1
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Friedhoff R, Elfayres G, Mérindol N, Desgagné-Penix I, Berthoux L. RNA replication-independent, DNA linearization-dependent expression of reporter genes from a SARS-CoV-2 replicon-encoding DNA in human cells. PLoS One 2024; 19:e0300491. [PMID: 39150942 PMCID: PMC11329111 DOI: 10.1371/journal.pone.0300491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/13/2024] [Indexed: 08/18/2024] Open
Abstract
Replicons, derived from RNA viruses, are genetic constructs retaining essential viral enzyme genes while lacking key structural protein genes. Upon introduction into cells, the genes carried by the replicon RNA are expressed, and the RNA self-replicates, yet viral particle production does not take place. Typically, RNA replicons are transcribed in vitro and are then electroporated in cells. However, it would be advantageous for the replicon to be generated in cells following DNA transfection instead of RNA. In this study, a bacterial artificial chromosome (BAC) DNA encoding a SARS-CoV-2 replicon under control of a T7 promoter was transfected into HEK293T cells engineered to functionally express the T7 RNA polymerase (T7 RNAP). Upon transfection of the BAC DNA, we observed low, but reproducible expression of reporter proteins GFP and luciferase carried by this replicon. Expression of the reporter proteins required linearization of the BAC DNA prior to transfection. Moreover, expression occurred independently of T7 RNAP. Gene expression was also insensitive to remdesivir treatment, suggesting that it did not involve self-replication of replicon RNA. Similar results were obtained in highly SARS-CoV-2 infection-permissive Calu-3 cells. Strikingly, prior expression of the SARS-CoV-2 N protein boosted expression from transfected SARS-CoV-2 RNA replicon but not from the replicon BAC DNA. In conclusion, transfection of a large DNA encoding a coronaviral replicon led to reproducible replicon gene expression through an unidentified mechanism. These findings highlight a novel pathway toward replicon gene expression from transfected replicon cDNA, offering valuable insights for the development of methods for DNA-based RNA replicon applications.
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Affiliation(s)
- Ronja Friedhoff
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Ghada Elfayres
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Natacha Mérindol
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Lionel Berthoux
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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2
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Marinho MDS, Zhang YN, Cassani NM, Santos IA, Costa Oliveira AL, dos Santos Pereira AK, Corbi PP, Zhang B, Jardim ACG. Development and validation of Mayaro virus with luciferase reporter genes as a tool for antiviral assays. Heliyon 2024; 10:e33885. [PMID: 39071632 PMCID: PMC11283106 DOI: 10.1016/j.heliyon.2024.e33885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
Arboviruses are etiological agents in an extensive group of emerging diseases with great clinical relevance in Brazil, due to the wide distribution of their vectors and the favorable environmental conditions. Among them, the Mayaro virus (MAYV) has drawn attention since its emergence as the etiologic agent of Mayaro fever, a highly debilitating disease. To study viral replication and identify new drug candidates, traditional antiviral assays based on viral antigens and/or plaque assays have been demonstrating low throughput, making it difficult to carry out larger-scale assays. Therefore, we developed and characterized two DNA-launched infectious clones reporter viruses based on the MAYV strain BeAr 20290 containing the reporter genes of firefly luciferase (FLuc) and nanoluciferase (NLuc), designated as MAYV-firefly and MAYV-nanoluc, respectively. The viruses replicated efficiently with similar properties to the parental wild-type MAYV, and luminescence expression levels reflected viral replication. Reporter genes were also preserved during passage in cell culture, remaining stably expressed for one round of passage for MAYV-firefly and three rounds for MAYV-nanoluc. Employing the infectious clone, we described the effect of Rimantadine, an FDA-approved Alzheimer's drug, as a repurposing agent for MAYV but with a broad-spectrum activity against Zika virus infection. Additionally, we validated MAYV-nanoluc as a tool for antiviral drug screening using the compound EIDD-2749 (4'-Fluorouridine), which acts as an inhibitor of alphavirus RNA-dependent RNA polymerase.
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Affiliation(s)
- Mikaela dos Santos Marinho
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
| | - Ya-Nan Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Natasha Marques Cassani
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
| | - Igor Andrade Santos
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
| | - Ana Laura Costa Oliveira
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
| | | | - Pedro Paulo Corbi
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bo Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
- Institute of Biosciences, Humanities, and Exact Sciences, São Paulo State University (UNESP), Campus, São José do Rio Preto, SP, Brazil
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3
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Karan S, Durán-Meza AL, Chapman A, Tanimoto C, Chan SK, Knobler CM, Gelbart WM, Steinmetz NF. In Vivo Delivery of Spherical and Cylindrical In Vitro Reconstituted Virus-like Particles Containing the Same Self-Amplifying mRNA. Mol Pharm 2024; 21:2727-2739. [PMID: 38709860 PMCID: PMC11250921 DOI: 10.1021/acs.molpharmaceut.3c01105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The dramatic effectiveness of recent mRNA (mRNA)-based COVID vaccines delivered in lipid nanoparticles has highlighted the promise of mRNA therapeutics in general. In this report, we extend our earlier work on self-amplifying mRNAs delivered in spherical in vitro reconstituted virus-like particles (VLPs), and on drug delivery using cylindrical virus particles. In particular, we carry out separate in vitro assemblies of a self-amplifying mRNA gene in two different virus-like particles: one spherical, formed with the capsid protein of cowpea chlorotic mottle virus (CCMV), and the other cylindrical, formed from the capsid protein of tobacco mosaic virus (TMV). The mRNA gene is rendered self-amplifying by genetically fusing it to the RNA-dependent RNA polymerase (RdRp) of Nodamura virus, and the relative efficacies of cell uptake and downstream protein expression resulting from their CCMV- and TMV-packaged forms are compared directly. This comparison is carried out by their transfections into cells in culture: expressions of two self-amplifying genes, enhanced yellow fluorescent protein (EYFP) and Renilla luciferase (Luc), packaged alternately in CCMV and TMV VLPs, are quantified by fluorescence and chemiluminescence levels, respectively, and relative numbers of the delivered mRNAs are measured by quantitative real-time PCR. The cellular uptake of both forms of these VLPs is further confirmed by confocal microscopy of transfected cells. Finally, VLP-mediated delivery of the self-amplifying-mRNA in mice following footpad injection is shown by in vivo fluorescence imaging to result in robust expression of EYFP in the draining lymph nodes, suggesting the potential of these plant virus-like particles as a promising mRNA gene and vaccine delivery modality. These results establish that both CCMV and TMV VLPs can deliver their in vitro packaged mRNA genes to immune cells and that their self-amplifying forms significantly enhance in situ expression. Choice of one VLP (CCMV or TMV) over the other will depend on which geometry of nucleocapsid is self-assembled more efficiently for a given length and sequence of RNA, and suggests that these plant VLP gene delivery systems will prove useful in a wide variety of medical applications, both preventive and therapeutic.
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Affiliation(s)
- Sweta Karan
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, California 92093, United States
| | - Ana Luisa Durán-Meza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Abigail Chapman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Cheylene Tanimoto
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Soo Khim Chan
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- UCLA Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, California 92093, United States
- Institute for Materials Discovery and Design, University of California San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
- Center for Engineering in Cancer, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, California 92093, United States
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4
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Wang X, Zhu Y, Wu Q, Jiang N, Xie Y, Deng Q. Development of a Cell Culture Model for Inducible SARS-CoV-2 Replication. Viruses 2024; 16:708. [PMID: 38793589 PMCID: PMC11125939 DOI: 10.3390/v16050708] [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: 04/01/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces direct cytopathic effects, complicating the establishment of low-cytotoxicity cell culture models for studying its replication. We initially developed a DNA vector-based replicon system utilizing the CMV promoter to generate a recombinant viral genome bearing reporter genes. However, this system frequently resulted in drug resistance and cytotoxicity, impeding model establishment. Herein, we present a novel cell culture model with SARS-CoV-2 replication induced by Cre/LoxP-mediated DNA recombination. An engineered SARS-CoV-2 transcription unit was subcloned into a bacterial artificial chromosome (BAC) vector. To enhance biosafety, the viral spike protein gene was deleted, and the nucleocapsid gene was replaced with a reporter gene. An exogenous sequence was inserted within NSP1 as a modulatory cassette that is removable after Cre/LoxP-mediated DNA recombination and subsequent RNA splicing. Using the PiggyBac transposon strategy, the transcription unit was integrated into host cell chromatin, yielding a stable cell line capable of inducing recombinant SARS-CoV-2 RNA replication. The model exhibited sensitivity to the potential antivirals forsythoside A and verteporfin. An innovative inducible SARS-CoV-2 replicon cell model was introduced to further explore the replication and pathogenesis of the virus and facilitate screening and assessment of anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Xiaoyan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (X.W.); (Y.Z.); (Q.W.); (N.J.)
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China
| | - Yuanfei Zhu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (X.W.); (Y.Z.); (Q.W.); (N.J.)
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China
| | - Qiong Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (X.W.); (Y.Z.); (Q.W.); (N.J.)
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China
| | - Nan Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (X.W.); (Y.Z.); (Q.W.); (N.J.)
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (X.W.); (Y.Z.); (Q.W.); (N.J.)
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China
| | - Qiang Deng
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China; (X.W.); (Y.Z.); (Q.W.); (N.J.)
- Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Fudan University, Shanghai 200032, China
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5
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Sergio MC, Ricciardi S, Guarino AM, Giaquinto L, De Matteis MA. Membrane remodeling and trafficking piloted by SARS-CoV-2. Trends Cell Biol 2024:S0962-8924(23)00256-8. [PMID: 38262893 DOI: 10.1016/j.tcb.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
The molecular mechanisms underlying SARS-CoV-2 host cell invasion and life cycle have been studied extensively in recent years, with a primary focus on viral entry and internalization with the aim of identifying antiviral therapies. By contrast, our understanding of the molecular mechanisms involved in the later steps of the coronavirus life cycle is relatively limited. In this review, we describe what is known about the host factors and viral proteins involved in the replication, assembly, and egress phases of SARS-CoV-2, which induce significant host membrane rearrangements. We also discuss the limits of the current approaches and the knowledge gaps still to be addressed.
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Affiliation(s)
- Maria Concetta Sergio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | | | - Andrea M Guarino
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy.
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6
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Yin C, Yang P, Xiao Q, Sun P, Zhang X, Zhao J, Hu X, Shan C. Novel antiviral discoveries for Japanese encephalitis virus infections through reporter virus-based high-throughput screening. J Med Virol 2024; 96:e29382. [PMID: 38235833 DOI: 10.1002/jmv.29382] [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: 11/07/2023] [Revised: 12/11/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
Japanese encephalitis (JE) caused by JE virus (JEV), remains a global public health concern. Currently, there is no specific antiviral drug approved for the treatment of JE. While vaccines are available for prevention, they may not cover all at-risk populations. This underscores the urgent need for prophylaxis and potent anti-JEV drugs. In this context, a high-content JEV reporter system expressing Nanoluciferase (Nluc) was developed and utilized for a high-throughput screening (HTS) of a commercial antiviral library to identify potential JEV drug candidates. Remarkably, this screening process led to the discovery of five drugs with outstanding antiviral activity. Further mechanism of action analysis revealed that cepharanthine, an old clinically approved drug, directly inhibited virus replication by blocking GTP binding to the JEV RNA-dependent RNA polymerase. Additionally, treatment with cepharanthine in mice models alleviated JEV infection. These findings warrant further investigation into the potential anti-JEV activity of cepharanthine as a new therapeutic approach for the treatment of JEV infection. The HTS method employed here proves to be an accurate and convenient approach that facilitates the rapid development of antiviral drugs.
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Affiliation(s)
- Chunhong Yin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Peipei Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qingcui Xiao
- School of Basic Medical Sciences, Cixi Biomedical Research Institute, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Peng Sun
- School of Basic Medical Sciences, Cixi Biomedical Research Institute, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuekai Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jiaxuan Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chao Shan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Hubei Jiangxia Laboratory, Wuhan, China
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7
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Cai HL, Huang YW. Reverse genetics systems for SARS-CoV-2: Development and applications. Virol Sin 2023; 38:837-850. [PMID: 37832720 PMCID: PMC10786661 DOI: 10.1016/j.virs.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.
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Affiliation(s)
- Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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8
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Wang L, Guzman M, Muñoz-Santos D, Honrubia JM, Ripoll-Gomez J, Delgado R, Sola I, Enjuanes L, Zuñiga S. Cell type dependent stability and virulence of a recombinant SARS-CoV-2, and engineering of a propagation deficient RNA replicon to analyze virus RNA synthesis. Front Cell Infect Microbiol 2023; 13:1268227. [PMID: 37942479 PMCID: PMC10628495 DOI: 10.3389/fcimb.2023.1268227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Engineering of reverse genetics systems for newly emerged viruses allows viral genome manipulation, being an essential tool for the study of virus life cycle, virus-host interactions and pathogenesis, as well as for the development of effective antiviral strategies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent human coronavirus that has caused the coronavirus disease (COVID-19) pandemic. The engineering of a full-length infectious cDNA clone and a fluorescent replicon of SARS-CoV-2 Wuhan-Hu-1, using a bacterial artificial chromosome, is reported. Viral growth and genetic stability in eleven cell lines were analyzed, showing that both VeroE6 cells overexpressing transmembrane serin protease 2 (TMPRSS2) and human lung derived cells resulted in the optimization of a cell system to preserve SARS-CoV-2 genetic stability. The recombinant SARS-CoV-2 virus and a point mutant expressing the D614G spike protein variant were virulent in a mouse model. The RNA replicon was propagation-defective, allowing its use in BSL-2 conditions to analyze viral RNA synthesis. The SARS-CoV-2 reverse genetics systems developed constitute a useful tool for studying the molecular biology of the virus, the development of genetically defined vaccines and to establish systems for antiviral compounds screening.
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Affiliation(s)
- Li Wang
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - María Guzman
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Jose Manuel Honrubia
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Jorge Ripoll-Gomez
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Rafael Delgado
- Laboratory of Molecular Microbiology, Instituto de Investigación Hospital 12 de Octubre (Imas12), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
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9
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Nagashima S, Primadharsini PP, Nishiyama T, Takahashi M, Murata K, Okamoto H. Development of a HiBiT-tagged reporter hepatitis E virus and its utility as an antiviral drug screening platform. J Virol 2023; 97:e0050823. [PMID: 37681960 PMCID: PMC10537679 DOI: 10.1128/jvi.00508-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/15/2023] [Indexed: 09/09/2023] Open
Abstract
Previously, we developed an infectious hepatitis E virus (HEV) harboring the nanoKAZ gene in the hypervariable region of the open reading frame 1 (ORF1) of the HEV3b (JE03-1760F/P10) genome and demonstrated the usefulness for screening anti-HEV drugs that inhibit the early infection process. In the present study, we constructed another reporter HEV (HEV3b-HiBiT) by placing a minimized HiBiT tag derived from NanoLuc luciferase at the 3'-end of the viral capsid (ORF2) coding sequence. It replicated efficiently in PLC/PRF/5 cells, produced membrane-associated particles identical to those of the parental virus, and was genetically stable and infectious. The HiBiT tag was fused to both secreted ORF2s (ORF2s-HiBiT) and ORF2c capsid protein (ORF2c-HiBiT). The ORF2c-HiBiT formed membrane-associated HEV particles (eHEV3b-HiBiT). By treating these particles with digitonin, we demonstrated that the HiBiT tag was expressed on the surface of capsid and was present inside the lipid membrane. To simplify the measurement of luciferase activity and provide a more convenient screening platform, we constructed an ORF2s-defective mutant (HEV3b-HiBiT/ΔORF2s) in which the secreted ORF2s are suppressed. We used this system to evaluate the effects of introducing small interfering RNAs and treatment with an inhibitor or accelerator of exosomal release on HEV egress and demonstrated that the effects on virus release can readily be analyzed. Therefore, HEV3b-HiBiT and HEV3b-HiBiT/ΔORF2s reporters may be useful for investigating the virus life cycle and can serve as a more convenient screening platform to search for candidate drugs targeting the late stage of HEV infection such as particle formation and release. IMPORTANCE The construction of recombinant infectious viruses harboring a stable luminescence reporter gene is essential for investigations of the viral life cycle, such as viral replication and pathogenesis, and the development of novel antiviral drugs. However, it is difficult to maintain the stability of a large foreign gene inserted into the viral genome. In the present study, we successfully generated a recombinant HEV harboring the 11-amino acid HiBiT tag in the ORF2 coding region and demonstrated the infectivity, efficient virus growth, particle morphology, and genetic stability, suggesting that this recombinant HEV is useful for in vitro assays. Furthermore, this system can serve as a more convenient screening platform for anti-HEV drugs. Thus, an infectious recombinant HEV is a powerful approach not only for elucidating the molecular mechanisms of the viral life cycle but also for the screening and development of novel antiviral agents.
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Affiliation(s)
- Shigeo Nagashima
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Putu Prathiwi Primadharsini
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Takashi Nishiyama
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Kazumoto Murata
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
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10
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Shi YJ, Li JQ, Zhang HQ, Deng CL, Zhu QX, Zhang B, Li XD. A high throughput antiviral screening platform for alphaviruses based on Semliki Forest virus expressing eGFP reporter gene. Virol Sin 2023; 38:585-594. [PMID: 37390870 PMCID: PMC10436050 DOI: 10.1016/j.virs.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
Alphaviruses, which contain a variety of mosquito-borne pathogens, are important pathogens of emerging/re-emerging infectious diseases and potential biological weapons. Currently, no specific antiviral drugs are available for the treatment of alphaviruses infection. For most highly pathogenic alphaviruses are classified as risk group-3 agents, the requirement of biosafety level 3 (BSL-3) facilities limits the live virus-based antiviral study. To facilitate the antiviral development of alphaviruses, we developed a high throughput screening (HTS) platform based on a recombinant Semliki Forest virus (SFV) which can be manipulated in BSL-2 laboratory. Using the reverse genetics approach, the recombinant SFV and SFV reporter virus expressing eGFP (SFV-eGFP) were successfully rescued. The SFV-eGFP reporter virus exhibited robust eGFP expression and remained relatively stable after four passages in BHK-21 cells. Using a broad-spectrum alphavirus inhibitor ribavirin, we demonstrated that the SFV-eGFP can be used as an effective tool for antiviral study. The SFV-eGFP reporter virus-based HTS assay in a 96-well format was then established and optimized with a robust Z' score. A section of reference compounds that inhibit highly pathogenic alphaviruses were used to validate that the SFV-eGFP reporter virus-based HTS assay enables rapid screening of potent broad-spectrum inhibitors of alphaviruses. This assay provides a safe and convenient platform for antiviral study of alphaviruses.
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Affiliation(s)
- Yu-Jia Shi
- Hunan Normal University, School of Medicine, Changsha, 410081, China
| | - Jia-Qi Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Lin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin-Xuan Zhu
- Hunan Normal University, School of Medicine, Changsha, 410081, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Dan Li
- Hunan Normal University, School of Medicine, Changsha, 410081, China.
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11
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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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12
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Lin D, Chen Y, Koksal AR, Dash S, Aydin Y. Targeting ER stress/PKA/GSK-3β/β-catenin pathway as a potential novel strategy for hepatitis C virus-infected patients. Cell Commun Signal 2023; 21:102. [PMID: 37158967 PMCID: PMC10165818 DOI: 10.1186/s12964-023-01081-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 02/13/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Chronic hepatitis C virus (HCV) infection causes hepatocellular carcinoma (HCC). The HCC risk, while decreased compared with active HCV infection, persists in HCV-cured patients by direct-acting antiviral agents (DAA). We previously demonstrated that Wnt/β-catenin signaling remained activated after DAA-mediated HCV eradication. Developing therapeutic strategies to both eradicate HCV and reverse Wnt/β-catenin signaling is needed. METHODS Cell-based HCV long term infection was established. Chronically HCV infected cells were treated with DAA, protein kinase A (PKA) inhibitor H89 and endoplasmic reticulum (ER) stress inhibitor tauroursodeoxycholic acid (TUDCA). Western blotting analysis and fluorescence microscopy were performed to determine HCV levels and component levels involved in ER stress/PKA/glycogen synthase kinase-3β (GSK-3β)/β-catenin pathway. Meanwhile, the effects of H89 and TUDCA were determined on HCV infection. RESULTS Both chronic HCV infection and replicon-induced Wnt/β-catenin signaling remained activated after HCV and replicon eradication by DAA. HCV infection activated PKA activity and PKA/GSK-3β-mediated Wnt/β-catenin signaling. Inhibition of PKA with H89 both repressed HCV and replicon replication and reversed PKA/GSK-3β-mediated Wnt/β-catenin signaling in both chronic HCV infection and replicon. Both chronic HCV infection and replicon induced ER stress. Inhibition of ER stress with TUDCA both repressed HCV and replicon replication and reversed ER stress/PKA/GSK-3β-dependent Wnt/β-catenin signaling. Inhibition of either PKA or ER stress both inhibited extracellular HCV infection. CONCLUSION Targeting ER stress/PKA/GSK-3β-dependent Wnt/β-catenin signaling with PKA inhibitor could be a novel therapeutic strategy for HCV-infected patients to overcomes the issue of remaining activated Wnt/β-catenin signaling by DAA treatment. Video Abstract.
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Affiliation(s)
- Dong Lin
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| | - Yijia Chen
- The College of Liberal Arts and Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Ali Riza Koksal
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Srikanta Dash
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yucel Aydin
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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13
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Alquraan L, Alzoubi KH, Rababa'h SY. Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. INFORMATICS IN MEDICINE UNLOCKED 2023; 39:101256. [PMID: 37131549 PMCID: PMC10127666 DOI: 10.1016/j.imu.2023.101256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
Numerous variations of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), including D614G, B.1.1.7 (United Kingdom), B.1.1.28 (Brazil P1, P2), CAL.20C (Southern California), B.1.351 (South Africa), B.1.617 (B.1.617.1 Kappa & Delta B.1.617.2) and B.1.1.529, have been reported worldwide. The receptor-binding domain (RBD) of the spike (S) protein is involved in virus-cell binding, where virus-neutralizing antibodies (NAbs) react. Novel variants in the S-protein could maximize viral affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor and increase virus transmission. Molecular detection with false-negative results may refer to mutations in the part of the virus's genome used for virus diagnosis. Furthermore, these changes in S-protein structure alter the neutralizing ability of NAbs, resulting in a reduction in vaccine efficiency. Further information is needed to evaluate how new mutations may affect vaccine efficacy.
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Affiliation(s)
- Laiali Alquraan
- Department of Biology, Faculty of Science, Yarmouk University, Irbid, Jordan
| | - Karem H Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Suzie Y Rababa'h
- Department of Medical Science, Irbid Faculty, Al-Balqa Applied University (BAU), Irbid, Jordan
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14
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Saito K, Shimasaki K, Fukasawa M, Suzuki R, Okemoto-Nakamura Y, Katoh K, Takasaki T, Hanada K. Establishment of Vero cell lines persistently harboring a yellow fever virus 17D subgenomic replicon. Virus Res 2022; 322:198935. [PMID: 36152929 DOI: 10.1016/j.virusres.2022.198935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 12/24/2022]
Abstract
Yellow fever virus (YFV), a member of the genus Flavivirus, family Flaviviridae, is the etiological agent for an acute viral hemorrhagic disease, yellow fever. Although effective live attenuated vaccines based on the strain YFV 17D are currently available, no specific antiviral drug is available, and the disease remains a major public health concern. Hence, the discovery and development of antiviral drugs should lead to great benefits in controlling the disease. To provide a screening platform for antiviral agents targeting YFV RNA translation/replication, we have established and characterized two Vero cell lines that persistently harbor a subgenomic replicon derived from YFV 17D-204 (referred to as replicon cells). The replicon carries YFV nucleotides (1 - 176 and 2382-10,862) and a green fluorescent protein (GFP)-Zeocin resistance fusion gene as a selection marker and indicator of persistent replication. Immunofluorescence analysis revealed that both replicon cells and YFV 17D-infected cells showed similar distribution patterns of viral NS4B protein and replication intermediate, double-stranded RNA. Sequencing analysis of persistent replicons from the two replicon cell lines suggested that their nucleotide sequences did not vary greatly following multiple passages. We examined the effect of five agents, the antiviral cytokines interferon-β and -γ, the nucleoside analog ribavirin, the squalene synthase inhibitor zaragozic acid A, and the antibiotic rifapentine, a recently reported entry and replication inhibitor against YFV, on the persistent replication in the two replicon cell lines. These agents were selected because they inhibited both production of YFV 17D and transient replication of a luciferase-expressing replicon in Vero cells, without greatly affecting cell viability. We found that each of the agents decreased GFP fluorescence in the replicon cells, albeit to varying degrees. The agents other than rifapentine also showed a decrease in viral RNA levels in the replicon cells comparable to that seen for GFP fluorescence. These results indicate that persistent replication is susceptible to each of these five agents, although their mechanisms of action may differ. Taken together, these results provide evidence that translation/replication of the replicon in the replicon cells mimics that of the viral genome upon YFV 17D infection, indicating that the replicon cell lines can serve as a useful tool for high-throughput antiviral drug screening.
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Affiliation(s)
- Kyoko Saito
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.
| | - Kentaro Shimasaki
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Masayoshi Fukasawa
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo, Japan
| | - Yuko Okemoto-Nakamura
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kaoru Katoh
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba-shi, Ibaragi, Japan; AIRC, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, Chigasaki-shi, Kanagawa, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan; Department of Quality Assurance, Radiation Safety, and Information System, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
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15
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Watanabe Y, Suzuki Y, Emi A, Murakawa T, Hishiki T, Kato F, Sakaguchi S, Wu H, Yano T, Lim CK, Takasaki T, Nakano T. Identification of the corticotropin-releasing factor receptor 1 antagonists as inhibitors of Chikungunya virus replication using a Gaussia luciferase–expressing subgenomic replicon. Biochem Biophys Res Commun 2022; 637:181-188. [DOI: 10.1016/j.bbrc.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
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16
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Characterization of the RNA-dependent RNA polymerase from Chikungunya virus and discovery of a novel ligand as a potential drug candidate. Sci Rep 2022; 12:10601. [PMID: 35732685 PMCID: PMC9217121 DOI: 10.1038/s41598-022-14790-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of Chikungunya fever, an acute febrile and arthritogenic illness with no effective treatments available. The development of effective therapeutic strategies could be significantly accelerated with detailed knowledge of the molecular components behind CHIKV replication. However, drug discovery is hindered by our incomplete understanding of their main components. The RNA-dependent RNA-polymerase (nsP4-CHIKV) is considered the key enzyme of the CHIKV replication complex and a suitable target for antiviral therapy. Herein, the nsP4-CHIKV was extensively characterized through experimental and computational biophysical methods. In the search for new molecules against CHIKV, a compound designated LabMol-309 was identified as a strong ligand of the nsp4-CHIKV and mapped to bind to its active site. The antiviral activity of LabMol-309 was evaluated in cellular-based assays using a CHIKV replicon system and a reporter virus. In conclusion, this study highlights the biophysical features of nsP4-CHIKV and identifies a new compound as a promising antiviral agent against CHIKV infection.
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17
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The Antifungal Itraconazole Is a Potent Inhibitor of Chikungunya Virus Replication. Viruses 2022; 14:v14071351. [PMID: 35891332 PMCID: PMC9317443 DOI: 10.3390/v14071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of chikungunya fever, a disabling disease that can cause long-term severe arthritis. Since the last large CHIKV outbreak in 2015, the reemergence of the virus represents a serious public health concern. The morbidity associated with viral infection emphasizes the need for the development of specific anti-CHIKV drugs. Herein, we describe the development and characterization of a CHIKV reporter replicon cell line and its use in replicon-based screenings. We tested 960 compounds from MMV/DNDi Open Box libraries and identified four candidates with interesting antiviral activities, which were confirmed in viral infection assays employing CHIKV-nanoluc and BHK-21 cells. The most noteworthy compound identified was itraconazole (ITZ), an orally available, safe, and cheap antifungal, that showed high selectivity indexes of >312 and >294 in both replicon-based and viral infection assays, respectively. The antiviral activity of this molecule has been described against positive-sense single stranded RNA viruses (+ssRNA) and was related to cholesterol metabolism that could affect the formation of the replication organelles. Although its precise mechanism of action against CHIKV still needs to be elucidated, our results demonstrate that ITZ is a potent inhibitor of the viral replication that could be repurposed as a broad-spectrum antiviral.
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18
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Joshi N, Shukla S, Narayan RJ. Novel photonic methods for diagnosis of SARS-CoV-2 infection. TRANSLATIONAL BIOPHOTONICS 2022; 4:e202200001. [PMID: 35602265 PMCID: PMC9111306 DOI: 10.1002/tbio.202200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
The COVID-19 pandemic that began in March 2020 continues in many countries. The ongoing pandemic makes early diagnosis a crucial part of efforts to prevent the spread of SARS-CoV-2 infections. As such, the development of a rapid, reliable, and low-cost technique with increased sensitivity for detection of SARS-CoV-2 is an important priority of the scientific community. At present, nucleic acid-based techniques are primarily used as the reference approach for the detection of SARS-CoV-2 infection. However, in several cases, false positive results have been observed with these techniques. Due to the drawbacks associated with existing techniques, the development of new techniques for the diagnosis of COVID-19 is an important research activity. We provide an overview of novel diagnostic methods for SARS-CoV-2 diagnosis that integrate photonic technology with artificial intelligence. Recent developments in emerging diagnostic techniques based on the principles of advanced molecular spectroscopy and microscopy are considered.
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Affiliation(s)
- Naveen Joshi
- Department of Materials Science and EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Shubhangi Shukla
- Joint Department of Biomedical EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Roger J. Narayan
- Joint Department of Biomedical EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
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19
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Zhang H, Fischer DK, Shuda M, Moore PS, Gao SJ, Ambrose Z, Guo H. Construction and characterization of two SARS-CoV-2 minigenome replicon systems. J Med Virol 2022; 94:2438-2452. [PMID: 35137972 PMCID: PMC9088700 DOI: 10.1002/jmv.27650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/10/2022]
Abstract
The ongoing COVID-19 pandemic severely impacts global public health and economies. In order to facilitate research on SARS-CoV-2 virology and antiviral discovery, a non-infectious viral replicon system operating under biosafety level 2 containment is warranted. We report herein the construction and characterization of two SARS-CoV-2 minigenome replicon systems. First, we constructed the IVT-CoV2-Rep cDNA template to generate a replicon mRNA with nanoluciferase (NLuc) reporter via in vitro transcription (IVT). The replicon mRNA transfection assay demonstrated a rapid and transient replication of IVT-CoV2-Rep in a variety of cell lines, which could be completely abolished by known SARS-CoV-2 replication inhibitors. Our data also suggests that the transient phenotype of IVT-CoV2-Rep is not due to host innate antiviral responses. In addition, we have developed a DNA-launched replicon BAC-CoV2-Rep, which supports the in-cell transcription of a replicon mRNA as initial replication template. The BAC-CoV2-Rep transient transfection system exhibited a much stronger and longer replicon signal compared to the IVT-CoV2-Rep version. We also found that a portion of the NLuc reporter signal was derived from the spliced BAC-CoV2-Rep mRNA and was resistant to antiviral treatment, especially during the early phase after transfection. In summary, the established SARS-CoV-2 transient replicon systems are suitable for basic and antiviral research, and hold promise for stable replicon cell line development with further optimization. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hu Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Douglas K Fischer
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Masahiro Shuda
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Patrick S Moore
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Shou-Jiang Gao
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
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20
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Zhou L, Zhou J, Chen T, Chi X, Liu X, Pan S, Chen W, Wu T, Lin T, Zhang X, Li YP, Yang W. Identification of Ascomycin against Zika virus infection through screening of natural product library. Antiviral Res 2021; 196:105210. [PMID: 34801589 DOI: 10.1016/j.antiviral.2021.105210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/27/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
Zika virus (ZIKV) infection could lead to Guillain-Barré syndrome in adults and microcephaly in the newborns from infected pregnant women. To date, there is no specific drug for the treatment of ZIKV infection. In this study, we sought to screen inhibitors against ZIKV infection from a natural product library. A ZIKV replicon was used to screen a library containing 1680 natural compounds. We explored the antiviral mechanism of the compound candidate in vitro and in vivo infection models. Ascomycin, a macrolide from Streptomyces hygroscopicus, was identified with inhibitory effect against ZIKV in Vero cells (IC50 = 0.11 μM), hepatoma cell Huh7 (IC50 = 0.38 μM), and glioblastoma cell SNB-19 (IC50 = 0.06 μM), far below the cytotoxic concentrations. Mechanistic study revealed that Ascomycin suppressed ZIKV RNA replication step during the life cycle and the regulation of calcineurin-NFAT pathway maybe involved in this inhibitory effect, independent of innate immunity activation. Moreover, we found that Ascomycin also inhibited the infection of other Flaviviridae members, such as hepatitis C virus and dengue virus. Ascomycin reduced ZIKV load in blood by up to 3500-fold in A129 mice. Meanwhile, the infection in the mice brain was undetectable by immunohistochemistry staining. Together, these findings reveal a critical role of Ascomycin in the inhibition of ZIKV and related viruses, facilitating the development of novel antiviral agents.
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Affiliation(s)
- Liang Zhou
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Jia Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tongling Chen
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaojing Chi
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Xiuying Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Shengnan Pan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Wenfang Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Tiantian Wu
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Tianli Lin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Xinhui Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Wei Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China.
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21
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Fernandes RS, de Godoy AS, Santos IA, Noske GD, de Oliveira KIZ, Gawriljuk VO, Gomes Jardim AC, Oliva G. Discovery of an imidazonaphthyridine and a riminophenazine as potent anti-Zika virus agents through a replicon-based high-throughput screening. Virus Res 2021; 299:198388. [PMID: 33887282 DOI: 10.1016/j.virusres.2021.198388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/19/2021] [Accepted: 03/06/2021] [Indexed: 12/17/2022]
Abstract
The 2015/16 Zika virus (ZIKV) epidemic led to almost 1 million confirmed cases in 84 countries and was associated to the development of congenital microcephaly and Guillain-Barré syndrome. More recently, a ZIKV African lineage was identified in Brazil raising concerns about a future outbreak. The long-term consequences of viral infection emphasizes the need for the development of effective anti-ZIKV drugs. In this study, we developed and characterized a ZIKV replicon cell line for the screening of viral replication inhibitors. The replicon system was developed by engineering the IRES-Neo cassette into the 3' UTR terminus of the ZIKV Rluc DNA construct. After in vitro transcription, replicon RNA was used to transfect BHK-21 cells, that were selected with G418, thus generating the BHK-21-RepZIKV_IRES-Neo cell line. Through this replicon-based cell system, we identified two molecules with potent anti-ZIKV activities, an imidazonaphthyridine and a riminophenazine, both from the MMV/DNDi Pandemic Response Box library of 400 drug-like compounds. The imidazonaphthyridine, known as RO8191, showed remarkable selectivity against ZIKV, while the riminophenazine, the antibiotic Clofazimine, could act as a non-nucleoside analog inhibitor of viral RNA-dependent RNA polymerase (RdRp), as evidenced both in vitro and in silico. The data showed herein supports the use of replicon-based assays in high-throughput screening format as a biosafe and reliable tool for antiviral drug discovery.
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Affiliation(s)
- Rafaela Sachetto Fernandes
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil.
| | - Andre Schutzer de Godoy
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Igor Andrade Santos
- Institute of Biomedical Sciences, Federal University of Uberlândia, Av. Amazonas, 1700, bloco 4C sala 216, Umuarama, Uberlândia, 38405-317, Brazil
| | - Gabriela Dias Noske
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ketllyn Irene Zagato de Oliveira
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Sciences, Federal University of Uberlândia, Av. Amazonas, 1700, bloco 4C sala 216, Umuarama, Uberlândia, 38405-317, Brazil
| | - Glaucius Oliva
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
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22
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Generation of SARS-CoV-2 reporter replicon for high-throughput antiviral screening and testing. Proc Natl Acad Sci U S A 2021; 118:2025866118. [PMID: 33766889 PMCID: PMC8053989 DOI: 10.1073/pnas.2025866118] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research and antiviral discovery are hampered by the lack of a cell-based virus replication system that can be readily adopted without biosafety level 3 (BSL-3) restrictions. Here, the construction of a noninfectious SARS-CoV-2 reporter replicon and its application in deciphering viral replication mechanisms and evaluating SARS-CoV-2 inhibitors are presented. The replicon genome is replication competent but does not produce progeny virions. Its replication can be inhibited by RdRp mutations or by known SARS-CoV-2 antiviral compounds. Using this system, a high-throughput antiviral assay has also been developed. Significant differences in potencies of several SARS-CoV-2 inhibitors in different cell lines were observed, which highlight the challenges of discovering antivirals capable of inhibiting viral replication in vivo and the importance of testing compounds in multiple cell culture models. The generation of a SARS-CoV-2 replicon provides a powerful platform to expand the global research effort to combat COVID-19.
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