untranslated region (UTR) secondary RNA structures in the replication of tick-borne encephalitis virus in mammalian cells. PLoS Negl Trop Dis 2023; 17:e0011098. [PMID: 36689554 PMCID: PMC9894543 DOI: 10.1371/journal.pntd.0011098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 02/02/2023] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
Tick-borne Encephalitis Virus (TBEV) is an emerging flavivirus that causes neurological disorders including viral encephalitis of varying severity. Whilst secondary RNA structures within the 5' untranslated regions (UTRs) of many flaviviruses determine both virus replication and pathogenic outcomes in humans, these elements have not been systematically investigated for TBEV. In this study, we investigated the role of predicted RNA secondary elements of the first 107 nucleotides (nts) of the viral genome forming the stem-loop A (SLA). Experiments were performed in replicons and infectious TBEV system. This region comprises three distinct structures: 5' stem 0 (S0), stem-loop 1 (SL1) and stem-loop 2 (SL2). S0 was found to be essential for virus infection as mutations in the lower stem of this region significantly reduced virus replication. Point mutations in SL1 that preserved the Y-shape confirmation delayed viral RNA replication but did not abolish virus infectivity. Deletion of SL2 did not abolish infectivity but had a negligible effect on virus propagation. No correlation was observed between in vitro translation efficiency and virus infectivity, suggesting that the 5'UTR functions independently to virus translation. Together, these findings reveal distinct RNA elements within the 5'UTR that are essential for the stability and replication of viral RNA. We further identify changes in RNA folding that lead to altered TBEV infectivity and pathogenesis.
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Affiliation(s)
- Laura Upstone
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Robin Colley
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Niluka Goonawardane
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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6
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Predictive validity in drug discovery: what it is, why it matters and how to improve it. Nat Rev Drug Discov 2022; 21:915-931. [PMID: 36195754 DOI: 10.1038/s41573-022-00552-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 11/08/2022]
Abstract
Successful drug discovery is like finding oases of safety and efficacy in chemical and biological deserts. Screens in disease models, and other decision tools used in drug research and development (R&D), point towards oases when they score therapeutic candidates in a way that correlates with clinical utility in humans. Otherwise, they probably lead in the wrong direction. This line of thought can be quantified by using decision theory, in which 'predictive validity' is the correlation coefficient between the output of a decision tool and clinical utility across therapeutic candidates. Analyses based on this approach reveal that the detectability of good candidates is extremely sensitive to predictive validity, because the deserts are big and oases small. Both history and decision theory suggest that predictive validity is under-managed in drug R&D, not least because it is so hard to measure before projects succeed or fail later in the process. This article explains the influence of predictive validity on R&D productivity and discusses methods to evaluate and improve it, with the aim of supporting the application of more effective decision tools and catalysing investment in their creation.
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7
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Goonawardane N, Upstone L, Harris M, Jones IM. Identification of Host Factors Differentially Induced by Clinically Diverse Strains of Tick-Borne Encephalitis Virus. J Virol 2022; 96:e0081822. [PMID: 36098513 PMCID: PMC9517736 DOI: 10.1128/jvi.00818-22] [Citation(s) in RCA: 3] [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: 05/24/2022] [Accepted: 08/19/2022] [Indexed: 11/20/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an important human arthropod-borne virus that causes tick-borne encephalitis (TBE) in humans. TBEV acutely infects the central nervous system (CNS), leading to neurological symptoms of various severity. No therapeutics are currently available for TBEV-associated disease. Virus strains of various pathogenicity have been described, although the basis of their diverse clinical outcome remains undefined. Work with infectious TBEV requires high-level biocontainment, meaning model systems that can recapitulate the virus life cycle are highly sought. Here, we report the generation of a self-replicating, noninfectious TBEV replicon used to study properties of high (Hypr) and low (Vs) pathogenic TBEV isolates. Using a Spinach2 RNA aptamer and luciferase reporter system, we perform the first direct comparison of Hypr and Vs in cell culture. Infectious wild-type (WT) viruses and chimeras of the nonstructural proteins 3 (NS3) and 5 (NS5) were investigated in parallel to validate the replicon data. We show that Hypr replicates to higher levels than Vs in mammalian cells, but not in arthropod cells, and that the basis of these differences map to the NS5 region, encoding the methyltransferase and RNA polymerase. For both Hypr and Vs strains, NS5 and the viral genome localized to intracellular structures typical of positive-strand RNA viruses. Hypr was associated with significant activation of IRF-3, caspase-3, and caspase-8, while Vs activated Akt, affording protection against caspase-mediated apoptosis. Higher activation of stress-granule proteins TIAR and G3BPI were an additional early feature of Vs but not for Hypr. These findings highlight novel host cell responses driven by NS5 that may dictate the differential clinical characteristics of TBEV strains. This highlights the utility of the TBEV replicons for further virological characterization and antiviral drug screening. IMPORTANCE Tick-borne encephalitis virus (TBEV) is an emerging virus of the flavivirus family that is spread by ticks and causes neurological disease of various severity. No specific therapeutic treatments are available for TBE, and control in areas of endemicity is limited to vaccination. The pathology of TBEV ranges from mild to fatal, depending on the virus genotype. Characterization of TBEV isolates is challenging due to the requirement for high-containment facilities. Here, we described the construction of novel TBEV replicons that permit a molecular comparison of TBEV isolates of high and low pathogenicity.
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Affiliation(s)
- Niluka Goonawardane
- School of Biological Sciences, University of Reading, Reading, United Kingdom
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Laura Upstone
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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8
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Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Kurhade C, Plante JA, Bopp NE, Kalveram B, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi PY. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. Nat Commun 2022; 13:4337. [PMID: 35896528 PMCID: PMC9326133 DOI: 10.1038/s41467-022-31930-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/08/2022] [Indexed: 12/27/2022] Open
Abstract
We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcription regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (∆3678). The ∆3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The ∆3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the ∆3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the ∆3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter ∆3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that ∆3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio E Muruato
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte Kalveram
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander Bukreyev
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, Galveston, TX, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Tian Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA. .,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA. .,World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA. .,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA. .,World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA. .,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. .,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA. .,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA. .,Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA. .,Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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9
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Liu Y, Li L, Timani KA, He JJ. A Unique Robust Dual-Promoter-Driven and Dual-Reporter-Expressing SARS-CoV-2 Replicon: Construction and Characterization. Viruses 2022; 14:974. [PMID: 35632716 PMCID: PMC9143625 DOI: 10.3390/v14050974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, SARS2) remains a great global health threat and demands identification of more effective and SARS2-targeted antiviral drugs, even with successful development of anti-SARS2 vaccines. Viral replicons have proven to be a rapid, safe, and readily scalable platform for high-throughput screening, identification, and evaluation of antiviral drugs against positive-stranded RNA viruses. In the study, we report a unique robust HIV long terminal repeat (LTR)/T7 dual-promoter-driven and dual-reporter firefly luciferase (fLuc) and green fluorescent protein (GFP)-expressing SARS2 replicon. The genomic organization of the replicon was designed with quite a few features that were to ensure the replication fidelity of the replicon, to maximize the expression of the full-length replicon, and to offer the monitoring flexibility of the replicon replication. We showed the success of the construction of the replicon and expression of reporter genes fLuc and GFP and SARS structural N from the replicon DNA or the RNA that was in vitro transcribed from the replicon DNA. We also showed detection of the negative-stranded genomic RNA (gRNA) and subgenomic RNA (sgRNA) intermediates, a hallmark of replication of positive-stranded RNA viruses from the replicon. Lastly, we showed that expression of the reporter genes, N gene, gRNA, and sgRNA from the replicon was sensitive to inhibition by Remdesivir. Taken together, our results support use of the replicon for identification of anti-SARS2 drugs and development of new anti-SARS strategies targeted at the step of virus replication.
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Affiliation(s)
- Ying Liu
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Lu Li
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Khalid A. Timani
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Johnny J. He
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
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10
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Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Plante JA, Bopp NE, Kurhade C, Bukreyev A, Ren P, Wang T, Vineet D. M, Plante KS, Xie X, Weaver SC, Shi P. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions.. [PMID: 35194609 PMCID: PMC8863145 DOI: 10.1101/2022.02.14.480460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcriptional regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (Δ3678). The Δ3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The Δ3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the Δ3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the Δ3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter Δ3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that Δ3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.
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11
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Enhanced Seroconversion to West Nile Virus Proteins in Mice by West Nile Kunjin Replicon Virus-like Particles Expressing Glycoproteins from Crimean–Congo Hemorrhagic Fever Virus. Pathogens 2022; 11:pathogens11020233. [PMID: 35215177 PMCID: PMC8874638 DOI: 10.3390/pathogens11020233] [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: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/18/2022] Open
Abstract
Removal of genes coding for major parts of capsid (C), premembrane (prM), and envelope (E) proteins on the flavivirus genome aborts the production of infectious virus particles where the remaining genome forms a replicon that retains replicability in host cells. The C-prM-E proteins can also be expressed in trans with the flavivirus replicons to generate single-round infectious replicon virus-like particles (RVPs). In this study, we characterized the use of RVPs based on the Kunjin strain of WNV (WNVKUN) as a putative WNV vaccine candidate. In addition, the WNVKUN C-prM-E genes were substituted with the Crimean–Congo hemorrhagic fever virus (CCHFV) genes encoding the glycoproteins Gn and Gc to generate a WNVKUN replicon expressing the CCHFV proteins. To generate RVPs, the WNVKUN replicon was transfected into a cell line expressing the WNVKUN C-prM-E. Using immunoblotting and immunofluorescence assays, we showed that the replicon can express the CCHFV Gn and Gc proteins and the RVPs can transduce cells to express WNVKUN proteins and the CCHFV Gn and Gc proteins. Our study also revealed that these RVPs have potential as a vaccine platform with low risk of recombination as it infects cells only in one cycle. The immunization of mice with the RVPs resulted in high seroconversion to both WNV E and NS1 but limited seroconversion to CCHFV Gn and Gc proteins. Interestingly, we found that there was enhanced production of WNV E, NS1 antibodies, and neutralizing antibodies by the inclusion of CCHFV Gc and Gn into WNVKUN RVPs. Thus, this study indicates a complementary effect of the CCHFV Gn and Gc proteins on the immunogenicity by WNVKUN RVPs, which may be applied to develop a future vaccine against the WNV.
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12
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Oreshkova N, Myeni SK, Mishra N, Albulescu IC, Dalebout TJ, Snijder EJ, Bredenbeek PJ, Dallmeier K, Kikkert M. A Yellow Fever 17D Virus Replicon-Based Vaccine Platform for Emerging Coronaviruses. Vaccines (Basel) 2021; 9:1492. [PMID: 34960238 PMCID: PMC8704410 DOI: 10.3390/vaccines9121492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/15/2021] [Accepted: 12/13/2021] [Indexed: 01/14/2023] Open
Abstract
The tremendous global impact of the current SARS-CoV-2 pandemic, as well as other current and recent outbreaks of (re)emerging viruses, emphasize the need for fast-track development of effective vaccines. Yellow fever virus 17D (YF17D) is a live-attenuated virus vaccine with an impressive efficacy record in humans, and therefore, it is a very attractive platform for the development of novel chimeric vaccines against various pathogens. In the present study, we generated a YF17D-based replicon vaccine platform by replacing the prM and E surface proteins of YF17D with antigenic subdomains from the spike (S) proteins of three different betacoronaviruses: MERS-CoV, SARS-CoV and MHV. The prM and E proteins were provided in trans for the packaging of these RNA replicons into single-round infectious particles capable of expressing coronavirus antigens in infected cells. YF17D replicon particles expressing the S1 regions of the MERS-CoV and SARS-CoV spike proteins were immunogenic in mice and elicited (neutralizing) antibody responses against both the YF17D vector and the coronavirus inserts. Thus, YF17D replicon-based vaccines, and their potential DNA- or mRNA-based derivatives, may constitute a promising and particularly safe vaccine platform for current and future emerging coronaviruses.
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Affiliation(s)
- Nadia Oreshkova
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
| | - Sebenzile K. Myeni
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
| | - Niraj Mishra
- Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49 Box 1043, 3000 Leuven, Belgium; (N.M.); (K.D.)
| | - Irina C. Albulescu
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
| | - Tim J. Dalebout
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
| | - Eric J. Snijder
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
| | - Peter J. Bredenbeek
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
| | - Kai Dallmeier
- Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49 Box 1043, 3000 Leuven, Belgium; (N.M.); (K.D.)
| | - Marjolein Kikkert
- Center of Infectious Diseases LU-CID, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (N.O.); (S.K.M.); (I.C.A.); (T.J.D.); (E.J.S.); (P.J.B.)
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13
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Tran PTH, Asghar N, Johansson M, Melik W. Roles of the Endogenous Lunapark Protein during Flavivirus Replication. Viruses 2021; 13:v13071198. [PMID: 34206552 PMCID: PMC8310331 DOI: 10.3390/v13071198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 12/19/2022] Open
Abstract
The endoplasmic reticulum (ER) of eukaryotic cells is a dynamic organelle, which undergoes continuous remodeling. At the three-way tubular junctions of the ER, the lunapark (LNP) protein acts as a membrane remodeling factor to stabilize these highly curved membrane junctions. In addition, during flavivirus infection, the ER membrane is invaginated to form vesicles (Ve) for virus replication. Thus, LNP may have roles in the generation or maintenance of the Ve during flavivirus infection. In this study, our aim was to characterize the functions of LNP during flavivirus infection and investigate the underlying mechanisms of these functions. To specifically study virus replication, we generated cell lines expressing replicons of West Nile virus (Kunjin strain) or Langat virus. By using these replicon platforms and electron microscopy, we showed that depletion of LNP resulted in reduced virus replication, which is due to its role in the generation of the Ve. By using biochemical assays and high-resolution microscopy, we found that LNP is recruited to the Ve and the protein interacts with the nonstructural protein (NS) 4B. Therefore, these data shed new light on the interactions between flavivirus and host factors during viral replication.
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14
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Mikulasova A, Gillespie LK, Ambrose RL, Aktepe TE, Trenerry AM, Liebscher S, Mackenzie JM. A Putative Lipid-Associating Motif in the West Nile Virus NS4A Protein Is Required for Efficient Virus Replication. Front Cell Dev Biol 2021; 9:655606. [PMID: 34055786 PMCID: PMC8149610 DOI: 10.3389/fcell.2021.655606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/07/2021] [Indexed: 01/06/2023] Open
Abstract
Flavivirus replication is intimately associated with re-organized cellular membranes. These virus-induced changes in membrane architecture form three distinct membranous “organelles” that have specific functions during the flavivirus life cycle. One of these structures is the replication complex in which the flaviviral RNA is replicated to produce progeny genomes. We have previously observed that this process is strictly dependent on cellular cholesterol. In this study we have identified a putative cholesterol recognition/interaction amino acid consensus (CRAC) motif within the West Nile virus strain Kunjin virus (WNVKUN) NS4A protein. Site-directed mutagenesis of this motif within a WNVKUN infectious clone severely attenuated virus replication and the capacity of the mutant viruses to form the replication complex. Replication of the mutant viruses also displayed reduced co-localization with cellular markers recruited to replication sites during wild-type virus replication. In addition, we observed that the mutant viruses were significantly impaired in their ability to remodel cytoplasmic membranes. However, after extensive analysis we are unable to conclusively reveal a role for the CRAC motif in direct cholesterol binding to NS4A, suggesting additional complex lipid-protein and protein-protein interactions. We believe this study highlights the crucial role for this region within NS4A protein in recruitment of cellular and viral proteins to specialized subdomains on membrane platforms to promote efficient virus replication.
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Affiliation(s)
- Andrea Mikulasova
- Department of Physiology Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Leah K Gillespie
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Rebecca L Ambrose
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Turgut E Aktepe
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Alice M Trenerry
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Susann Liebscher
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
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15
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Zhang X, Liu Y, Liu J, Bailey AL, Plante KS, Plante JA, Zou J, Xia H, Bopp NE, Aguilar PV, Ren P, Menachery VD, Diamond MS, Weaver SC, Xie X, Shi PY. A trans-complementation system for SARS-CoV-2 recapitulates authentic viral replication without virulence. Cell 2021; 184:2229-2238.e13. [PMID: 33691138 PMCID: PMC7901297 DOI: 10.1016/j.cell.2021.02.044] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/25/2022]
Abstract
The biosafety level 3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research. Here, we report a trans-complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. The trans-complementation system consists of two components: a genomic viral RNA containing ORF3 and envelope gene deletions, as well as mutated transcriptional regulator sequences, and a producer cell line expressing the two deleted genes. Trans-complementation of the two components generates virions that can infect naive cells for only one round but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. Thus, the trans-complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.
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Affiliation(s)
- Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam L Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael S Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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16
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Zhang X, Liu Y, Liu J, Bailey AL, Plante KS, Plante JA, Zou J, Xia H, Bopp N, Aguilar P, Ren P, Menachery VD, Diamond MS, Weaver SC, Xie X, Shi PY. A trans -complementation system for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33501436 DOI: 10.1101/2021.01.16.426970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The biosafety level-3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research and countermeasure development. Here we report a trans -complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. The trans -complementation system consists of two components: a genomic viral RNA containing a deletion of ORF3 and envelope gene, and a producer cell line expressing the two deleted genes. Trans- complementation of the two components generates virions that can infect naive cells for only one round, but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. The results suggest that the trans -complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.
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17
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Tran PTH, Asghar N, Höglund U, Larsson O, Haag L, Mirazimi A, Johansson M, Melik W. Development of a Multivalent Kunjin Virus Reporter Virus-Like Particle System Inducing Seroconversion for Ebola and West Nile Virus Proteins in Mice. Microorganisms 2020; 8:E1890. [PMID: 33260425 PMCID: PMC7760487 DOI: 10.3390/microorganisms8121890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/26/2022] Open
Abstract
Kunjin virus (KUNV) is an attenuated strain of the severe neurotropic West Nile virus (WNV). The virus has a single-strand positive-sense RNA genome that encodes a polyprotein. Following gene expression, the polyprotein is cleaved into structural proteins for viral packaging and nonstructural proteins for viral replication and expression. Removal of the structural genes generate subgenomic replicons that maintain replication capacity. Co-expression of these replicons with the viral structural genes produces reporter virus-like particles (RVPs) which infect cells in a single round. In this study, we aimed to develop a system to generate multivalent RVPs based on KUNV to elicit an immune response against different viruses. We selected the Ebola virus (EBOV) glycoprotein (GP) and the matrix protein (VP40) genes, as candidates to be delivered by KUNV RVPs. Initially, we enhanced the production of KUNV RVPs by generating a stable cell line expressing the KUNV packaging system comprising capsid, precursor membrane, and envelope. Transfection of the DNA-based KUNV replicon into this cell line resulted in an enhanced RVP production. The replicon was expressed in the stable cell line to produce the RVPs that allowed the delivery of EBOV GP and VP40 genes into other cells. Finally, we immunized BALB/cN mice with RVPs, resulting in seroconversion for EBOV GP, EBOV VP40, WNV nonstructural protein 1, and WNV E protein. Thus, our study shows that KUNV RVPs may function as a WNV vaccine candidate and RVPs can be used as a gene delivery system in the development of future EBOV vaccines.
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Affiliation(s)
- Pham-Tue-Hung Tran
- School of Medical Science, Inflammatory Response and Infection Susceptibility Centre (iRiSC), Örebro University, 703 62 Örebro, Sweden; (P.-T.-H.T.); (N.A.); (M.J.)
| | - Naveed Asghar
- School of Medical Science, Inflammatory Response and Infection Susceptibility Centre (iRiSC), Örebro University, 703 62 Örebro, Sweden; (P.-T.-H.T.); (N.A.); (M.J.)
| | - Urban Höglund
- Adlego Biomedical AB, P.O. Box 42, 751 03 Uppsala, Sweden; (U.H.); (O.L.)
| | - Olivia Larsson
- Adlego Biomedical AB, P.O. Box 42, 751 03 Uppsala, Sweden; (U.H.); (O.L.)
| | - Lars Haag
- EM Unit (EMil), Department of Laboratory Medicine, Karolinska Institute, 171 77 Solna, Sweden;
| | - Ali Mirazimi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden;
- National Veterinary Institute, 751 89 Uppsala, Sweden
| | - Magnus Johansson
- School of Medical Science, Inflammatory Response and Infection Susceptibility Centre (iRiSC), Örebro University, 703 62 Örebro, Sweden; (P.-T.-H.T.); (N.A.); (M.J.)
| | - Wessam Melik
- School of Medical Science, Inflammatory Response and Infection Susceptibility Centre (iRiSC), Örebro University, 703 62 Örebro, Sweden; (P.-T.-H.T.); (N.A.); (M.J.)
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18
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Baker C, Shi PY. Construction of Stable Reporter Flaviviruses and Their Applications. Viruses 2020; 12:v12101082. [PMID: 32992987 PMCID: PMC7599567 DOI: 10.3390/v12101082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/28/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Flaviviruses are significant human pathogens that cause frequent emerging and reemerging epidemics around the world. Better molecular tools for studying, diagnosing, and treating these diseases are needed. Reporter viruses represent potent tools to fill this gap but have been hindered by genetic instability. Recent advances have overcome these hurdles, opening the way for increased use of stable reporter flaviviruses to diagnose infections, screen and study antiviral compounds, and serve as potential vaccine vectors.
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Affiliation(s)
- Coleman Baker
- Microbiology and Immunology Department, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Pei-Yong Shi
- Biochemistry and Molecular Biology Department, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections & Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Correspondence:
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19
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Liu Y, Zhang Y, Wang M, Cheng A, Yang Q, Wu Y, Jia R, Liu M, Zhu D, Chen S, Zhang S, Zhao X, Huang J, Mao S, Ou X, Gao Q, Wang Y, Xu Z, Chen Z, Zhu L, Luo Q, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. Structures and Functions of the 3' Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals. Front Cell Infect Microbiol 2020; 10:453. [PMID: 32974223 PMCID: PMC7481400 DOI: 10.3389/fcimb.2020.00453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022] Open
Abstract
The 3′ untranslated region (3′ UTR) of positive-sense single-stranded RNA [ssRNA(+)] viruses is highly structured. Multiple elements in the region interact with other nucleotides and proteins of viral and cellular origin to regulate various aspects of the virus life cycle such as replication, translation, and the host-cell response. This review attempts to summarize the primary and higher order structures identified in the 3′UTR of ssRNA(+) viruses and their functional roles.
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Affiliation(s)
- Yuanzhi Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - XinXin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yin Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhiwen Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qihui Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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20
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Baker C, Xie X, Zou J, Muruato A, Fink K, Shi PY. Using recombination-dependent lethal mutations to stabilize reporter flaviviruses for rapid serodiagnosis and drug discovery. EBioMedicine 2020; 57:102838. [PMID: 32574959 PMCID: PMC7317239 DOI: 10.1016/j.ebiom.2020.102838] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 01/11/2023] Open
Abstract
Background Many flaviviruses are significant human pathogens that cause global public health threats. Developing research tools for studying and diagnosing these pathogens is a top priority. Reporter flaviviruses are useful tools for studying viral pathogenesis, diagnosing disease, and screening antiviral compounds. However, the stability of reporter flaviviruses has been challenged by viral RNA recombination, leading to deletion of the engineered reporter gene during viral replication. The instability of reporter viruses has limited their application to research and countermeasure development. Thus, new approaches to overcome the instability of reporter flaviviruses are critically needed to advance the flavivirus field. Methods To create a stable flavivirus bearing a reporter gene, we engineered mutations in the viral capsid gene that are rendered virus-lethal upon recombination. Thus, only non-recombined reporter virus propagates. We tested this strategy using Zika virus (ZIKV) bearing a nano-luciferase (NanoLuc) gene and passaged both virus with capsid mutations and virus without mutations. Findings The recombination-dependent lethal mutations succeeded in stabilizing the NanoLuc ZIKV through ten passages, while WT reporter virus showed instability as early as five passages. The stability of NanoLuc ZIKV was supported by RT-PCR, sequencing, focus forming assay, and luciferase assay. The success of this method was reconfirmed by also establishing a stable NanoLuc Yellow Fever 17D virus, indicating that the recombination-dependent lethal approach can be applied to other flaviviruses. To demonstrate the utility of the stable reporter viruses, we showed that NanoLuc ZIKV and YFV17D could be used to measure neutralizing antibody titers with a turnaround time as short as four hours. Importantly, the neutralizing antibody titers derived from the reporter virus assay were equivalent to those derived from the conventional plaque assay, indicating the new assay maintains the gold standard of serology testing. Furthermore, using a known inhibitor, we showed that the reporter viruses could be reliably used for antiviral evaluation. Interpretation The study has developed a recombination-dependent lethal approach to produce stable reporter flaviviruses that may be used for rapid serodiagnosis, trans-gene delivery, vaccine evaluation, and antiviral discovery. Funding National Institute of Health, Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation; John S. Dunn Foundation; Amon G. Carter Foundation; Gillson Longenbaugh Foundation; Summerfield G. Roberts Foundation.
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Affiliation(s)
- Coleman Baker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biology and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Jing Zou
- Department of Biology and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio Muruato
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Pei-Yong Shi
- Department of Biology and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
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21
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Hannemann H. Viral replicons as valuable tools for drug discovery. Drug Discov Today 2020; 25:1026-1033. [PMID: 32272194 PMCID: PMC7136885 DOI: 10.1016/j.drudis.2020.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/28/2020] [Accepted: 03/13/2020] [Indexed: 12/15/2022]
Abstract
RNA viruses can cause severe diseases such as dengue, Lassa, chikungunya and Ebola. Many of these viruses can only be propagated under high containment levels, necessitating the development of low containment surrogate systems such as subgenomic replicons and minigenome systems. Replicons are self-amplifying recombinant RNA molecules expressing proteins sufficient for their own replication but which do not produce infectious virions. Replicons can persist in cells and are passed on during cell division, enabling quick, efficient and high-throughput testing of drug candidates that act on viral transcription, translation and replication. This review will explore the history and potential for drug discovery of hepatitis C virus, dengue virus, respiratory syncytial virus, Ebola virus and norovirus replicon and minigenome systems.
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Affiliation(s)
- Holger Hannemann
- The Native Antigen Company, Langford Locks, Kidlington OX5 1LH, UK.
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22
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Bhatia M, Gupta E. Emerging resistance to directly-acting antiviral therapy in treatment of chronic Hepatitis C infection-A brief review of literature. J Family Med Prim Care 2020; 9:531-538. [PMID: 32318377 PMCID: PMC7113931 DOI: 10.4103/jfmpc.jfmpc_943_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022] Open
Abstract
Hepatitis caused by Hepatitis C virus (HCV) is a major cause of chronic liver disease. HCV is transmitted by injection drug use, blood transfusion, hemodialysis, organ transplantation and less frequently sexual intercourse. It has been recognized as a global health problem because of the progression to cirrhosis and hepatocellular carcinoma. Globally, about 170 million people are infected with HCV. Since the discovery of this virus in 1989, the clinical management of chronic hepatitis C infection has undergone a paradigm shift from alpha interferon to direct-acting antiviral (DAA) therapy. However, resistance to many of these antiviral agents has been reported increasingly from all over the globe. This review article focuses on the emerging HCV resistance to DAAs and the relevance of in vitro DAA resistance testing in clinical practice.
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Affiliation(s)
- Mohit Bhatia
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Ekta Gupta
- Department of Virology, Institute of Liver and Biliary Sciences, New Delhi, India
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23
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Rana J, Slon Campos JL, Poggianella M, Burrone OR. Dengue virus capsid anchor modulates the efficiency of polyprotein processing and assembly of viral particles. J Gen Virol 2019; 100:1663-1673. [DOI: 10.1099/jgv.0.001346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The assembly and secretion of flaviviruses are part of an elegantly regulated process. During maturation, the viral polyprotein undergoes several co- and post-translational cleavages mediated by both viral and host proteases. Among these, sequential cleavage at the N and C termini of the hydrophobic capsid anchor (Ca) is crucial in deciding the fate of viral infection. Here, using a refined dengue pseudovirus production system, along with cleavage and furin inhibition assays, immunoblotting and secondary structure prediction analysis, we show that Ca plays a key role in the processing efficiency of dengue virus type 2 (DENV2) structural proteins and viral particle assembly. Replacement of the DENV2 Ca with the homologous regions from West nile or Zika viruses or, alternatively, increasing its length, improved cleavage and hence particle assembly. Further, we showed that substitution of the Ca conserved proline residue (P110) to alanine abolishes pseudovirus production, regardless of the Ca sequence length. Besides providing the results of a biochemical analysis of DENV2 structural polyprotein processing, this study also presents a system for efficient production of dengue pseudoviruses.
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Affiliation(s)
- Jyoti Rana
- Present address: Gene and Cell Therapy group, IU School of Medicine, Wells Center of Pediatric Research, IUPUI, Indianapolis, IN 46202, USA
- International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
| | - José Luis Slon Campos
- Present address: Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
| | - Monica Poggianella
- International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
| | - Oscar R. Burrone
- International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
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24
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Abstract
The flavivirus virion consists of an envelope outer layer, formed by envelope (E) and membrane (M) proteins on a lipid bilayer, and an internal core, formed by capsid (C) protein and genomic RNA. The molecular mechanism of flavivirus assembly is not well understood. Here, we show that Zika virus (ZIKV) NS2A protein recruits genomic RNA, the structural protein prM/E complex, and the NS2B/NS3 protease complex to the virion assembly site and orchestrates virus morphogenesis. Coimmunoprecipitation analysis showed that ZIKV NS2A binds to prM, E, NS2B, and NS3 (but not C, NS4B, or NS5) in a viral RNA-independent manner, whereas prM/E complex does not interact with NS2B/NS3 complex. Remarkably, a single-amino-acid mutation (E103A) of NS2A impairs its binding to prM/E and NS2B/NS3 and abolishes virus production, demonstrating the indispensable role of NS2A/prM/E and NS2A/NS2B/NS3 interactions in virion assembly. In addition, RNA-protein pulldown analysis identified a stem-loop RNA from the 3' untranslated region (UTR) of the viral genome as an "RNA recruitment signal" for ZIKV assembly. The 3' UTR RNA binds to a cytoplasmic loop of NS2A protein. Mutations of two positively charged residues (R96A and R102A) from the cytoplasmic loop reduce NS2A binding to viral RNA, leading to a complete loss of virion assembly. Collectively, our results support a virion assembly model in which NS2A recruits viral NS2B/NS3 protease and structural C-prM-E polyprotein to the virion assembly site; once the C-prM-E polyprotein has been processed, NS2A presents viral RNA to the structural proteins for virion assembly.IMPORTANCE ZIKV is a recently emerged mosquito-borne flavivirus that can cause devastating congenital Zika syndrome in pregnant women and Guillain-Barré syndrome in adults. The molecular mechanism of ZIKV virion assembly is largely unknown. Here, we report that ZIKV NS2A plays a central role in recruiting viral RNA, structural protein prM/E, and viral NS2B/NS3 protease to the virion assembly site and orchestrating virion morphogenesis. One mutation that impairs these interactions does not significantly affect viral RNA replication but selectively abolishes virion assembly, demonstrating the specific role of these interactions in virus morphogenesis. We also show that the 3' UTR of ZIKV RNA may serve as a "recruitment signal" through binding to NS2A to enter the virion assembly site. Following a coordinated cleavage of C-prM-E at the virion assembly site, NS2A may present the viral RNA to C protein for nucleocapsid formation followed by envelopment with prM/E proteins. The results have provided new insights into flavivirus virion assembly.
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25
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Dengue NS2A Protein Orchestrates Virus Assembly. Cell Host Microbe 2019; 26:606-622.e8. [PMID: 31631053 DOI: 10.1016/j.chom.2019.09.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/04/2019] [Accepted: 09/25/2019] [Indexed: 01/12/2023]
Abstract
Dengue virus assembly requires cleavage of viral C-prM-E polyprotein into three structural proteins (capsid, premembrane, and envelope), packaging of viral RNA with C protein into nucleocapsid, and budding of prM and E proteins into virions. The molecular mechanisms underlying these assembly events are unclear. Here, we show that dengue nonstructural protein 2A (NS2A protein) recruits viral RNA, structural proteins, and protease to the site of virion assembly and coordinates nucleocapsid and virus formation. The last 285 nucleotides of viral 3' UTR serve as a "recruiting signal for packaging" that binds to a cytosolic loop of NS2A. This interaction allows NS2A to recruit nascent RNA from the replication complex to the virion assembly site. NS2A also recruits the C-prM-E polyprotein and NS2B-NS3 protease to the virion assembly site by interacting with prM, E, and NS3, leading to coordinated C-prM-E cleavage. Mature C protein assembles onto genomic RNA to form nucleocapsid, followed by prM and E envelopment and virion formation.
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26
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Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication. J Virol 2019; 93:JVI.00292-19. [PMID: 31243132 PMCID: PMC6714791 DOI: 10.1128/jvi.00292-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023] Open
Abstract
TBEV infection causes a broad spectrum of symptoms, ranging from mild fever to severe encephalitis. Similar to other flaviviruses, TBEV exploits intracellular membranes to build RCs for viral replication. The viral NS proteins have been suggested to be involved in this process; however, the mechanism of RC formation and the roles of individual NS proteins remain unclear. To study how TBEV induces membrane remodeling, we developed an inducible stable cell system expressing the TBEV NS polyprotein in the absence of viral RNA replication. Using this system, we were able to reproduce RC-like vesicles that resembled the RCs formed in flavivirus-infected cells, in terms of morphology and size. This cell system is a robust tool to facilitate studies of flavivirus RC formation and is an ideal model for the screening of antiviral agents at a lower biosafety level. Flavivirus is a positive-sense, single-stranded RNA viral genus, with members causing severe diseases in humans such as tick-borne encephalitis, yellow fever, and dengue fever. Flaviviruses are known to cause remodeling of intracellular membranes into small cavities, where replication of the viral RNA takes place. Nonstructural (NS) proteins are not part of the virus coat and are thought to participate in the formation of these viral replication compartments (RCs). Here, we used tick-borne encephalitis virus (TBEV) as a model for the flaviviruses and developed a stable human cell line in which the expression of NS proteins can be induced without viral RNA replication. The model system described provides a novel and benign tool for studies of the viral components under controlled expression levels. We show that the expression of six NS proteins is sufficient to induce infection-like dilation of the endoplasmic reticulum (ER) and the formation of RC-like membrane invaginations. The NS proteins form a membrane-associated complex in the ER, and electron tomography reveals that the dilated areas of the ER are closely associated with lipid droplets and mitochondria. We propose that the NS proteins drive the remodeling of ER membranes and that viral RNA, RNA replication, viral polymerase, and TBEV structural proteins are not required. IMPORTANCE TBEV infection causes a broad spectrum of symptoms, ranging from mild fever to severe encephalitis. Similar to other flaviviruses, TBEV exploits intracellular membranes to build RCs for viral replication. The viral NS proteins have been suggested to be involved in this process; however, the mechanism of RC formation and the roles of individual NS proteins remain unclear. To study how TBEV induces membrane remodeling, we developed an inducible stable cell system expressing the TBEV NS polyprotein in the absence of viral RNA replication. Using this system, we were able to reproduce RC-like vesicles that resembled the RCs formed in flavivirus-infected cells, in terms of morphology and size. This cell system is a robust tool to facilitate studies of flavivirus RC formation and is an ideal model for the screening of antiviral agents at a lower biosafety level.
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27
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Luna JM, Saeed M, Rice CM. Taming a beast: lessons from the domestication of hepatitis C virus. Curr Opin Virol 2019; 35:27-34. [PMID: 30875640 PMCID: PMC6556422 DOI: 10.1016/j.coviro.2019.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/05/2019] [Accepted: 02/12/2019] [Indexed: 12/13/2022]
Abstract
"What I cannot create, I do not understand." Richard Feynman may have championed reasoning from first principles in his famous blackboard missive, but he could just as well have been referring to the plight of a molecular virologist. What cannot be grown in a controlled laboratory setting, we cannot fully understand. The story of the laboratory domestication of hepatitis C virus (HCV) is now a classic example of virologists applying all manner of inventive skill to create cell-based models of infection in order to clarify prospective drug targets. In this review, we highlight key successes and failures that were instructive in achieving cell-based models for HCV studies and drug development. We also emphasize the lessons learned from the ∼40 year saga that may be applicable to viruses yet unknown and uncultured.
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Affiliation(s)
- Joseph M Luna
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, United States
| | - Mohsan Saeed
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, United States
| | - Charles M Rice
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, United States.
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28
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Zou J, Shi PY. Strategies for Zika drug discovery. Curr Opin Virol 2019; 35:19-26. [PMID: 30852345 DOI: 10.1016/j.coviro.2019.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) can cause devastating congenital syndrome in fetuses from pregnant women and autoimmune disorder Guillain-Barré syndrome in adults. No clinically approved vaccine or drug is currently available for ZIKV. This unmet medical need has motivated a global effort to develop countermeasures. Several promising ZIKV vaccine candidates have already entered clinical trials. In contrast, antiviral development of ZIKV is lagging behind. Here, we review the overall strategies for ZIKV drug discovery, including (i) repurposing of clinically approved drugs, (ii) viral replication-based phenotypic screening for inhibitors, and (iii) targeted drug discovery of viral proteins. Along with vaccines, the development of antiviral treatment will provide a complementary means to control ZIKV infections.
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Affiliation(s)
- Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Department of Phamarcology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
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29
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Ávila-Pérez G, Nogales A, Martín V, Almazán F, Martínez-Sobrido L. Reverse Genetic Approaches for the Generation of Recombinant Zika Virus. Viruses 2018; 10:E597. [PMID: 30384426 PMCID: PMC6266887 DOI: 10.3390/v10110597] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/26/2018] [Accepted: 10/28/2018] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV) is an emergent mosquito-borne member of the Flaviviridae family that was responsible for a recent epidemic in the Americas. ZIKV has been associated with severe clinical complications, including neurological disorder such as Guillain-Barré syndrome in adults and severe fetal abnormalities and microcephaly in newborn infants. Given the significance of these clinical manifestations, the development of tools and reagents to study the pathogenesis of ZIKV and to develop new therapeutic options are urgently needed. In this respect, the implementation of reverse genetic techniques has allowed the direct manipulation of the viral genome to generate recombinant (r)ZIKVs, which have provided investigators with powerful systems to answer important questions about the biology of ZIKV, including virus-host interactions, the mechanism of transmission and pathogenesis or the function of viral proteins. In this review, we will summarize the different reverse genetic strategies that have been implemented, to date, for the generation of rZIKVs and the applications of these platforms for the development of replicon systems or reporter-expressing viruses.
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Affiliation(s)
- Ginés Ávila-Pérez
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| | - Verónica Martín
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 3 Darwin street, 28049 Madrid, Spain.
| | - Fernando Almazán
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 3 Darwin street, 28049 Madrid, Spain.
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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30
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Role of Capsid Anchor in the Morphogenesis of Zika Virus. J Virol 2018; 92:JVI.01174-18. [PMID: 30158295 DOI: 10.1128/jvi.01174-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/22/2018] [Indexed: 01/24/2023] Open
Abstract
The flavivirus capsid protein (C) is separated from the downstream premembrane (PrM) protein by a hydrophobic sequence named capsid anchor (Ca). During polyprotein processing, Ca is sequentially cleaved by the viral NS2B/NS3 protease on the cytosolic side and by signal peptidase on the luminal side of the endoplasmic reticulum (ER). To date, Ca is considered important mostly for directing translocation of PrM into the ER lumen. In this study, the role of Ca in the assembly and secretion of Zika virus was investigated using a pseudovirus-based approach. Our results show that, while Ca-mediated anchoring of C to the ER membrane is not needed for the production of infective particles, Ca expression in cis with respect to PrM is strictly required to allow proper assembly of infectious particles. Finally, we show that the presence of heterologous, but not homologous, Ca induces degradation of E through the autophagy/lysosomal pathway.IMPORTANCE The capsid anchor (Ca) is a single-pass transmembrane domain at the C terminus of the capsid protein (C) known to function as a signal for the translocation of PrM into the ER lumen. The objective of this study was to further examine the role of Ca in Zika virus life cycle, whether involved in the formation of nucleocapsid through association with C or in the formation of viral envelope. In this study, we show that Ca has a function beyond the one of translocation signal, controlling protein E stability and therefore its availability for assembly of infectious particles.
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31
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Hepatitis C virus cell culture models: an encomium on basic research paving the road to therapy development. Med Microbiol Immunol 2018; 208:3-24. [PMID: 30298360 DOI: 10.1007/s00430-018-0566-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022]
Abstract
Chronic hepatitis C virus (HCV) infections affect 71 million people worldwide, often resulting in severe liver damage. Since 2014 highly efficient therapies based on directly acting antivirals (DAAs) are available, offering cure rates of almost 100%, if the infection is diagnosed in time. It took more than a decade to discover HCV in 1989 and another decade to establish a cell culture model. This review provides a personal view on the importance of HCV cell culture models, particularly the replicon system, in the process of therapy development, from drug screening to understanding of mode of action and resistance, with a special emphasis on the contributions of Ralf Bartenschlager's group. It summarizes the tremendous efforts of scientists in academia and industry required to achieve efficient DAAs, focusing on the main targets, protease, polymerase and NS5A. It furthermore underpins the importance of strong basic research laying the ground for translational medicine.
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32
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Klitting R, Fischer C, Drexler JF, Gould EA, Roiz D, Paupy C, de Lamballerie X. What Does the Future Hold for Yellow Fever Virus? (II). Genes (Basel) 2018; 9:E425. [PMID: 30134625 PMCID: PMC6162518 DOI: 10.3390/genes9090425] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023] Open
Abstract
As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas with low vaccination coverage but that are suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization's initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately viral dissemination, and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more yellow fever (YF) cases in the upcoming years. Hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of a two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
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Affiliation(s)
- Raphaëlle Klitting
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
| | - Carlo Fischer
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany.
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany.
| | - Jan F Drexler
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany.
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany.
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119991 Moscow, Russia.
| | - Ernest A Gould
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
| | - David Roiz
- UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Univ. Montpellier), 34394 Montpellier, France.
| | - Christophe Paupy
- UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Univ. Montpellier), 34394 Montpellier, France.
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
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Barrows NJ, Campos RK, Liao KC, Prasanth KR, Soto-Acosta R, Yeh SC, Schott-Lerner G, Pompon J, Sessions OM, Bradrick SS, Garcia-Blanco MA. Biochemistry and Molecular Biology of Flaviviruses. Chem Rev 2018; 118:4448-4482. [PMID: 29652486 DOI: 10.1021/acs.chemrev.7b00719] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA-protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes. In this review, we examine the molecular biology of flaviviruses touching on the structure and function of viral components and how these interact with host factors. The latter are functionally divided into pro-viral and antiviral factors, both of which, not surprisingly, include many RNA binding proteins. In the interface between the virus and the hosts we highlight the role of a noncoding RNA produced by flaviviruses to impair antiviral host immune responses. Throughout the review, we highlight areas of intense investigation, or a need for it, and potential targets and tools to consider in the important battle against pathogenic flaviviruses.
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Affiliation(s)
- Nicholas J Barrows
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Rafael K Campos
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Kuo-Chieh Liao
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Ruben Soto-Acosta
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Shih-Chia Yeh
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Geraldine Schott-Lerner
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Julien Pompon
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore.,MIVEGEC, IRD, CNRS, Université de Montpellier , Montpellier 34090 , France
| | - October M Sessions
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
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Establishment and Application of Flavivirus Replicons. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:165-173. [PMID: 29845532 DOI: 10.1007/978-981-10-8727-1_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Dengue virus (DENV) and Zika virus (ZIKV) are enveloped, positive-strand RNA viruses belonging to the genus Flavivirus in the family Flaviviridae. The genome of ~11 kb length encodes one long open reading frame flanked by a 5' and a 3' untranslated region (UTR). The 5' end is capped and the 3' end lacks a poly(A) tail. The encoded single polyprotein is cleaved co-and posttranslationally by cellular and viral proteases. The first one-third of the genome encodes the structural proteins (C-prM-E), whereas the nonstructural (NS) proteins NS1-NS2A-NS3-NS4A-2K-NS4B-NS5 are encoded by the remaining two-thirds of the genome.Research on flaviviruses was driven forward by the ability to produce recombinant viruses using reverse genetics technology. It is known that the purified RNA of flaviviruses is per se infectious, which allows initiation of a complete viral life cycle by transfecting the genomic RNA into susceptible cells. In 1989, the first infectious flavivirus RNA was transcribed from full-length cDNA templates of yellow fever virus (YFV) facilitating molecular genetic analyses of this virus. In addition to the production of infectious recombinant viruses, reverse genetics can also be used to establish non-infectious replicons. Replicons contain an in-frame deletion in the structural protein genes but still encode all nonstructural proteins and contain the UTRs necessary to mediate efficient replication, a factor that enables their analyses under Biosafety Level (BSL) 1 conditions. This is particularly important since many flaviviruses are BSL3 agents.The review will cover strategies for generating flavivirus replicons, including the establishment of bacteriophage (T7 or SP6) promoter-driven constructs as well as cytomegalovirus (CMV) promoter-driven constructs. Furthermore, different reporter replicons or replicons expressing selectable marker proteins will be outlined using examples of their application to answer basic questions of the flavivirus replication cycle, to select and test antiviral compounds or to produce virus replicon particles. The establishment and application of flavivirus replicons will further be exemplified by my own data using an established YFV reporter replicon to study the role of YFV NS2A in the viral life cycle. In addition, we established a reporter replicon of a novel insect-specific flavivirus, namely Niénokoué virus (NIEV), to define the barrier(s) involved in host range restriction.
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Helicase Domain of West Nile Virus NS3 Protein Plays a Role in Inhibition of Type I Interferon Signalling. Viruses 2017; 9:v9110326. [PMID: 29099073 PMCID: PMC5707533 DOI: 10.3390/v9110326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022] Open
Abstract
West Nile virus (WNV) is a neurotropic flavivirus that can cause encephalitis in mammalian and avian hosts. In America, the virulent WNV strain (NY99) is causing yearly outbreaks of encephalitis in humans and horses, while in Australia the less virulent Kunjin strain of WNV strain has not been associated with significant disease outbreaks until a recent 2011 large outbreak in horses (but not in humans) caused by NSW2011 strain. Using chimeric viruses between NY99 and NSW2011 strains we previously identified a role for the non-structural proteins of NY99 strain and especially the NS3 protein, in enhanced virus replication in type I interferon response-competent cells and increased virulence in mice. To further define the role of NY99 NS3 protein in inhibition of type I interferon response, we have generated and characterised additional chimeric viruses containing the protease or the helicase domains of NY99 NS3 on the background of the NSW2011 strain. The results identified the role for the helicase but not the protease domain of NS3 protein in the inhibition of type I interferon signalling and showed that helicase domain of the more virulent NY99 strain performs this function more efficiently than helicase domain of the less virulent NSW2011 strain. Further analysis with individual amino acid mutants identified two amino acid residues in the helicase domain primarily responsible for this difference. Using chimeric replicons, we also showed that the inhibition of type I interferon (IFN) signalling was independent of other known functions of NS3 in RNA replication and assembly of virus particles.
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Zhang QY, Li XD, Liu SQ, Deng CL, Zhang B, Ye HQ. Development of a stable Japanese encephalitis virus replicon cell line for antiviral screening. Arch Virol 2017; 162:3417-3423. [PMID: 28779235 DOI: 10.1007/s00705-017-3508-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Japanese encephalitis virus (JEV), an important pathogen in Eastern and Southern Asia and the Pacific, has spread to Australia and other territories in recent years. Although the vaccine for JEV has been used in some countries, development of efficient antiviral drugs is still an urgent requirement. Replicon systems have been widely used in the research of viral replication and antiviral screening for West Nile virus (WNV), yellow fever virus (YFV) and dengue virus (DENV). Here, a novel JEV replicon harboring the Rluc and Pac gene (JEV-Pac-Rluc-Rep) was constructed. Furthermore, we established a BHK-21 cell line harboring JEV-Pac-Rluc-Rep (BHK-21/PAC/Rluc cell line) through continuous puromycin selection. Characterization of cell line stability showed that the replicon RNA could persistently replicate in this cell line for at least up to 10 rounds of passage. Using a known flavivirus inhibitor, the JEV replicon cell line was validated for antiviral screening. The JEV replicon cell line will be a valuable tool for both compound screening and viral replication studies.
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Affiliation(s)
- Qiu-Yan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Dan Li
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si-Qing Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Cheng-Lin Deng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Han-Qing Ye
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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Yudhaputri FA, Trimarsanto H, Perkasa A, Yohan B, Haryanto S, Wiyatno A, Soebandrio A, Myint KS, Ledermann JP, Rosenberg R, Powers AM, Sasmono RT. Genomic characterization of Zika virus isolated from Indonesia. Virology 2017; 510:248-251. [PMID: 28755588 DOI: 10.1016/j.virol.2017.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 01/06/2023]
Abstract
Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000. We observed high nucleotide sequence identity between Indonesia, Thailand, Singapore, and American strains although unique amino acid substitutions were also observed. This report provides information on the genomic characteristics of Indonesian ZIKV which may be used for further studies.
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Affiliation(s)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Agency for Assessment and Application of Technology, Jakarta, Indonesia
| | - Aditya Perkasa
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Ageng Wiyatno
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Khin Saw Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Ronald Rosenberg
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Ann M Powers
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
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Piyasena TBH, Setoh YX, Hobson-Peters J, Newton ND, Bielefeldt-Ohmann H, McLean BJ, Vet LJ, Khromykh AA, Hall RA. Infectious DNAs derived from insect-specific flavivirus genomes enable identification of pre- and post-entry host restrictions in vertebrate cells. Sci Rep 2017; 7:2940. [PMID: 28592864 PMCID: PMC5462777 DOI: 10.1038/s41598-017-03120-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/24/2017] [Indexed: 02/06/2023] Open
Abstract
Flaviviruses such as West Nile virus (WNV), dengue virus and Zika virus are mosquito-borne pathogens that cause significant human diseases. A novel group of insect-specific flaviviruses (ISFs), which only replicate in mosquitoes, have also been identified. However, little is known about the mechanisms of ISF host restriction. We report the generation of infectious cDNA from two Australian ISFs, Parramatta River virus (PaRV) and Palm Creek virus (PCV). Using circular polymerase extension cloning (CPEC) with a modified OpIE2 insect promoter, infectious cDNA was generated and transfected directly into mosquito cells to produce infectious virus indistinguishable from wild-type virus. When infectious PaRV cDNA under transcriptional control of a mammalian promoter was used to transfect mouse embryo fibroblasts, the virus failed to initiate replication even when cell entry steps were by-passed and the type I interferon response was lacking. We also used CPEC to generate viable chimeric viruses between PCV and WNV. Analysis of these hybrid viruses revealed that ISFs are also restricted from replication in vertebrate cells at the point of entry. The approaches described here to generate infectious ISF DNAs and chimeric viruses provide unique tools to further dissect the mechanisms of their host restriction.
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Affiliation(s)
- Thisun B H Piyasena
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Yin X Setoh
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Natalee D Newton
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Breeanna J McLean
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Laura J Vet
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Alexander A Khromykh
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia.
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia.
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The 5' and 3' Untranslated Regions of the Flaviviral Genome. Viruses 2017; 9:v9060137. [PMID: 28587300 PMCID: PMC5490814 DOI: 10.3390/v9060137] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/16/2017] [Accepted: 05/29/2017] [Indexed: 01/30/2023] Open
Abstract
Flaviviruses are enveloped arthropod-borne viruses with a single-stranded, positive-sense RNA genome that can cause serious illness in humans and animals. The 11 kb 5′ capped RNA genome consists of a single open reading frame (ORF), and is flanked by 5′ and 3′ untranslated regions (UTR). The ORF is a polyprotein that is processed into three structural and seven non-structural proteins. The UTRs have been shown to be important for viral replication and immune modulation. Both of these regions consist of elements that are essential for genome cyclization, resulting in initiation of RNA synthesis. Genome mutation studies have been employed to investigate each component of the essential elements to show the necessity of each component and its role in viral RNA replication and growth. Furthermore, the highly structured 3′UTR is responsible for the generation of subgenomic flavivirus RNA (sfRNA) that helps the virus evade host immune response, thereby affecting viral pathogenesis. In addition, changes within the 3′UTR have been shown to affect transmissibility between vector and host, which can influence the development of vaccines.
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40
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Fernández-Sanlés A, Ríos-Marco P, Romero-López C, Berzal-Herranz A. Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes. Front Microbiol 2017; 8:546. [PMID: 28421048 PMCID: PMC5376627 DOI: 10.3389/fmicb.2017.00546] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/15/2017] [Indexed: 02/05/2023] Open
Abstract
The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle. The efficiency of this storage system is attributable to supracoding elements, i.e., discrete, structural units with essential functions. This information storage system overlaps and complements the protein coding sequence and is highly conserved across the genus. It therefore offers interesting potential targets for novel therapeutic strategies. This review summarizes our knowledge of the features of flavivirus genome functional RNA domains. It also provides a brief overview of the main achievements reported in the design of antiviral nucleic acid-based drugs targeting functional genomic RNA elements.
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Affiliation(s)
- Alba Fernández-Sanlés
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Pablo Ríos-Marco
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Cristina Romero-López
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Alfredo Berzal-Herranz
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
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41
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Lopez-Denman AJ, Mackenzie JM. The IMPORTance of the Nucleus during Flavivirus Replication. Viruses 2017; 9:v9010014. [PMID: 28106839 PMCID: PMC5294983 DOI: 10.3390/v9010014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
Flaviviruses are a large group of arboviruses of significant medical concern worldwide. With outbreaks a common occurrence, the need for efficient viral control is required more than ever. It is well understood that flaviviruses modulate the composition and structure of membranes in the cytoplasm that are crucial for efficient replication and evading immune detection. As the flavivirus genome consists of positive sense RNA, replication can occur wholly within the cytoplasm. What is becoming more evident is that some viral proteins also have the ability to translocate to the nucleus, with potential roles in replication and immune system perturbation. In this review, we discuss the current understanding of flavivirus nuclear localisation, and the function it has during flavivirus infection. We also describe-while closely related-the functional differences between similar viral proteins in their nuclear translocation.
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Affiliation(s)
- Adam J Lopez-Denman
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne 3086, Australia.
| | - Jason M Mackenzie
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
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Abstract
Vaccination is essential in livestock farming and in companion animal ownership. Nucleic acid vaccines based on DNA or RNA provide an elegant alternative to those classical veterinary vaccines that have performed suboptimally. Recent advances in terms of rational design, safety, and efficacy have strengthened the position of nucleic acid vaccines in veterinary vaccinology. The present review focuses on replicon vaccines designed for veterinary use. Replicon vaccines are self-amplifying viral RNA sequences that, in addition to the sequence encoding the antigen of interest, contain all elements necessary for RNA replication. Vaccination results in high levels of in situ antigen expression and induction of potent immune responses. Both positive- and negative-stranded viruses have been used to construct replicons, and they can be delivered as RNA, DNA, or viral replicon particles. An introduction to the biology and the construction of different viral replicon vectors is given, and examples of veterinary replicon vaccine applications are discussed.
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Affiliation(s)
- Mia C Hikke
- Laboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands;
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands;
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43
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Abstract
Replication of positive-strand RNA viruses occurs in tight association with reorganized host cell membranes. In a concerted fashion, viral and cellular factors generate distinct organelle-like structures, designated viral replication factories. These virus-induced compartments promote highly efficient genome replication, allow spatiotemporal coordination of the different steps of the viral replication cycle, and protect viral RNA from the hostile cytoplasmic environment. The combined use of ultrastructural and functional studies has greatly increased our understanding of the architecture and biogenesis of viral replication factories. Here, we review common concepts and distinct differences in replication organelle morphology and biogenesis within the Flaviviridae family, exemplified by dengue virus and hepatitis C virus. We discuss recent progress made in our understanding of the complex interplay between viral determinants and subverted cellular membrane homeostasis in biogenesis and maintenance of replication factories of this virus family.
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Affiliation(s)
- David Paul
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany; ,
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany; , .,Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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44
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Xie X, Zou J, Shan C, Yang Y, Kum DB, Dallmeier K, Neyts J, Shi PY. Zika Virus Replicons for Drug Discovery. EBioMedicine 2016; 12:156-160. [PMID: 27658737 PMCID: PMC5078599 DOI: 10.1016/j.ebiom.2016.09.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023] Open
Abstract
The current epidemic of Zika virus (ZIKV) has underscored the urgency to establish experimental systems for studying viral replication and pathogenesis, and countermeasure development. Here we report two ZIKV replicon systems: a luciferase replicon that can differentiate between viral translation and RNA synthesis; and a stable luciferase replicon carrying cell line that can be used to screen and characterize inhibitors of viral replication. The transient replicon was used to evaluate the effect of an NS5 polymerase mutation on viral RNA synthesis and to analyze a known ZIKV inhibitor. The replicon cell line was developed into a 96-well format for antiviral testing. Compare with virus infection-based assay, the replicon cell line allows antiviral screening without using infectious virus. Collectively, the replicon systems have provided critical tools for both basic and translational research. A Zika virus replicon has been developed to study antivirals and to differentiate between viral translation and replication. A cell line carrying Zika virus replicon has been developed to screen and characterize antiviral inhibitors.
Experimental systems are urgently needed to study Zika virus and to develop countermeasures. In this communication, we report the development of Zika virus replicon systems that can be used to study viral replication and pathogenesis as well as to screen and characterize antiviral inhibitors.
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Affiliation(s)
- Xuping Xie
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Chao Shan
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yujiao Yang
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Dieudonné Buh Kum
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, University of Leuven, Leuven, Belgium
| | - Kai Dallmeier
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, University of Leuven, Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, University of Leuven, Leuven, Belgium
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Department of Pharmacology & Toxicology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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45
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Schott JW, Morgan M, Galla M, Schambach A. Viral and Synthetic RNA Vector Technologies and Applications. Mol Ther 2016; 24:1513-27. [PMID: 27377044 DOI: 10.1038/mt.2016.143] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Use of RNA is an increasingly popular method to transiently deliver genetic information for cell manipulation in basic research and clinical therapy. In these settings, viral and nonviral RNA platforms are employed for delivery of small interfering RNA and protein-coding mRNA. Technological advances allowing RNA modification for increased stability, improved translation and reduced immunogenicity have led to increased use of nonviral synthetic RNA, which is delivered in naked form or upon formulation. Alternatively, highly efficient viral entry pathways are exploited to transfer genes of interest as RNA incorporated into viral particles. Current viral RNA transfer technologies are derived from Retroviruses, nonsegmented negative-strand RNA viruses or positive-stranded Alpha- and Flaviviruses. In retroviral particles, the genes of interest can either be incorporated directly into the viral RNA genome or as nonviral RNA. Nonsegmented negative-strand virus-, Alpha- and Flavivirus-derived vectors support prolonged expression windows through replication of viral RNA encoding genes of interest. Mixed technologies combining viral and nonviral components are also available. RNA transfer is ideal for all settings that do not require permanent transgene expression and excludes potentially detrimental DNA integration into the target cell genome. Thus, RNA-based technologies are successfully applied for reprogramming, transdifferentiation, gene editing, vaccination, tumor therapy, and gene therapy.
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Affiliation(s)
- Juliane W Schott
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Dengue Virus Reporter Replicon is a Valuable Tool for Antiviral Drug Discovery and Analysis of Virus Replication Mechanisms. Viruses 2016; 8:v8050122. [PMID: 27164125 PMCID: PMC4885077 DOI: 10.3390/v8050122] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/23/2022] Open
Abstract
Dengue, the most prevalent arthropod-borne viral disease, is caused by the dengue virus (DENV), a member of the Flaviviridae family, and is a considerable public health threat in over 100 countries, with 2.5 billion people living in high-risk areas. However, no specific antiviral drug or licensed vaccine currently targets DENV infection. The replicon system has all the factors needed for viral replication in cells. Since the development of replicon systems, transient and stable reporter replicons, as well as reporter viruses, have been used in the study of various virological aspects of DENV and in the identification of DENV inhibitors. In this review, we summarize the DENV reporter replicon system and its applications in high-throughput screening (HTS) for identification of anti-DENV inhibitors. We also describe the use of this system in elucidation of the mechanisms of virus replication and viral dynamics in vivo and in vitro.
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47
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Alsaleh K, Khou C, Frenkiel MP, Lecollinet S, Vàzquez A, de Arellano ER, Després P, Pardigon N. The E glycoprotein plays an essential role in the high pathogenicity of European-Mediterranean IS98 strain of West Nile virus. Virology 2016; 492:53-65. [PMID: 26896935 DOI: 10.1016/j.virol.2016.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/08/2016] [Accepted: 02/11/2016] [Indexed: 01/25/2023]
Abstract
West Nile virus (WNV) is the most widespread arbovirus in the world. Several recent outbreaks and epizootics have been reported in Europe and the Mediterranean basin with increased virulence. In contrast to the well-characterized American and Australian strains, little is known about the virulence determinants of the WNV European-Mediterranean strains. To investigate the viral factors involved in the virulence of these strains, we generated chimeras between the highly neuropathogenic Israel 1998 (IS-98-ST1, IS98) strain and the non-pathogenic Malaysian Kunjin virus (KJMP-502). In vivo analyses in a mouse model of WNV pathogenesis shows that chimeric virus where KJMP-502 E glycoprotein was replaced by that of IS98 is neuropathogenic, demonstrating that this protein is a major virulence determinant. Presence of the N-glycosylation site had limited impact on virus virulence and the 5'UTR does not seem to influence pathogenesis. Finally, mice inoculated with KJMP-502 virus were protected against lethal IS98 infection.
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Affiliation(s)
| | - Cécile Khou
- Institut Pasteur, URE ERI/CIBU, Paris, France
| | | | - Sylvie Lecollinet
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Animal Health Laboratory, UMR1161 Virology, INRA, ANSES, ENVA, Maisons-Alfort, France
| | - Ana Vàzquez
- Arbovirus & Imported Viral Diseases, Centro Nacional de Microbiología, Ctra. Pozuelo, Madrid, Spain
| | - Eva Ramírez de Arellano
- Arbovirus & Imported Viral Diseases, Centro Nacional de Microbiología, Ctra. Pozuelo, Madrid, Spain
| | - Philippe Després
- University of La Réunion Island, UM134 PIMIT, INSERM U1187, CNRS UMR9192, IRD UMR249, Technology Platform CYROI, 97490 Saint-Clotilde, La Réunion, France
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48
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Wang J, Liu W, Meng G, Zhao K, Gu J, Chen P, Cao R. Isolation and genome characterization of a novel duck Tembusu virus with a 74 nucleotide insertion in the 3' non-translated region. Avian Pathol 2015; 44:92-102. [PMID: 25582834 DOI: 10.1080/03079457.2015.1006167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
During investigations into the outbreak of duck Tembusu virus (DTMUV) infection in 2011 in China, a DTMUV strain (DTMUV-AH2011) was isolated from the affected ducks. The length of the genome of the DTMUV-AH2011 strain was found to be 11,064 nucleotides and to possess 10,278 nucleotides of one open reading frame (ORF), flanked by 94 nucleotides of the 5' non-translated region (NTR) and 692 nucleotides of the 3' NTR. In comparison with five fully sequenced TMUV genomes, the genome of DTMUV-AH2011 had a 74 nucleotide insertion in the 3' NTR. Comparison of the DTMUV-AH2011 fully deduced amino acid sequences with those of other Tembusu virus strains reported recently in China showed they had a highly conserved polyprotein precursor, sharing 98.9% amino acid identities, at least. The overall divergences of amino acid substitutions were randomly distributed among viral proteins except for the protein NS4B, the protein NS4B was unchanged. Knowledge of the biological characters of DTMUV and the potential role of the insertion in the 3' NTR in RNA replication will be useful for further studies of the mechanisms of virus replication and pathogenesis.
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Affiliation(s)
- Jingman Wang
- a Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine , Nanjing Agricultural University , Nanjing , China
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Yamshchikov V. Development of a human live attenuated West Nile infectious DNA vaccine: conceptual design of the vaccine candidate. Virology 2015; 484:59-68. [PMID: 26071925 DOI: 10.1016/j.virol.2015.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 11/19/2022]
Abstract
West Nile virus has become an important epidemiological problem attracting significant attention of health authorities, mass media, and the public. Although there are promising advancements toward addressing the vaccine need, the perspectives of the commercial availability of the vaccine remain uncertain. To a large extent this is due to lack of a sustained interest for further commercial development of the vaccines already undergoing the preclinical and clinical development, and a predicted insignificant cost effectiveness of mass vaccination. There is a need for a safe, efficacious and cost effective vaccine, which can improve the feasibility of a targeted vaccination program. In the present report, we summarize the background, the rationale, and the choice of the development pathway that we selected for the design of a live attenuated human West Nile vaccine in a novel infectious DNA format.
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Affiliation(s)
- Vladimir Yamshchikov
- Southern Research, Division of Drug Discovery, Birmingham, Alabama, United States.
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50
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Douam F, Ploss A. Proteomic approaches to analyzing hepatitis C virus biology. Proteomics 2015; 15:2051-65. [PMID: 25809442 PMCID: PMC4559851 DOI: 10.1002/pmic.201500009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/25/2015] [Accepted: 03/19/2015] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of liver disease worldwide. Acute infection often progresses to chronicity resulting frequently in fibrosis, cirrhosis, and in rare cases, in the development of hepatocellular carcinoma. Although HCV has proven to be an arduous object of research and has raised important technical challenges, several experimental models have been developed all over the last two decades in order to improve our understanding of the virus life cycle, pathogenesis and virus-host interactions. The recent development of direct acting-agents, leading to considerable progress in treatment of patients, represents the direct outcomes of these achievements. Proteomic approaches have been of critical help to shed light on several aspect of the HCV biology such as virion composition, viral replication, and virus assembly and to unveil diagnostic or prognostic markers of HCV-induced liver disease. Here, we review how proteomic approaches have led to improve our understanding of HCV life cycle and liver disease, thus highlighting the relevance of these approaches for studying the complex interactions between other challenging human viral pathogens and their host.
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Affiliation(s)
- Florian Douam
- Department of Molecular Biology, Princeton University, 110 Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, 110 Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544
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