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Silva Júnior JVJ, da Silva ANMR, da Silva Santos JJ, Gil LHVG. Reverse Genetics of Dengue Virus. Methods Mol Biol 2024; 2733:231-248. [PMID: 38064036 DOI: 10.1007/978-1-0716-3533-9_14] [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] [Indexed: 12/18/2023]
Abstract
Dengue virus (DENV) is one of the most important and widespread arthropod-borne viruses, causing millions of infections over the years. Considering its epidemiological importance, efforts have been directed towards understanding various aspects of DENV biology, which have been facilitated by the development of different molecular strategies for engineering viral genomes, such as reverse genetics approaches. Reverse genetic systems are a powerful tool for investigating virus-host interaction, for vaccine development, and for high-throughput screening of antiviral compounds. However, stable manipulation of DENV genomes is a major molecular challenge, especially when using conventional cloning systems. To circumvent this issue, we describe a simple and efficient yeast-based reverse genetics system to recover infectious DENV clones.
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Affiliation(s)
- José Valter Joaquim Silva Júnior
- Virology Sector, Department of Preventive Veterinary Medicine, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Virology Sector, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Recife, PE, Brazil
| | | | | | - Laura Helena Vega Gonzales Gil
- Laboratory of Virology and Experimental Therapy, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, Brazil.
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2
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Hu M, Li WF, Wu T, Yang Y, Chen G, Chen T, Liu Y, Mei Y, Wu D, Wei Y, Luo T, Zhang HJ, Li YP. Identification of an Arylnaphthalene Lignan Derivative as an Inhibitor against Dengue Virus Serotypes 1 to 4 (DENV-1 to -4) Using a Newly Developed DENV-3 Infectious Clone and Replicon. Microbiol Spectr 2023; 11:e0042323. [PMID: 37378517 PMCID: PMC10434217 DOI: 10.1128/spectrum.00423-23] [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: 02/07/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Dengue virus (DENV) is the most widespread arbovirus, causing symptoms ranging from dengue fever to severe dengue, including hemorrhagic fever and shock syndrome. Four serotypes of DENV (DENV-1 to -4) can infect humans; however, no anti-DENV drug is available. To facilitate the study of antivirals and viral pathogenesis, here we developed an infectious clone and a subgenomic replicon of DENV-3 strains for anti-DENV drug discovery by screening a synthetic compound library. The viral cDNA was amplified from a serum sample from a DENV-3-infected individual during the 2019 epidemic; however, fragments containing the prM-E-partial NS1 region could not be cloned until a DENV-3 consensus sequence with 19 synonymous substitutions was introduced to reduce putative Escherichia coli promoter activity. Transfection of the resulting cDNA clone, plasmid DV3syn, released an infectious virus titer of 2.2 × 102 focus-forming units (FFU)/mL. Through serial passages, four adaptive mutations (4M) were identified, and addition of 4M generated recombinant DV3syn_4M, which produced viral titers ranging from 1.5 × 104 to 6.7 × 104 FFU/mL and remained genetically stable in transformant bacteria. Additionally, we constructed a DENV-3 subgenomic replicon and screened an arylnaphthalene lignan library, from which C169-P1 was identified as exhibiting inhibitory effects on viral replicon. A time-of-drug addition assay revealed that C169-P1 also impeded the internalization process of cell entry. Furthermore, we demonstrated that C169-P1 inhibited the infectivity of DV3syn_4M, as well as DENV-1, DENV-2, and DENV-4, in a dose-dependent manner. This study provides an infectious clone and a replicon for the study of DENV-3 and a candidate compound for future development against DENV-1 to -4 infections. IMPORTANCE Dengue virus (DENV) is the most prevalent mosquito-transmitted virus, and there is no an anti-dengue drug. Reverse genetic systems representative of different serotype viruses are invaluable tools for the study of viral pathogenesis and antiviral drugs. Here, we developed an efficient infectious clone of a clinical DENV-3 genotype III isolate. We successfully overcame the instability of flavivirus genome-length cDNA in transformant bacteria, an unsolved issue for construction of cDNA clones of flaviviruses, and adapted this clone to efficiently produce infectious viruses following plasmid transfection of cell culture. Moreover, we constructed a DENV-3 subgenomic replicon and screened a compound library. An arylnaphthalene lignan, C169-P1, was identified as an inhibitor of virus replication and cell entry. Finally, we demonstrated that C169-P1 exhibited a broad-spectrum antiviral effect against the infections with DENV-1 to -4. The reverse genetic systems and the compound candidate described here facilitate the study of DENV and related RNA viruses.
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Affiliation(s)
- Mingyue Hu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning, China
| | - Wan-Fei Li
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Tiantian Wu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yang Yang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guoquan Chen
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning, China
| | - Tongling Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yongchen Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yaqing Mei
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - De Wu
- Institute of Pathogenic Microbiology, Center for Disease Control and Prevention of Guangdong, Guangzhou, China
| | - Youchuan Wei
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning, China
| | - Tingrong Luo
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning, China
| | - Hong-Jie Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Fang E, Li M, Liu X, Hu K, Liu L, Zhang Z, Li X, Peng Q, Li Y. NS1 Protein N-Linked Glycosylation Site Affects the Virulence and Pathogenesis of Dengue Virus. Vaccines (Basel) 2023; 11:vaccines11050959. [PMID: 37243063 DOI: 10.3390/vaccines11050959] [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: 03/21/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Live attenuated vaccine is one of the most effective vaccines against flavivirus. Recently, site-directed mutation of the flavivirus genome using reverse genetics techniques has been used for the rapid development of attenuated vaccines. However, this technique relies on basic research of critical virulence loci of the virus. To screen the attenuated sites in dengue virus, a total of eleven dengue virus type four mutant strains with deletion of N-glycosylation sites in the NS1 protein were designed and constructed. Ten of them (except for the N207-del mutant strain) were successfully rescued. Out of the ten strains, one mutant strain (N130del+207-209QQA) was found to have significantly reduced virulence through neurovirulence assay in suckling mice, but was genetically unstable. Further purification using the plaque purification assay yielded a genetically stable attenuated strain #11-puri9 with mutations of K129T, N130K, N207Q, and T209A in the NS1 protein and E99D in the NS2A protein. Identifying the virulence loci by constructing revertant mutant and chimeric viruses revealed that five amino acid adaptive mutations in the dengue virus type four non-structural proteins NS1 and NS2A dramatically affected its neurovirulence and could be used in constructing attenuated dengue chimeric viruses. Our study is the first to obtain an attenuated dengue virus strain through the deletion of amino acid residues at the N-glycosylation site, providing a theoretical basis for understanding the pathogenesis of the dengue virus and developing its live attenuated vaccines.
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Affiliation(s)
- Enyue Fang
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
| | - Miao Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
- Vaccines R&D Department, Changchun Institute of Biological Products Co., Ltd., Changchun 130000, China
| | - Xiaohui Liu
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
- Vaccines R&D Department, Changchun Institute of Biological Products Co., Ltd., Changchun 130000, China
| | - Kongxin Hu
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Lijuan Liu
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Zelun Zhang
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
| | - Xingxing Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
| | - Qinhua Peng
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
| | - Yuhua Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China
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Holliday M, Corliss L, Lennemann NJ. Construction and Rescue of a DNA-Launched DENV2 Infectious Clone. Viruses 2023; 15:275. [PMID: 36851490 PMCID: PMC9959642 DOI: 10.3390/v15020275] [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: 08/29/2022] [Revised: 12/15/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Flaviviruses represent a large group of globally significant, insect-borne pathogens. For many of these viruses, there is a lack of antivirals and vaccines. Thus, there is a need to continue the development of tools to further advance our efforts to combat these pathogens, including reverse genetics techniques. Traditionally, reverse genetics methods for flaviviruses rely on producing infectious RNA from in vitro transcription reactions followed by electroporation or transfection into permissive cell lines. However, the production of Zika virus has been successful from CMV promoter-driven expression plasmids, which provides cost and time advantages. In this report, we describe the design and construction of a DNA-launched infectious clone for dengue virus (DENV) serotype 2 strain 16681. An artificial intron was introduced in the nonstructural protein 1 segment of the viral genome to promote stability in bacteria. We found that rescued viruses maintained the ability to form plaques and replicate efficiently in commonly used cell lines. Thus, we present a rapid and cost-effective method for producing DENV2 strain 16681 from plasmid DNA. This construct will be a useful platform for the continued development of anti-DENV therapeutics and vaccines.
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Affiliation(s)
| | | | - Nicholas J. Lennemann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Lindenbach BD. Reinventing positive-strand RNA virus reverse genetics. Adv Virus Res 2022; 112:1-29. [PMID: 35840179 PMCID: PMC9273853 DOI: 10.1016/bs.aivir.2022.03.001] [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] [Indexed: 12/09/2022]
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
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Petit MJ, Kenaston MW, Pham OH, Nagainis AA, Fishburn AT, Shah PS. Nuclear dengue virus NS5 antagonizes expression of PAF1-dependent immune response genes. PLoS Pathog 2021; 17:e1010100. [PMID: 34797876 PMCID: PMC8641875 DOI: 10.1371/journal.ppat.1010100] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/03/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022] Open
Abstract
Dengue virus (DENV) disruption of the innate immune response is critical to establish infection. DENV non-structural protein 5 (NS5) plays a central role in this disruption, such as antagonism of STAT2. We recently found that DENV serotype 2 (DENV2) NS5 interacts with Polymerase associated factor 1 complex (PAF1C). The primary members of PAF1C are PAF1, LEO1, CTR9, and CDC73. This nuclear complex is an emerging player in the immune response. It promotes the expression of many genes, including genes related to the antiviral, antimicrobial and inflammatory responses, through close association with the chromatin of these genes. Our previous work demonstrated that NS5 antagonizes PAF1C recruitment to immune response genes. However, it remains unknown if NS5 antagonism of PAF1C is complementary to its antagonism of STAT2. Here, we show that knockout of PAF1 enhances DENV2 infectious virion production. By comparing gene expression profiles in PAF1 and STAT2 knockout cells, we find that PAF1 is necessary to express immune response genes that are STAT2-independent. Finally, we mapped the viral determinants for the NS5-PAF1C protein interaction. We found that NS5 nuclear localization and the C-terminal region of the methyltransferase domain are required for its interaction with PAF1C. Mutation of these regions rescued the expression of PAF1-dependent immune response genes that are antagonized by NS5. In sum, our results support a role for PAF1C in restricting DENV2 replication that NS5 antagonizes through its protein interaction with PAF1C. Dengue virus (DENV) is a pathogen that infects nearly 400 million people a year and thus represents a major challenge for public health. Productive infection by DENV relies on the effective evasion of intrinsic antiviral defenses and is often accomplished through virus-host protein interactions. Here, we investigate the recently discovered interaction between DENV non-structural protein 5 (NS5) and the transcriptional regulator Polymerase associated factor 1 complex (PAF1C). Our work demonstrates PAF1C member PAF1 acts as an antiviral factor and inhibits DENV replication. In parallel, we identified immune response genes involved in intrinsic antiviral defense that depend on PAF1 for expression. We further identified the regions of NS5 required for the protein interaction with PAF1C. Breaking the NS5-PAF1C protein interaction restores the expression of PAF1-dependent immune response genes. Together, our work establishes the antiviral role of PAF1C in DENV infection and NS5 antagonism of PAF1-dependent gene expression through a virus-host protein interaction.
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Affiliation(s)
- Marine J. Petit
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
- Department of Chemical Engineering, University of California, Davis, California, United States of America
| | - Matthew W. Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Oanh H. Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Ariana A. Nagainis
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
- Department of Chemical Engineering, University of California, Davis, California, United States of America
| | - Adam T. Fishburn
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Priya S. Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
- Department of Chemical Engineering, University of California, Davis, California, United States of America
- * E-mail:
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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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Abstract
Dengue virus (DENV) belongs to the family Flaviviridae, genus Flavivirus. It is a single-stranded positive-sense ribonucleic acid virus with 10,700 bases. The genus Flavivirus includes other arthropod borne viruses such as yellow fever virus, West Nile virus, Zika virus, tick-borne encephalitis virus. It infects ~50–200 million people annually, putting over 3.6 billion people living in tropical regions at risk and causing ~20,000 deaths annually. The expansion of dengue is attributed to factors such as the modern dynamics of climate change, globalization, travel, trade, socioeconomics, settlement, and also viral evolution. There are four antigenically different serotypes of DENV based on the differences in their viral structural and nonstructural proteins. DENV infection causes a spectrum of illness ranging from asymptomatic to dengue fever to severe dengue shock syndrome. Infection with one serotype confers lifelong immunity against that serotype, but heterologus infection leads to severe dengue hemorrhagic fever due to antibody-dependent enhancement. Diagnosis of dengue infections is based mainly on serological detection of either antigen in acute cases or antibodies in both acute and chronic infection. Viral detection and real-time PCR detection though helpful is not feasible in resource poor setup. Treatment of dengue depends on symptomatic management along with fluid resuscitation and may require platelet transfusion. Although vaccine development is in late stages of development, developing a single vaccine against four serotypes often causes serious challenges to researchers; hence, the main stay of prevention is vector control and management.
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Chen Y, Liu T, Zhang Z, Chen M, Rong L, Ma L, Yu B, Wu D, Zhang P, Zhu X, Huang X, Zhang H, Li YP. Novel genetically stable infectious clone for a Zika virus clinical isolate and identification of RNA elements essential for virus production. Virus Res 2018; 257:14-24. [PMID: 30144463 DOI: 10.1016/j.virusres.2018.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 01/19/2023]
Abstract
Zika virus (ZIKV) is an Aedes mosquitoes-transmitted flavivirus, and its infection may cause severe neurological diseases. A genetically stable infectious clone is essential for ZIKV research, however the toxicity and instability of the viral cDNA in bacteria potentially due to its bacterial promoter activity are major challenges. Here, we constructed a full-length cDNA clone for isolate ZG01 by introducing non-coding changes T1865C/A1868G to reduce the bacterial promoter activity. Wild-type and recombinant ZG01 were highly attenuated in Vero cells, thus we serially passaged wild-type ZG01 through neonatal mice and Vero cells to generate high-titer virus, from which four mutations (4m, C2178T/G2913A/T4991C/T10561C) were identified. Addition of 4m greatly enhanced the infectivity, as ZG01_4m released ZIKV of 107.0-107.5 plaque-forming unit (PFU)/ml in infected Vero and A549 cells. ZG01_4m resembled the infectivity of high-titer ZG01 in vitro and in vivo. Notably, ZG01_4m plasmid was genetically stable after multiple rounds of transformation-purification in bacteria. Using ZG01_4m, we identified a potential RNA-RNA interaction between 5'UTR and 3'UTR and demonstrated that the nucleotides involved were essential for ZIKV production. The genetically stable ZG01 cDNA clone provides a reliable tool for the study of this important virus, and the strategy used here is feasible for the development of reverse genetics systems for other ZIKV isolates and related flaviviruses.
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Affiliation(s)
- Yiyi 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
| | - Ting Liu
- Department of Immunology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhenzhen Zhang
- 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
| | - Mingxiao 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
| | - Liang Rong
- 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
| | - Ling Ma
- 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
| | - Bolan Yu
- Key Lab for Major Obstetric Diseases of Guangdong Province, Guangzhou Medical University, Guangzhou 510150, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Ping Zhang
- Department of Immunology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xun Zhu
- 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
| | - Xi Huang
- The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Hui Zhang
- 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
| | - 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; Program in Pathobiology, The Fifth Affiliated Hospital and Zhongshan School of Medicine, Sun Yat-sen University, Guangdong, China.
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Deng CL, Zhang QY, Chen DD, Liu SQ, Qin CF, Zhang B, Ye HQ. Recovery of the Zika virus through an in vitro ligation approach. J Gen Virol 2017; 98:1739-1743. [PMID: 28703698 DOI: 10.1099/jgv.0.000862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, an in vitro ligation method was developed to assemble a full-length infectious cDNA clone of the Zika virus (ZIKV). Four contiguous cDNA subclones covering the complete ZIKV genome were constructed with unique BglI restriction sites at the ends of each fragment. The BglI restriction sites only allow in vitro ligation to happen between interconnecting restriction sites from adjacent cDNA fragments, resulting in an intact full-length cDNA of ZIKV. RNA transcripts derived from the full-length cDNA were infectious. The recombinant virus replicated as efficiently as the wild-type virus with similar growth kinetics and plaque morphologies in Vero and C6/36 cells. Both viruses were inhibited by NITD008 treatment. This in vitro ligation method will facilitate manipulation of the viral genome through genetic modifications of four separated subclones of ZIKV for the rapid and rational development of candidate vaccines and viral replication study.
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Affiliation(s)
- Cheng-Lin Deng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Qiu-Yan Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Dong-Dong Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Si-Qing Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Bo Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Han-Qing Ye
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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Weger-Lucarelli J, Duggal NK, Brault AC, Geiss BJ, Ebel GD. Rescue and Characterization of Recombinant Virus from a New World Zika Virus Infectious Clone. J Vis Exp 2017. [PMID: 28654045 DOI: 10.3791/55857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infectious cDNA clones allow for genetic manipulation of a virus, thus facilitating work on vaccines, pathogenesis, replication, transmission and viral evolution. Here we describe the construction of an infectious clone for Zika virus (ZIKV), which is currently causing an explosive outbreak in the Americas. To prevent toxicity to bacteria that is commonly observed with flavivirus-derived plasmids, we generated a two-plasmid system which separates the genome at the NS1 gene and is more stable than full-length constructs that could not be successfully recovered without mutations. After digestion and ligation to join the two fragments, full-length viral RNA can be generated by in vitro transcription with T7 RNA polymerase. Following electroporation of transcribed RNA into cells, virus was recovered that exhibited similar in vitro growth kinetics and in vivo virulence and infection phenotypes in mice and mosquitoes, respectively.
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Affiliation(s)
| | - Nisha K Duggal
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University;
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12
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Santos JJDS, Cordeiro MT, Bertani GR, Marques ETDA, Gil LHVG. Construction and characterisation of a complete reverse genetics system of dengue virus type 3. Mem Inst Oswaldo Cruz 2015; 108:983-91. [PMID: 24402142 PMCID: PMC4005542 DOI: 10.1590/0074-0276130298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/12/2013] [Indexed: 11/27/2022] Open
Abstract
Dengue virulence and fitness are important factors that determine disease outcome.
However, dengue virus (DENV) molecular biology and pathogenesis are not completely
elucidated. New insights on those mechanisms have been facilitated by the development
of reverse genetic systems in the past decades. Unfortunately, instability of
flavivirus genomes cloned in Escherichia coli has been a major
problem in these systems. Here, we describe the development of a complete reverse
genetics system, based on the construction of an infectious clone and replicon for a
low passage DENV-3 genotype III of a clinical isolate. Both constructs were assembled
into a newly designed yeast- E. coli shuttle vector by homologous
recombination technique and propagated in yeast to prevent any possible genome
instability in E. coli . RNA transcripts derived from the infectious
clone are infectious upon transfection into BHK-21 cells even after repeated passages
of the plasmid in yeast. Transcript-derived DENV-3 exhibited growth kinetics,
focus formation size comparable to original DENV-3 in mosquito
C6/36 cell culture. In vitro characterisation of DENV-3 replicon confirmed its
identity and ability to replicate transiently in BHK-21 cells. The reverse genetics
system reported here is a valuable tool that will facilitate further molecular
studies in DENV replication, virus attenuation and pathogenesis.
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13
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Flavivirus reverse genetic systems, construction techniques and applications: a historical perspective. Antiviral Res 2014; 114:67-85. [PMID: 25512228 PMCID: PMC7173292 DOI: 10.1016/j.antiviral.2014.12.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022]
Abstract
The study of flaviviruses, which cause some of the most important emerging tropical and sub-tropical human arbovirus diseases, has greatly benefited from the use of reverse genetic systems since its first development for yellow fever virus in 1989. Reverse genetics technology has completely revolutionized the study of these viruses, making it possible to manipulate their genomes and evaluate the direct effects of these changes on their biology and pathogenesis. The most commonly used reverse genetics system is the infectious clone technology. Whilst flavivirus infectious clones provide a powerful tool, their construction as full-length cDNA molecules in bacterial vectors can be problematic, laborious and time consuming, because they are often unstable, contain unwanted induced substitutions and may be toxic for bacteria due to viral protein expression. The incredible technological advances that have been made during the past 30years, such as the use of PCR or new sequencing methods, have allowed the development of new approaches to improve preexisting systems or elaborate new strategies that overcome these problems. This review summarizes the evolution and major technical breakthroughs in the development of flavivirus reverse genetics technologies and their application to the further understanding and control of these viruses and their diseases.
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14
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Alcaraz-Estrada SL, Del Angel R, Padmanabhan R. Construction of self-replicating subgenomic dengue virus 4 (DENV4) replicon. Methods Mol Biol 2014; 1138:131-50. [PMID: 24696335 DOI: 10.1007/978-1-4939-0348-1_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dengue virus serotypes 1-4 are members of mosquito-borne flavivirus genus of Flaviviridae family that encode one long open reading frame (ORF) that is translated to a polyprotein. Both host and virally encoded proteases function in the processing of the polyprotein by co-translational and posttranslational mechanisms to yield 10 mature proteins prior to viral RNA replication. To study cis- and trans-acting factors involved in viral RNA replication, many groups [1-8] have constructed cDNAs encoding West Nile virus (WNV), DENV, or yellow fever virus reporter replicon RNAs. The replicon plasmids constructed in our laboratory for WNV [9] and the DENV4 replicon described here are arranged in the order of 5'-untranslated region (UTR), the N-terminal coding sequence of capsid (C), Renilla luciferase (Rluc) reporter gene with a translation termination codon, and an internal ribosome entry site (IRES) element from encephalomyocarditis virus (EMCV) for cap-independent translation of the downstream ORF that codes for a polyprotein precursor, CterE-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5, followed by the 3'-UTR. In the second DENV4 replicon, the Rluc gene is fused sequentially downstream to the 20 amino acid (aa) FMDV 2A protease coding sequence, neomycin resistance gene (Neo(r)), a termination codon, and the EMCV leader followed by the same polyprotein coding sequence and 3'-UTR as in the first replicon. The first replicon is useful to study by transient transfection experiments the cis-acting elements and trans-acting factors involved in viral RNA replication. The second DENV4 replicon is used to establish a stable monkey kidney (Vero) cell line by transfection of replicon RNA and selection in the presence of the G418, an analog of neomycin. This replicon is useful for screening and identifying antiviral compounds that are potential inhibitors of viral replication.
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Affiliation(s)
- Sofia L Alcaraz-Estrada
- Division de Medicina Genomica, Centro Medico Nacional"20 de Noviembre"-ISSSTE, Mexico, D.F., Mexico
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15
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Manzano M, Padmanabhan R. Targeted mutagenesis of dengue virus type 2 replicon RNA by yeast in vivo recombination. Methods Mol Biol 2014; 1138:151-60. [PMID: 24696336 DOI: 10.1007/978-1-4939-0348-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The use of cDNA infectious clones or subgenomic replicons is indispensable in studying flavivirus biology. Mutating nucleotides or amino acid residues gives important clues to their function in the viral life cycle. However, a major challenge to the establishment of a reverse genetics system for flaviviruses is the instability of their nucleotide sequences in Escherichia coli. Thus, direct cloning using conventional restriction enzyme-based procedures usually leads to unwanted rearrangements of the construct. In this chapter, we discuss a cloning strategy that bypasses traditional cloning procedures. We take advantage of the observations from previous studies that (1) unstable sequences in bacteria can be cloned in eukaryotic systems and (2) Saccharomyces cerevisiae has a well-studied genetics system to introduce sequences using homologous recombination. We describe a protocol to perform targeted mutagenesis in a subgenomic dengue virus 2 replicon. Our method makes use of homologous recombination in yeast using a linearized replicon and a PCR product containing the desired mutation. Constructs derived from this method can be propagated in E. coli with improved stability. Thus, yeast in vivo recombination provides an excellent strategy to genetically engineer flavivirus infectious clones or replicons because this system is compatible with inherently unstable sequences of flaviviruses and is not restricted by the limitations of traditional cloning procedures.
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Affiliation(s)
- Mark Manzano
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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16
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Santos JJS, Cordeiro MT, Bertani GR, Marques ETA, Gil LHVG. A two-plasmid strategy for engineering a dengue virus type 3 infectious clone from primary Brazilian isolate. AN ACAD BRAS CIENC 2014; 86:1749-59. [PMID: 25590713 DOI: 10.1590/0001-3765201420130332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 05/05/2014] [Indexed: 11/22/2022] Open
Abstract
Dengue infections represent one of the most prevalent arthropod-borne diseases worldwide, causing a wide spectrum of clinical outcomes. Engineered infectious clone is an important tool to study Dengue virus (DENV) biology. Functional full-length cDNA clones have been constructed for many positive-strand RNA viruses and have provided valuable tools for studying the molecular mechanisms involved in viral genome replication, virion assembly, virus pathogenesis and vaccine development. We report herein the successful development of an infectious clone from a primary Brazilian isolate of dengue virus 3 (DENV3) of the genotype III. Using a two-plasmid strategy, DENV3 genome was divided in two parts and cloned separately into a yeast-bacteria shuttle vector. All plasmids were assembled in yeast by homologous recombination technique and a full-length template for transcription was obtained by in vitro ligation of the two parts of the genome. Transcript-derived DENV3 is infectious upon transfection into BHK-21 cells and in vitro characterization confirmed its identity. Growth kinetics of transcript-derived DENV3 was indistinguishable from wild type DENV3. This system is a powerful tool that will help shed light on molecular features of DENV biology, as the relationship of specific mutations and DENV pathogenesis.
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Affiliation(s)
- Jefferson J S Santos
- Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães, FIOCRUZ, Recife, PE, Brasil
| | - Marli T Cordeiro
- Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães, FIOCRUZ, Recife, PE, Brasil
| | - Giovani R Bertani
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | - Ernesto T A Marques
- Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães, FIOCRUZ, Recife, PE, Brasil
| | - Laura H V G Gil
- Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães, FIOCRUZ, Recife, PE, Brasil
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17
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Pu SY, Wu RH, Tsai MH, Yang CC, Chang CM, Yueh A. A novel approach to propagate flavivirus infectious cDNA clones in bacteria by introducing tandem repeat sequences upstream of virus genome. J Gen Virol 2014; 95:1493-1503. [DOI: 10.1099/vir.0.064915-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Despite tremendous efforts to improve the methodology for constructing flavivirus infectious cDNAs, the manipulation of flavivirus cDNAs remains a difficult task in bacteria. Here, we successfully propagated DNA-launched type 2 dengue virus (DENV2) and Japanese encephalitis virus (JEV) infectious cDNAs by introducing seven repeats of the tetracycline-response element (7×TRE) and a minimal cytomegalovirus (CMVmin) promoter upstream of the viral genome. Insertion of the 7×TRE-CMVmin sequence upstream of the DENV2 or JEV genome decreased the cryptic E. coli promoter (ECP) activity of the viral genome in bacteria, as measured using fusion constructs containing DENV2 or JEV segments and the reporter gene Renilla luciferase in an empty vector. The growth kinetics of recombinant viruses derived from DNA-launched DENV2 and JEV infectious cDNAs were similar to those of parental viruses. Similarly, RNA-launched DENV2 infectious cDNAs were generated by inserting 7×TRE-CMVmin, five repeats of the GAL4 upstream activating sequence, or five repeats of BamHI linkers upstream of the DENV2 genome. All three tandem repeat sequences decreased the ECP activity of the DENV2 genome in bacteria. Notably, 7×TRE-CMVmin stabilized RNA-launched JEV infectious cDNAs and reduced the ECP activity of the JEV genome in bacteria. The growth kinetics of recombinant viruses derived from RNA-launched DENV2 and JEV infectious cDNAs displayed patterns similar to those of the parental viruses. These results support a novel methodology for constructing flavivirus infectious cDNAs, which will facilitate research in virology, viral pathogenesis and vaccine development of flaviviruses and other RNA viruses.
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Affiliation(s)
- Szu-Yuan Pu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan, R.O.C
| | - Ren-Huang Wu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan, R.O.C
| | - Ming-Han Tsai
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan, R.O.C
| | - Chi-Chen Yang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan, R.O.C
| | - Chung-Ming Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan, R.O.C
| | - Andrew Yueh
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan, R.O.C
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18
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Evaluation of single-round infectious, chimeric dengue type 1 virus as an antigen for dengue functional antibody assays. Vaccine 2014; 32:4289-95. [DOI: 10.1016/j.vaccine.2014.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/19/2014] [Accepted: 06/06/2014] [Indexed: 12/26/2022]
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19
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RNA virus reverse genetics and vaccine design. Viruses 2014; 6:2531-50. [PMID: 24967693 PMCID: PMC4113782 DOI: 10.3390/v6072531] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 12/22/2022] Open
Abstract
RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines.
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20
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Kumar A, Bühler S, Selisko B, Davidson A, Mulder K, Canard B, Miller S, Bartenschlager R. Nuclear localization of dengue virus nonstructural protein 5 does not strictly correlate with efficient viral RNA replication and inhibition of type I interferon signaling. J Virol 2013; 87:4545-57. [PMID: 23408610 PMCID: PMC3624364 DOI: 10.1128/jvi.03083-12] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 01/29/2013] [Indexed: 12/30/2022] Open
Abstract
Dengue virus (DENV) is an important human pathogen, especially in the tropical and subtropical parts of the world, causing considerable morbidity and mortality. DENV replication occurs in the cytoplasm; however, a high proportion of nonstructural protein 5 (NS5), containing methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) activities, accumulates in the nuclei of infected cells. The present study investigates the impact of nuclear localization of NS5 on its known functions, including viral RNA replication and subversion of the type I interferon response. By using a mutation analysis approach, we identified the most critical residues within the αβ nuclear localization signal (αβNLS), which are essential for the nuclear accumulation of this protein. Although we observed an overall correlation between reduced nuclear accumulation of NS5 and impaired RNA replication, we identified one mutant with drastically reduced amounts of nuclear NS5 and virtually unaffected RNA replication, arguing that nuclear localization of NS5 does not correlate strictly with DENV replication, at least in cell culture. Because NS5 plays an important role in blocking interferon signaling via STAT-2 (signal transducer and activator of transcription 2) degradation, the abilities of the NLS mutants to block this pathway were investigated. All mutants were able to degrade STAT-2, with accordingly similar type I interferon resistance phenotypes. Since the NLS is contained within the RdRp domain, the MTase and RdRp activities of the mutants were determined by using recombinant full-length NS5. We found that the C-terminal region of the αβNLS is a critical functional element of the RdRp domain required for polymerase activity. These results indicate that efficient DENV RNA replication requires only minimal, if any, nuclear NS5, and they identify the αβNLS as a structural element required for proper RdRp activity.
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Affiliation(s)
- Anil Kumar
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Sandra Bühler
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Barbara Selisko
- Centre National de la Recherche Scientifique and Aix-Marseille Université, UMR 7257, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol, United Kingdom
| | - Klaas Mulder
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Bruno Canard
- Centre National de la Recherche Scientifique and Aix-Marseille Université, UMR 7257, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Sven Miller
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
- F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
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21
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Queiroz SRA, Silva ANMR, Santos JJS, Marques ETA, Bertani GR, Gil LHVG. Construction of yellow fever virus subgenomic replicons by yeast-based homologous recombination cloning technique. AN ACAD BRAS CIENC 2013; 85:159-68. [PMID: 23460439 DOI: 10.1590/s0001-37652013005000008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 09/13/2011] [Indexed: 11/22/2022] Open
Abstract
RNA replicon derived from Flavivirus genome is a valuable tool for studying viral replication independent of virion assembly and maturation, besides being a great potential for heterologous gene expression. In this study we described the construction of subgenomic replicons of yellow fever virus by yeast-based homologous recombination technique. The plasmid containing the yellow fever 17D strain replicon (pBSC-repYFV-17D), previously characterized, was handled to heterologous expression of the green fluorescent protein (repYFV-17D-GFP) and firefly luciferase (repYFV-17D-Luc) reporter genes. Both replicons were constructed by homologous recombination between the linearized vector pBSC-repYFV-17D and the PCR product containing homologous 25 nucleotides ends incorporated into PCR primers. The genomic organization of these constructs is similar to repYFV-17D, but with insertion of the reporter gene between the remaining 63 N-terminal nucleotides of the capsid protein and 72 C-terminal nucleotides of the E protein. The replicons repYFV-17D-GFP and repYFV-17D-Luc showed efficient replication and expression of the reporter genes. The yeast-based homologous recombination technique used in this study proved to be applicable for manipulation of the yellow fever virus genome in order to construct subgenomic replicons.
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Affiliation(s)
- Sabrina R A Queiroz
- Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Universidade Federal de Pernambuco, 50760-420 Recife, PE, Brasil
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22
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[Reverse genetics system for flaviviruses]. Uirusu 2013; 63:13-22. [PMID: 24769573 DOI: 10.2222/jsv.63.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Flaviviruses such as Japanese encephalitis virus, West Nile virus, yellow fever virus, dengue virus, and tick-borne encephalitis virus belong to a family Flaviviridae. These viruses are transmitted to vertebrates by infected mosquitoes or ticks, producing diseases, which have a serious impact on global public health. Reverse genetics is a powerful tool for studying the viruses. Although infectious full-length clones have been obtained for multiple flaviviruses, their early-stage development had the difficulty because of the instability problem of the viral cDNA in E. coli. Several strategies have been developed to circumvent the problem of infectious clone instability. The current knowledge accumulated on reverse genetics system of flaviviruses and its application are summarized in this review.
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Messer WB, Yount B, Hacker KE, Donaldson EF, Huynh JP, de Silva AM, Baric RS. Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization. PLoS Negl Trop Dis 2012; 6:e1486. [PMID: 22389731 PMCID: PMC3289595 DOI: 10.1371/journal.pntd.0001486] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/07/2011] [Indexed: 12/15/2022] Open
Abstract
Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ∼19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here are valuable for testing hypotheses on genetic determinants of DENV-3 immunopathogenesis.
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Affiliation(s)
- William B. Messer
- Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Boyd Yount
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kari E. Hacker
- Department of Microbiology and Immunology, and Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Eric F. Donaldson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeremy P. Huynh
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, and Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Pan M, Yang X, Du J, Zhou L, Ge X, Guo X, Liu J, Zhang D, Yang H. Recovery of duck hepatitis A virus 3 from a stable full-length infectious cDNA clone. Virus Res 2011; 160:439-43. [PMID: 21801768 DOI: 10.1016/j.virusres.2011.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 07/08/2011] [Accepted: 07/12/2011] [Indexed: 11/25/2022]
Abstract
Recently, duck hepatitis A virus 3 (DHAV-3) with genetically distinct characteristics from DHAV-1 and DHAV-2 was recognized in South Korea and China. In this short communication, we successfully constructed a stable full-length infectious cDNA clone derived from DHAV-3 by solving instability of cloned full-length cDNA in Escherichia coli (E. coli). The cDNA fragments amplified from the genome of DHAV-3 were assembled and inserted into a low-copy-number plasmid. Finally, a full-length cDNA clone containing an engineered SacII site that served as a genetic marker was obtained. The cDNA clone showed stable by serial passages in E. coli when propagated at 25°C under low level of antibiotic selection. BHK-21 cells were transfected with transcribed RNA from the full-length cDNA clone; infectious viral particles were rescued, showing its fatality to 10-day-old duck embryos. The results indicated that the constructed full-length cDNA clone of DHAV-3 is infectious. By various virological assays, our results indicated that the rescued virus exhibited similar biological properties with the parental virus. Animal experiments revealed that the rescued virus retained the high pathogenicity to 1-day-old ducklings and could induce a fatal hepatitis indistinguishable from its parental virus. Our present studies provide a useful tool for future research on genomic functions and molecular pathogenesis of DHAV-3.
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Affiliation(s)
- Meng Pan
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
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25
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Triyatni M, Berger EA, Saunier B. A new model to produce infectious hepatitis C virus without the replication requirement. PLoS Pathog 2011; 7:e1001333. [PMID: 21533214 PMCID: PMC3077361 DOI: 10.1371/journal.ppat.1001333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 03/14/2011] [Indexed: 02/06/2023] Open
Abstract
Numerous constraints significantly hamper the experimental study of hepatitis C virus (HCV). Robust replication in cell culture occurs with only a few strains, and is invariably accompanied by adaptive mutations that impair in vivo infectivity/replication. This problem complicates the production and study of authentic HCV, including the most prevalent and clinically important genotype 1 (subtypes 1a and 1b). Here we describe a novel cell culture approach to generate infectious HCV virions without the HCV replication requirement and the associated cell-adaptive mutations. The system is based on our finding that the intracellular environment generated by a West-Nile virus (WNV) subgenomic replicon rendered a mammalian cell line permissive for assembly and release of infectious HCV particles, wherein the HCV RNA with correct 5′ and 3′ termini was produced in the cytoplasm by a plasmid-driven dual bacteriophage RNA polymerase-based transcription/amplification system. The released particles preferentially contained the HCV-based RNA compared to the WNV subgenomic RNA. Several variations of this system are described with different HCV-based RNAs: (i) HCV bicistronic particles (HCVbp) containing RNA encoding the HCV structural genes upstream of a cell-adapted subgenomic replicon, (ii) HCV reporter particles (HCVrp) containing RNA encoding the bacteriophage SP6 RNA polymerase in place of HCV nonstructural genes, and (iii) HCV wild-type particles (HCVwt) containing unmodified RNA genomes of diverse genotypes (1a, strain H77; 1b, strain Con1; 2a, strain JFH-1). Infectivity was assessed based on the signals generated by the HCV RNA molecules introduced into the cytoplasm of target cells upon virus entry, i.e. HCV RNA replication and protein production for HCVbp in Huh-7.5 cells as well as for HCVwt in HepG2-CD81 cells and human liver slices, and SP6 RNA polymerase-driven firefly luciferase for HCVrp in target cells displaying candidate HCV surface receptors. HCV infectivity was inhibited by pre-incubation of the particles with anti-HCV antibodies and by a treatment of the target cells with leukocyte interferon plus ribavirin. The production of authentic infectious HCV particles of virtually any genotype without the adaptive mutations associated with in vitro HCV replication represents a new paradigm to decipher the requirements for HCV assembly, release, and entry, amenable to analyses of wild type and genetically modified viruses of the most clinically significant HCV genotypes. Two decades after its identification, hepatitis C virus (HCV) remains a leading cause of serious liver diseases worldwide. The poor in vitro propagation of patient isolates has impaired their study. Conversely, viral strains of the most prevalent (∼70% of total infections) and clinically problematic (∼45% cured with the standard of care) genotype 1 adapted for in vitro replication display mutations impairing yield and/or in vivo infectivity. We established a new cell culture model for producing infectious HCV in a cell line stably bearing a subgenomic replicon from West Nile virus (a flavivirus belonging to the same family as HCV) that circumvents the requirement for HCV RNA replication. To study viral infectivity in vitro, we devised several HCV genome-based constructs. This system produced wild type HCV particles of subtypes 1a, 1b, 2a and a 1b/2a chimera. All specifically infected permissive target cells, and HCV particles containing wild type genomes known to be infectious in vivo infected human liver slices ex vivo. The production of authentic HCV particles independent of HCV RNA replication represents a new paradigm to decipher requirements for HCV assembly, release, and entry, amenable to analyses of wild type and genetically modified viruses of the most clinically significant genotypes.
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Affiliation(s)
- Miriam Triyatni
- Molecular Structure Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Edward A. Berger
- Molecular Structure Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Bertrand Saunier
- Molecular Structure Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
- Paris-Descartes University, Faculty of Medicine, Paris, France
- Institut Cochin, Paris, France
- Inserm U1016, Paris, France
- * E-mail:
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Li D, Aaskov J, Lott WB. Identification of a cryptic prokaryotic promoter within the cDNA encoding the 5' end of dengue virus RNA genome. PLoS One 2011; 6:e18197. [PMID: 21483867 PMCID: PMC3069047 DOI: 10.1371/journal.pone.0018197] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 02/28/2011] [Indexed: 11/17/2022] Open
Abstract
Infectious cDNA clones of RNA viruses are important research tools, but flavivirus cDNA clones have proven difficult to assemble and propagate in bacteria. This has been attributed to genetic instability and/or host cell toxicity, however the mechanism leading to these difficulties has not been fully elucidated. Here we identify and characterize an efficient cryptic bacterial promoter in the cDNA encoding the dengue virus (DENV) 5' UTR. Following cryptic transcription in E. coli, protein expression initiated at a conserved in-frame AUG that is downstream from the authentic DENV initiation codon, yielding a DENV polyprotein fragment that was truncated at the N-terminus. A more complete understanding of constitutive viral protein expression in E. coli might help explain the cloning and propagation difficulties generally observed with flavivirus cDNA.
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Affiliation(s)
- Dongsheng Li
- Infectious Diseases Program, Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology, Brisbane, Australia
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Successful propagation of flavivirus infectious cDNAs by a novel method to reduce the cryptic bacterial promoter activity of virus genomes. J Virol 2011; 85:2927-41. [PMID: 21228244 DOI: 10.1128/jvi.01986-10] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reverse genetics is a powerful tool to study single-stranded RNA viruses. Despite tremendous efforts having been made to improve the methodology for constructing flavivirus cDNAs, the cause of toxicity of flavivirus cDNAs in bacteria remains unknown. Here we performed mutational analysis studies to identify Escherichia coli promoter (ECP) sequences within nucleotides (nt) 1 to 3000 of the dengue virus type 2 (DENV2) and Japanese encephalitis virus (JEV) genomes. Eight and four active ECPs were demonstrated within nt 1 to 3000 of the DENV2 and JEV genomes, respectively, using fusion constructs containing DENV2 or JEV segments and empty vector reporter gene Renilla luciferase. Full-length DENV2 and JEV cDNAs were obtained by inserting mutations reducing their ECP activity in bacteria without altering amino acid sequences. A severe cytopathic effect occurred when BHK21 cells were transfected with in vitro-transcribed RNAs from either a DENV2 cDNA clone with multiple silent mutations within the prM-E-NS1 region of dengue genome or a JEV cDNA clone with an A-to-C mutation at nt 90 of the JEV genome. The virions derived from the DENV2 or JEV cDNA clone exhibited infectivities similar to those of their parental viruses in C6/36 and BHK21 cells. A cis-acting element essential for virus replication was revealed by introducing silent mutations into the central portion (nt 160 to 243) of the core gene of DENV2 infectious cDNA or a subgenomic DENV2 replicon clone. This novel strategy of constructing DENV2 and JEV infectious clones could be applied to other flaviviruses or pathogenic RNA viruses to facilitate research in virology, viral pathogenesis, and vaccine development.
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Shiryaev SA, Strongin AY. Structural and functional parameters of the flaviviral protease: a promising antiviral drug target. Future Virol 2010; 5:593-606. [PMID: 21076642 DOI: 10.2217/fvl.10.39] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Flaviviruses have a single-strand, positive-polarity RNA genome that encodes a single polyprotein. The polyprotein is comprised of seven nonstructural (NS) and three structural proteins. The N- and C-terminal parts of NS3 represent the serine protease and the RNA helicase, respectively. The cleavage of the polyprotein by the protease is required to produce the individual viral proteins, which assemble a new viral progeny. Conversely, inactivation of the protease blocks viral infection. Both the protease and the helicase are conserved among flaviviruses. As a result, NS3 is a promising drug target in flaviviral infections. This article examines the West Nile virus NS3 with an emphasis on the structural and functional parameters of the protease, the helicase and their cofactors.
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Affiliation(s)
- Sergey A Shiryaev
- Inflammatory & Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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29
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Orlinger KK, Holzer GW, Schwaiger J, Mayrhofer J, Schmid K, Kistner O, Noel Barrett P, Falkner FG. An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system. Vaccine 2010; 28:3318-24. [PMID: 20211218 PMCID: PMC7115638 DOI: 10.1016/j.vaccine.2010.02.092] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/17/2010] [Accepted: 02/19/2010] [Indexed: 01/29/2023]
Abstract
A cDNA comprising the complete genome of West Nile Virus (WNV) was generated by chemical synthesis using published sequence data, independent of any preformed viral components. The synthetic WNV, produced by transfection of in vitro transcribed RNA into cell culture, exhibited undistinguishable biological properties compared to the corresponding animal-derived wild-type virus. No differences were found concerning viral growth in mammalian and insect cell lines and concerning expression of viral proteins in cells. There were also no significant differences in virulence in mice following intranasal challenge. After immunizations of mice with experimental vaccines derived from the synthetic and wild-type viruses, protection from lethal challenge was achieved with similar amounts of antigen. Both vaccine preparations also induced comparable levels of neutralizing antibodies in mice. In addition, the synthetic approach turned out to be very accurate, since the rescued WNV genome contained no undesired mutations. Thus, the first flavivirus based on chemical gene synthesis was indistinguishable from the parent virus. This demonstrates that virus isolates from animal sources are dispensable to derive seed viruses for vaccine production or research.
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Affiliation(s)
- Klaus K Orlinger
- Baxter Bioscience, Biomedical Research Center, Uferstrasse 15, A-2304 Orth/Donau, Austria
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30
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Abstract
Dengue poses an increasing threat to public health worldwide. Studies conducted over the past several decades have improved our knowledge of the mechanisms of dengue virus translation and replication. New methodologies have facilitated advances in our understanding of the RNA elements and viral and host factors that modulate dengue virus replication and translation. This review integrates research findings and explores future directions for research into the cellular and molecular mechanisms of dengue virus infection. Lessons learned from dengue virus will inform approaches to other viruses and expand our understanding of the ways in which viruses co-opt host cells during the course of infection. In addition, knowledge about the molecular mechanisms of dengue virus translation and replication and the role of host cell factors in these processes will facilitate development of antiviral strategies.
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Maeda A, Murata R, Akiyama M, Takashima I, Kariwa H, Watanabe T, Kurane I, Maeda J. A PCR-based protocol for the generation of a recombinant West Nile virus. Virus Res 2009; 144:35-43. [PMID: 19467726 DOI: 10.1016/j.virusres.2009.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 03/27/2009] [Accepted: 03/31/2009] [Indexed: 11/24/2022]
Abstract
Viral reverse genetics, particularly infectious cloning, is a valuable tool with applications to many areas of viral research including the generation of vaccine candidates. However, this technology is sometimes insufficient for the construction cDNA clones as the genome sequences and/or encoding proteins of some viral agents may be toxic to the host cells used for cloning. To circumvent this problem, we developed a polymerase chain reaction (PCR)-based protocol for generating a complete West Nile virus (WNV) cDNA. The fragmented cDNAs were synthesized from WNV RNA by reverse transcription-PCR, and subsequently cloned into plasmids for use as templates for WNV cDNA synthesis. The fragmented cDNAs were amplified and assembled by PCR to generate a full-length WNV cDNA. Using this cDNA as a template, WNV RNA was synthesized in vitro and transfected into mammalian cells. We also examined the generation of a mutant recombinant WNV containing a site-directed mutation within the viral genome sequence. Here, we discuss the possibility of developing a method for the generation of recombinant WNVs.
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Affiliation(s)
- Akihiko Maeda
- Department of Prion Diseases, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan.
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32
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Changing the protease specificity for activation of a flavivirus, tick-borne encephalitis virus. J Virol 2008; 82:8272-82. [PMID: 18562534 DOI: 10.1128/jvi.00587-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The infectivity of flavivirus particles depends on a maturation process that is triggered by the proteolytic cleavage of the precursor of the M protein (prM). This activation cleavage is naturally performed by ubiquitous cellular proteases of the furin family, which typically recognize the multibasic sequence motif R-X-R/K-R. Previously, we demonstrated that a tick-borne encephalitis virus (TBEV) mutant with an altered cleavage motif, R-X-R, produced immature, noninfectious particles that could be activated by exogenous trypsin, which cleaves after single basic residues. Here, we report the adaptation of this mutant to chymotrypsin, a protease specific for large, hydrophobic amino acid residues. Using selection pressure in cell culture, two different mutations conferring a chymotrypsin-dependent phenotype were identified. Surprisingly, one of these mutations (Ser85Phe) occurred three positions upstream of the natural cleavage site. The other mutation (Arg89His) arose at the natural cleavage position but involved a His residue, which is not a typical chymotrypsin cleavage site. Efficient cleavage of protein prM and activation by the heterologous protease were confirmed using various recombinant TBEV mutants. Mutants with only the originally selected mutations exhibited unimpaired export kinetics and were genotypically stable during at least six cell culture passages. However, in contrast to the wild-type virus or trypsin-dependent mutants, chymotrypsin-dependent mutants were not neurovirulent in suckling mice. Our results demonstrate that flaviviruses with altered protease specificities can be generated and suggest that this approach can be used for the construction of viral mutants or vectors that can be activated on demand and have restricted tissue tropism and virulence.
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Abstract
Dengue virus infection causes the most important arthropod-borne disease of humans. Currently, there are no dengue vaccines or antiviral therapies in clinical use, although their development is a global health priority. Using a technique known as ‘reverse genetics’, the dengue virus RNA genome can be manipulated, either by the introduction of specific mutations or the deletion and/or substitution of entire genes. This has led to the production of novel recombinant viruses that have potential as vaccines and the production of noninfectious viral subgenomes (termed replicons) useful for drug screening. Reverse genetics is also an invaluable tool for studying the role of dengue virus RNA elements and proteins in replication and pathogenesis. This review describes the contribution of reverse genetics to dengue virus research to date, highlighting the potential use of this technology in the development of effective control measures against dengue in the future.
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Affiliation(s)
- Rebecca Ward
- University of Bristol, Department of Cellular & Molecular Medicine, School of Medical & Veterinary Sciences, BS8 1TD, UK
| | - Andrew D Davidson
- University of Bristol, Department of Cellular & Molecular Medicine, School of Medical & Veterinary Sciences, BS8 1TD, UK
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Hu HP, Hsieh SC, King CC, Wang WK. Characterization of retrovirus-based reporter viruses pseudotyped with the precursor membrane and envelope glycoproteins of four serotypes of dengue viruses. Virology 2007; 368:376-87. [PMID: 17662331 PMCID: PMC7126519 DOI: 10.1016/j.virol.2007.06.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 05/14/2007] [Accepted: 06/19/2007] [Indexed: 11/16/2022]
Abstract
In this study, we successfully established retrovirus-based reporter viruses pseudotyped with the precursor membrane and envelope (PrM/E) proteins of each of the four serotypes of dengue viruses, which caused the most important arboviral diseases in this century. Co-sedimentation of the dengue E protein and HIV-1 core proteins by sucrose gradient analysis of the pseudotype reporter virus of dengue virus type 2, D2(HIVluc), and detection of HIV-1 core proteins by immunoprecipitation with anti-E monoclonal antibody suggested that dengue viral proteins were incorporated into the pseudotype viral particles. The infectivity in target cells, as assessed by the luciferase activity, can be inhibited by the lysosomotropic agents, suggesting a pH-dependent mechanism of entry. Amino acid substitutions of the leucine at position 107, a critical residue at the fusion loop of E protein, with lysine resulted in severe impairment in infectivity, suggesting that entry of the pseudotype reporter virus is mediated through the fusogenic properties of E protein. With more and more dengue viral sequences available from different outbreaks worldwide, this sensitive and convenient tool has the potential to facilitate molecular characterization of the PrM/E proteins of dengue field isolates.
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Affiliation(s)
- Hsien-Ping Hu
- Institute of Microbiology, College of Medicine, National Taiwan University, No 1 Sec1 Jen-Ai Rd, Taipei 100, Taiwan
| | - Szu-Chia Hsieh
- Institute of Microbiology, College of Medicine, National Taiwan University, No 1 Sec1 Jen-Ai Rd, Taipei 100, Taiwan
| | - Chwan-Chuen King
- Institute of Epidemiology, College of Public Health, National Taiwan University, No 1 Sec1 Jen-Ai Rd, Taipei 100, Taiwan
| | - Wei-Kung Wang
- Institute of Microbiology, College of Medicine, National Taiwan University, No 1 Sec1 Jen-Ai Rd, Taipei 100, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, No 7 Chung-Shan S Rd, Taipei 100, Taiwan
- Corresponding author. Institute of Microbiology, National Taiwan University, No 1 Sec1 Jen-Ai Rd, Taipei 100, Taiwan. Fax: +886 2 2391 5293.
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35
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Pierro DJ, Salazar MI, Beaty BJ, Olson KE. Infectious clone construction of dengue virus type 2, strain Jamaican 1409, and characterization of a conditional E6 mutation. J Gen Virol 2006; 87:2263-2268. [PMID: 16847122 DOI: 10.1099/vir.0.81958-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A full-length infectious cDNA clone (ic) was constructed from the genome of the dengue virus type 2 (DENV-2) Jamaica83 1409 strain, pBAC1409ic, by using a bacterial artifical chromosome plasmid system. Infectious virus was generated and characterized for growth in cell culture and for infection in Aedes aegypti mosquitoes. During construction, an isoleucine to methionine (Ile-->Met) change was found at position 6 in the envelope glycoprotein sequence between low- and high-passage DENV-2 1409 strains. In vitro-transcribed genomic RNA of 1409ic with E6-Ile produced infectious virions following electroporation in mosquito cells, but not mammalian cells, while 1409ic RNA with an E6-Met mutation produced virus in both cell types. Moreover, DENV-2 1409 with the E6-Ile residue produced syncytia in C6/36 cell culture, whereas viruses with E6-Met did not. However, in vitro cell culture-derived growth-curve data and in vivo mosquito-infection rates revealed that none of the analysed DENV-2 strains differed from each other.
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Affiliation(s)
- Dennis J Pierro
- Arthropod-borne and Infectious Disease Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Foothills Research Campus, Fort Collins, CO 80523, USA
| | - Ma Isabel Salazar
- Arthropod-borne and Infectious Disease Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Foothills Research Campus, Fort Collins, CO 80523, USA
| | - Barry J Beaty
- Arthropod-borne and Infectious Disease Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Foothills Research Campus, Fort Collins, CO 80523, USA
| | - Ken E Olson
- Arthropod-borne and Infectious Disease Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Foothills Research Campus, Fort Collins, CO 80523, USA
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36
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Zhu W, Chen S, Qin C, Yu M, Jiang T, Deng Y, Qin E. Construction and identification of reverse genetics system of Dengue type 2 virus isolated in China. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11434-006-2087-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Lee YR, Huang KJ, Lei HY, Chen SH, Lin YS, Yeh TM, Liu HS. Suckling mice were used to detect infectious dengue-2 viruses by intracerebral injection of the full-length RNA transcript. Intervirology 2005; 48:161-6. [PMID: 15812190 DOI: 10.1159/000081744] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Accepted: 07/05/2004] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE In this study we established a mouse brain injection system to detect infectious dengue-2 virus produced from the full-length RNA transcripts. METHODS In vitro transcription was used to synthesize full-length dengue-2 virus RNA from the plasmid pRS424FLDEN2NGC, which was intracerebrally injected into the 6-day-old suckling mice (ICR strains). Engineered dengue-2 viruses were detected in the brain sections using immunohistochemistry staining. RT-PCR followed by restriction endonuclease BstEII digestion was used to confirm the mosquito C6/36 cells cocultured with the mouse brain extract. RESULTS The mice inoculated with the full-length dengue-2 viral RNA transcript showed paralysis symptoms and died between day 10 and 13 postinjection. The dengue-2 virus-specific antigens (E, Core and NS1) were detected in all the brain and part of the liver sections of the paralyzed mice by immunohistochemistry staining, indicating the existence of dengue-2 virus in these tissues of the suckling mice. The viruses detected in the brains of suckling mice were indeed infectious, which was further confirmed by coculturing mosquito C6/36 cells with the brain extract of the injected mice. CONCLUSIONS We developed an in vivo approach to detect and produce engineered dengue viruses with infectivity from the full-length plasmid cDNA. This suckling mice system will also aid in screening the infectious viruses that are created by site-directed mutagenesis and is useful for the studies of dengue virus gene function and pathogenesis in the host.
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Affiliation(s)
- Ying-Ray Lee
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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McElroy KL, Tsetsarkin KA, Vanlandingham DL, Higgs S. Characterization of an infectious clone of the wild-type yellow fever virus Asibi strain that is able to infect and disseminate in mosquitoes. J Gen Virol 2005; 86:1747-1751. [PMID: 15914853 DOI: 10.1099/vir.0.80746-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Infectious clone technology provides an opportunity to study the molecular basis of arthropod-virus interactions in detail. This study describes the development of an infectious clone of the prototype yellow fever virus Asibi strain (YFV-As) with the purpose of identifying sequences or domains that influence infection dynamics in the mosquito vector. The full-length cDNA of YFV-As virus was produced from RT-PCR products of parental viral RNA. These were cloned into a low-copy-number plasmid previously used to develop the YFV-17D infectious clone (pACNR/FLYF-17D). Virus recovered from the infectious clone exhibited biological characteristics similar to those of the parental YFV-As, including replication kinetics, reactivity to flavivirus cross-reactive and YFV-specific antibodies and infection and dissemination rates in Aedes aegypti, the principal mosquito vector of YFV. These data provide the basis for future studies with chimeric Asibi/17D viruses to identify the determinants of vaccine attenuation in the vector.
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Affiliation(s)
- Kate L McElroy
- Department of Pathology, University of Texas Medical Branch, Keiller 2.104, 301 University Boulevard, Galveston, TX 77555-0609, USA
| | - Konstantin A Tsetsarkin
- Department of Pathology, University of Texas Medical Branch, Keiller 2.104, 301 University Boulevard, Galveston, TX 77555-0609, USA
| | - Dana L Vanlandingham
- Department of Pathology, University of Texas Medical Branch, Keiller 2.104, 301 University Boulevard, Galveston, TX 77555-0609, USA
| | - Stephen Higgs
- Department of Pathology, University of Texas Medical Branch, Keiller 2.104, 301 University Boulevard, Galveston, TX 77555-0609, USA
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Pierson TC, Diamond MS, Ahmed AA, Valentine LE, Davis CW, Samuel MA, Hanna SL, Puffer BA, Doms RW. An infectious West Nile Virus that expresses a GFP reporter gene. Virology 2005; 334:28-40. [PMID: 15749120 DOI: 10.1016/j.virol.2005.01.021] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Revised: 12/02/2004] [Accepted: 01/03/2005] [Indexed: 11/23/2022]
Abstract
West Nile virus is a mosquito-borne, neurotropic flavivirus that causes encephalitis in humans and animals. Since being introduced into the Western hemisphere in 1999, WNV has spread rapidly across North America, identifying this virus as an important emerging pathogen. In this study, we developed a DNA-launched infectious molecular clone of WNV that encodes a GFP reporter gene. Transfection of cells with the plasmid encoding this recombinant virus (pWNII-GFP) resulted in the production of infectious WNV capable of expressing GFP at high levels shortly after infection of a variety of cell types, including primary neurons and dendritic cells. Infection of cells with WNII-GFP virus was productive, and could be inhibited with both monoclonal antibodies and interferon-beta, highlighting the potential of this system in the development and characterization of novel inhibitors and therapeutics for WNV infection. As expected, insertion of the reporter gene into the viral genome was associated with a reduced rate of viral replication, providing the selective pressure for the development of variants that no longer encoded the full-length reporter gene cassette. We anticipate this DNA-based, infectious WNV reporter virus will allow novel approaches for the study of WNV infection and its inhibition both in vitro and in vivo.
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Affiliation(s)
- Theodore C Pierson
- Department of Microbiology, University of Pennsylvania, 225 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104, USA.
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40
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Hayasaka D, Gritsun TS, Yoshii K, Ueki T, Goto A, Mizutani T, Kariwa H, Iwasaki T, Gould EA, Takashima I. Amino acid changes responsible for attenuation of virus neurovirulence in an infectious cDNA clone of the Oshima strain of Tick-borne encephalitis virus. J Gen Virol 2004; 85:1007-1018. [PMID: 15039543 DOI: 10.1099/vir.0.19668-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A stable full-length infectious cDNA clone of the Oshima strain of Tick-borne encephalitis virus (Far-Eastern subtype) was developed by a long high-fidelity RT-PCR and one-step cloning procedure. The infectious clone (O-IC) had four amino acid substitutions and produced smaller plaques when compared with the parent Oshima 5-10 strain. Using site-directed mutagenesis, the substitutions were reverted to restore the parent virus sequence (O-IC-pt). Although genetically identical, parent virus Oshima 5-10 and virus recovered from O-IC-pt demonstrated some biological differences that are possibly explained by the presence of quasispecies with differing virulence characteristics within the original virus population. These observations may have implications for vaccines based on modified infectious clones. It was also demonstrated that the amino acid substitution E-S40→P at position 40 in the envelope (E) glycoprotein was responsible for plaque size reduction, reduced infectious virus yields in cell culture and reduced mouse neurovirulence. Additionally, two amino acid substitutions in the non-structural (NS)5 protein (virus RNA-dependent RNA polymerase) NS5-V378→A and NS5-R674→K also contributed to attenuation of virulence in mice, but did not demonstrate a noticeable biological effect in baby hamster kidney cell culture. Comparative neurovirulence tests revealed how the accumulation of individual mutations (E-S40→P, NS5-V378→A and NS5-R674→K) can result in the attenuation of a virus.
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Affiliation(s)
- Daisuke Hayasaka
- Department of Pathology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | | | - Kentarou Yoshii
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Tomotaka Ueki
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Akiko Goto
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Tetsuya Mizutani
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroaki Kariwa
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Takuya Iwasaki
- Department of Pathology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | | | - Ikuo Takashima
- Laboratory of Public Health, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
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41
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Affiliation(s)
- Brett D Lindenbach
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, Rockefeller University, New York, New York 10021, USA
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42
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Pugachev KV, Guirakhoo F, Trent DW, Monath TP. Traditional and novel approaches to flavivirus vaccines. Int J Parasitol 2003; 33:567-82. [PMID: 12782056 DOI: 10.1016/s0020-7519(03)00063-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Yellow fever, dengue, Japanese encephalitis and tick-borne encephalitis viruses are the medically most important members of the Flavivirus genus composed primarily of arboviruses. In this paper, we review the commercially available traditional flavivirus vaccines against yellow fever, Japanese encephalitis, and tick-borne encephalitis, as well as modern approaches to flavivirus vaccines. Formalin inactivation technology has been employed to produce killed vaccines. Flaviviruses have been attenuated by multiple passages in animal tissues and cell cultures to produce empirical live attenuated vaccines. The use of traditional methods is being pursued to develop vaccines against other flavivirus diseases, such as dengue, and to improve existing vaccines, such as for Japanese encephalitis. With the recent development of infectious clones, rational approaches to attenuated flavivirus vaccines have employed the introduction of specific mutations into wild type viruses and chimerisation between different viruses. Novel methods for delivery of live vaccines, such as inoculation of infectious DNA or RNA, have been described. Other approaches, such as the construction of protein subunit, expression vector-based and naked DNA vaccines, have been proposed to create alternate vaccine candidates.
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43
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Lai CJ, Monath TP. Chimeric Flaviviruses: Novel Vaccines against Dengue Fever, Tick-borne Encephalitis, and Japanese Encephalitis. Adv Virus Res 2003; 61:469-509. [PMID: 14714441 DOI: 10.1016/s0065-3527(03)61013-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many arthropod-borne flaviviruses are important human pathogens responsible for diverse illnesses, including YF, JE, TBE, and dengue. Live, attenuated vaccines have afforded the most effective and economical means of prevention and control, as illustrated by YF 17D and JE SA14-14-2 vaccines. Recent advances in recombinant DNA technology have made it possible to explore a novel approach for developing live attenuated flavivirus vaccines against other flaviviruses. Full-length cDNA clones allow construction of infectious virus bearing attenuating mutations or deletions incorporated in the viral genome. It is also possible to create chimeric flaviviruses in which the structural protein genes for the target antigens of a flavivirus are replaced by the corresponding genes of another flavivirus. By combining these molecular techniques, the DNA sequences of DEN4 strain 814669, DEN2 PDK-53 candidate vaccine and YF 17D vaccine have been used as the genetic backbone to construct chimeric flaviviruses with the required attenuation phenotype and expression of the target antigens. Encouraging results from preclinical and clinical studies have shown that several chimeric flavivirus vaccines have the safety profile and satisfactory immunogenicity and protective efficacy to warrant further evaluation in humans. The chimeric flavivirus strategy has led to the rapid development of novel live-attenuated vaccines against dengue, TBE, JE, and West Nile viruses.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Chimera/genetics
- Chimera/immunology
- DNA, Viral/genetics
- Dengue/immunology
- Dengue/prevention & control
- Dengue Virus/genetics
- Dengue Virus/immunology
- Encephalitis Viruses, Tick-Borne/genetics
- Encephalitis Viruses, Tick-Borne/immunology
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/prevention & control
- Encephalitis, Tick-Borne/immunology
- Encephalitis, Tick-Borne/prevention & control
- Flavivirus/genetics
- Flavivirus/immunology
- Genetic Engineering
- Humans
- Japanese Encephalitis Vaccines/genetics
- Japanese Encephalitis Vaccines/isolation & purification
- Molecular Sequence Data
- Vaccines, Attenuated/genetics
- Vaccines, Attenuated/isolation & purification
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/isolation & purification
- Viral Vaccines/genetics
- Viral Vaccines/isolation & purification
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Affiliation(s)
- Ching-Juh Lai
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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44
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Shi PY, Tilgner M, Lo MK, Kent KA, Bernard KA. Infectious cDNA clone of the epidemic west nile virus from New York City. J Virol 2002; 76:5847-56. [PMID: 12021317 PMCID: PMC136194 DOI: 10.1128/jvi.76.12.5847-5856.2002] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first full-length infectious clone of the current epidemic, lineage I, strain of West Nile virus (WNV). The full-length cDNA was constructed from reverse transcription-PCR products of viral RNA from an isolate collected during the year 2000 outbreak in New York City. It was cloned into plasmid pBR322 under the control of a T7 promoter and stably amplified in Escherichia coli HB101. RNA transcribed from the full-length cDNA clone was highly infectious upon transfection into BHK-21 cells, resulting in progeny virus with titers of 1 x 10(9) to 5 x 10(9) PFU/ml. The cDNA clone was engineered to contain three silent nucleotide changes to create a StyI site (C to A and A to G at nucleotides [nt] 8859 and 8862, respectively) and to knock out an EcoRI site (A to G at nt 8880). These genetic markers were retained in the recovered progeny virus. Deletion of the 3'-terminal 199 nt of the cDNA transcript abolished the infectivity of the RNA. The plaque morphology, in vitro growth characteristics in mammalian and insect cells, and virulence in adult mice were indistinguishable for the parental and recombinant viruses. The stable infectious cDNA clone of the epidemic lineage I strain will provide a valuable experimental system to study the pathogenesis and replication of WNV.
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Affiliation(s)
- Pei-Yong Shi
- Wadsworth Center, New York State Department of Health. Department of Biomedical Sciences, University at Albany, State University of New York, Albany, New York 12201, USA.
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45
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Kinney RM, Huang CY. Development of new vaccines against dengue fever and Japanese encephalitis. Intervirology 2002; 44:176-97. [PMID: 11509879 DOI: 10.1159/000050045] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mosquito-borne dengue (DEN) and Japanese encephalitis (JE) viruses are the leading causes of arthropod-transmitted viral disease in humans. A licensed tetravalent vaccine that provides effective, long-term immunity against all four serotypes of DEN virus is needed, but is currently unavailable. Improvements to currently available JE vaccines are also needed. Past and recent strategies for the development of new DEN and JE vaccines include inactivated and live attenuated viruses, engineered viruses and chimeric viruses derived from infectious cDNA clones of DEN or JE virus, recombinant poxviruses, recombinant baculoviruses, protein expression in Escherichia coli, and naked DNA vaccines. This report summarizes some of the recent developments in DEN and JE vaccinology, particularly vaccine strategies that involve live attenuated viruses, engineered viruses derived from infectious cDNA clones, and naked DNA vaccines.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Dengue/immunology
- Dengue/prevention & control
- Dengue/virology
- Dengue Virus/genetics
- Dengue Virus/immunology
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/virology
- Humans
- Molecular Sequence Data
- Vaccines, Attenuated/immunology
- Vaccines, DNA/genetics
- Vaccines, DNA/immunology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- R M Kinney
- Division of Vector-Borne Infectious Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, US Department of Health and Human Services, Fort Collins, Colo 80522, USA.
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46
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Shi PY, Tilgner M, Lo MK. Construction and characterization of subgenomic replicons of New York strain of West Nile virus. Virology 2002; 296:219-33. [PMID: 12069521 DOI: 10.1006/viro.2002.1453] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The lineage I strain of West Nile virus (WNV) frequently causes human epidemics, including the recent outbreak in North America (Lanciotti et al., 1999, Science 286:2333-2337). As an initial step in studying the replication and pathogenesis of WNV, we constructed several cDNA clones of a WNV replicon derived from an epidemic strain (lineage I) isolated from the epicenter of New York City in the year 2000. Replicon RNAs were in vitro transcribed from cDNA plasmids and transfected into BHK-21 cells. RNA replication in transfected cells was monitored by immunofluorescence analysis (IFA) and 5' nuclease real-time RT-PCR (TaqMan). The replicon RNAs contained large in-frame deletions (greater than 92%) of the C-prM-E structural region yet still replicated efficiently in BHK-21 cells. 5' nuclease real-time RT-PCR showed that a great excess of plus-sense replicon RNA over the minus-sense RNA was synthesized in transfected cells. Replication efficiency decreased upon insertion of a green fluorescent protein (GFP) reporter gene driven by an internal ribosomal entry site (IRES) in the upstream end of the 3' untranslated region of the replicon. Strong GFP expression was detected in cells transfected with a replicon containing IRES-GFP positioned in the plus-sense orientation. IFA showed that GFP and viral proteins were exclusively coexpressed in transfected cells. In contrast, no GFP fluorescence was observed in cells transfected with a replicon containing IRES-GFP positioned in the minus-sense orientation, despite high levels of synthesis of viral proteins and RNA in the cells. Substitution of the GFP gene in the plus-sense GFP replicon with the neomycin phosphotransferase gene allowed selection of geneticin-resistant cells in which WNV replicons persistently replicated without apparent cytopathic effect. These results suggest that WNV replicons may serve as a noncytopathic RNA virus expression system and should provide a valuable tool to study WNV replication.
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Affiliation(s)
- Pei-Yong Shi
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.
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47
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Abstract
The 'infectious DNA' approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Its use, however, is often limited by the instability of plasmids due to a transcriptional activity of eukaryotic promoters in Escherichia coli resulting in synthesis of products toxic for the bacterial host. Using a highly unstable representative infectious clone of Japanese encephalitis (JE) flavivirus, we tested a new approach in design of such problematic 'infectious DNA' constructs, which is based on minimizing unwanted transcription in the bacterial host. A plasmid containing full genome size JE cDNA under control of the minimal cytomegalovirus (CMV) promoter can be propagated in E. coli with growth and stability characteristics similar to that of constructs controlled by the T7 promoter. Transfection of this plasmid into susceptible cells leads to the establishment of a productive infectious cycle. Reinsertion of the CMV enhancer at the 3'-end of the JE cassette substantially increased the specific infectivity without affecting the stability and growth characteristics of the construct. This approach can be useful when stabilization of infectious clones by modification of a viral cDNA cassette is not the feasible or suitable alternative.
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MESH Headings
- 5' Untranslated Regions/genetics
- Cell Line
- Cloning, Molecular
- Cytomegalovirus/genetics
- DNA, Complementary/genetics
- DNA, Viral/genetics
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/growth & development
- Encephalitis Virus, Japanese/pathogenicity
- Enhancer Elements, Genetic
- Escherichia coli/genetics
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Transcription, Genetic
- Transfection
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48
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Bisht H, Chugh DA, Swaminathan S, Khanna N. Expression and purification of Dengue virus type 2 envelope protein as a fusion with hepatitis B surface antigen in Pichia pastoris. Protein Expr Purif 2001; 23:84-96. [PMID: 11570849 DOI: 10.1006/prep.2001.1474] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The methylotrophic yeast, Pichia pastoris, has been used as a host to express the envelope protein (Den2E) of dengue type 2 virus (NGC strain) as a chimera with hepatitis B surface antigen (HBsAg): a protein known to self assemble into virus-like particles (VLPs) and to be efficiently expressed in P. pastoris. The Den2E gene used in this study is a truncated version encoding the first 395 amino acid (aa) residues of the mature Den2E protein; the HBsAg gene encodes the full length 226 aa HBsAg protein. Two in-frame gene fusions were constructed for intracellular expression in P. pastoris. The first one contains the HBsAg gene as the 5' partner and the Den2E gene as the 3'partner (HBsAg-Den2E). In the second one, the relative positions of the two partners of the gene fusion were reversed to create the hybrid Den2E-HBsAg gene. These fusion genes were integrated into the genome of P. pastoris under the control of the methanol-inducible alcohol oxidase (AOX1) promoter. Of the two fusions, the Den2E-HBsAg gene was expressed at higher levels in P. pastoris based on Northern analysis. The hybrid protein ( approximately 68 kDa) expressed by this clone was purified to near homogeneity using a combination of acid precipitation, hydrophobic interaction, and immunoaffinity chromatographic steps. Final purification achieved was approximately 1400-fold with a yield of approximately 26%. The chimeric protein was found to possess the ability to assemble into high molecular weight aggregates (akin to HBsAg particles). The recombinant fusion protein eluted close to the void volume of a Sepharose CL-4B column indicating its macromolecular nature. On a CsCl density gradient the recombinant fusion protein sedimented to a position very similar to that of HBsAg VLPs. The hybrid protein is recognized by the two neutralizing monoclonals against the two components of the chimeric protein.
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Affiliation(s)
- H Bisht
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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49
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Zhang F, Huang Q, Ma W, Jiang S, Fan Y, Zhang H. Amplification and cloning of the full-length genome of Japanese encephalitis virus by a novel long RT-PCR protocol in a cosmid vector. J Virol Methods 2001; 96:171-82. [PMID: 11445147 DOI: 10.1016/s0166-0934(01)00331-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A novel and rapid full-length long RT-PCR technique was established to produce genome-length cDNA from Japanese encephalitis virus. In vitro positive strand RNA transcripts from the full-length RT-PCR amplicon including T7 promoter sequences at the 5' end were proved to be infectious upon transfection. The full-length amplicon without the T7 promoter was cloned into a cosmid vector under the SP6 promoter. This stable clone, designated as pJEV-1, was characterised further and used as a genetic resource for generation of infectious RNA transcripts, gene manipulation and expression. The 'run-off' transcript from pJEV-1 with vector sequences at the either end of the insert was not infectious, but transcripts of the full-length PCR amplicon from pJEV-1 produced infectious virus upon transfection. A transcript with an engineered Xho I site from two ligated PCR fragments amplified from pJEV-1 was also infectious. Furthermore, the coding region for premembrane and envelope proteins (preM-E) from pJEV-1 was subcloned and expressed in the Drosophila Expression System. The expressed protein showed correct molecular size and was immunoreactive with a Japanese encephalitis virus E protein-specific antibody. The derivation of genome-size cDNA from Japanese encephalitis virus and the stable clone will facilitate investigation of this virus and elucidation of its pathogenesis at the molecular level.
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MESH Headings
- Animals
- Cell Line
- Cloning, Molecular/methods
- Cosmids/genetics
- DNA, Complementary/genetics
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/pathogenicity
- Encephalitis, Japanese/virology
- Gene Amplification
- Genetic Vectors/genetics
- Genome, Viral
- Mice
- Mice, Inbred BALB C
- RNA, Viral/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- F Zhang
- Department of Microbiology, the Fourth Military Medical University, Xi'an, 710032, Shaanxi, People's Republic of China
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50
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Yamshchikov VF, Wengler G, Perelygin AA, Brinton MA, Compans RW. An infectious clone of the West Nile flavivirus. Virology 2001; 281:294-304. [PMID: 11277701 DOI: 10.1006/viro.2000.0795] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
West Nile (WN) virus is the most widespread among flaviviruses, but until recently it was not known on the American continent. We describe here design of a subgenomic replicon, as well as a full-length infectious clone of the lineage II WN strain, which appeared surprisingly stable compared to other flavivirus infectious clones. This infectious clone was used to investigate effects of 5'- and 3'-nonrelated sequences on virus replication and infectivity of synthetic RNA. While a long nonrelated sequence at the 3'-end delayed but did not prevent establishment of the productive infectious cycle, a much shorter extra sequence at the 5'-end completely abrogated virus replication. Replacement of the conserved 5'-adenosine residue substantially delayed, but did not prevent, establishment of virus infection. In all cases, the recovered virus had restored its authentic 5'- and 3'-end genome sequences. However, the presence of extensive nonrelated sequences at both 5'- and 3'-ends could not be repaired.
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Affiliation(s)
- V F Yamshchikov
- Department of Internal Medicine, University of Virginia, Charlottesville, Virginia 22908, USA.
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