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Cochin M, Driouich JS, Moureau G, Piorkowski G, de Lamballerie X, Nougairède A. In vivo rescue of arboviruses directly from subgenomic DNA fragments. Emerg Microbes Infect 2024; 13:2356140. [PMID: 38742328 PMCID: PMC11133884 DOI: 10.1080/22221751.2024.2356140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Reverse genetic systems are mainly used to rescue recombinant viral strains in cell culture. These tools have also been used to generate, by inoculating infectious clones, viral strains directly in living animals. We previously developed the "Infectious Subgenomic Amplicons" (ISA) method, which enables the rescue of single-stranded positive sense RNA viruses in vitro by transfecting overlapping subgenomic DNA fragments. Here, we provide proof-of-concept for direct in vivo generation of infectious particles following the inoculation of subgenomic amplicons. First, we rescued a strain of tick-borne encephalitis virus in mice to transpose the ISA method in vivo. Subgenomic DNA fragments were amplified using a 3-fragment reverse genetics system and inoculated intramuscularly. Almost all animals were infected when quantities of DNA inoculated were at least 20 µg. We then optimized our procedure in order to increase the animal infection rate. This was achieved by adding an electroporation step and/or using a simplified 2- fragment reverse genetics system. Under optimal conditions, a large majority of animals were infected with doses of 20 ng of DNA. Finally, we demonstrated the versatility of this method by applying it to Japanese encephalitis and Chikungunya viruses. This method provides an efficient strategy for in vivo rescue of arboviruses. Furthermore, in the context of the development of DNA-launched live attenuated vaccines, this new approach may facilitate the generation of attenuated strains in vivo. It also enables to deliver a substance free of any vector DNA, which seems to be an important criterion for the development of human vaccines.
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Affiliation(s)
- Maxime Cochin
- Unité des Virus Émergents, UVE: Aix Marseille Université, Marseille, France
| | | | - Grégory Moureau
- Unité des Virus Émergents, UVE: Aix Marseille Université, Marseille, France
| | | | | | - Antoine Nougairède
- Unité des Virus Émergents, UVE: Aix Marseille Université, Marseille, France
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2
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Cui D, Li S, Yin B, Li C, Zhang L, Li Z, Huang J. Rapid Rescue of Goose Astrovirus Genome via Red/ET Assembly. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:297-306. [PMID: 38582780 DOI: 10.1007/s12560-024-09593-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/28/2024] [Indexed: 04/08/2024]
Abstract
The host-specific infection of Avian Astrovirus (AAstVs) has posed significant challenges to the poultry industry, resulting in substantial economic losses. However, few reports exist on the functional consequences of genome diversity, cross-species infectivity and mechanisms governing virus replication of AAstVs, making it difficult to develop measures to control astrovirus transmission. Reverse genetics technique can be used to study the function of viruses at the molecular level, as well as investigating pathogenic mechanisms and guide vaccine development and disease treatment. Herein, the reverse genetics technique of goose astrovirus GAstV/JS2019 strain was developed based on use of a reconstructed vector including CMV promotor, hammerhead ribozyme (HamRz), hepatitis delta virus ribozyme (HdvRz), and SV40 tail, then the cloned viral genome fragments were connected using Red/ET recombineering. The recombinant rGAstV-JS2019 was readily rescued by transfected the infectious clone plasmid into LMH cells. Importantly, the rescued rGAstV/JS2019 exhibited similar growth kinetics comparable to those of the parental GAstV/JS2019 isolate in cultured cells. Our research results provide an alternative and more effective reverse genetic tool for a detailed understanding of viral replication, pathogenic mechanisms, and molecular mechanisms of evolution.
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Affiliation(s)
- Daqing Cui
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Shujun Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Boxuan Yin
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Changyan Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Zexing Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
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3
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Sanchez-Felipe L, Alpizar YA, Ma J, Coelmont L, Dallmeier K. YF17D-based vaccines - standing on the shoulders of a giant. Eur J Immunol 2024; 54:e2250133. [PMID: 38571392 DOI: 10.1002/eji.202250133] [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: 02/21/2023] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024]
Abstract
Live-attenuated yellow fever vaccine (YF17D) was developed in the 1930s as the first ever empirically derived human vaccine. Ninety years later, it is still a benchmark for vaccines made today. YF17D triggers a particularly broad and polyfunctional response engaging multiple arms of innate, humoral and cellular immunity. This unique immunogenicity translates into an extraordinary vaccine efficacy and outstanding longevity of protection, possibly by single-dose immunization. More recently, progress in molecular virology and synthetic biology allowed engineering of YF17D as a powerful vector and promising platform for the development of novel recombinant live vaccines, including two licensed vaccines against Japanese encephalitis and dengue, even in paediatric use. Likewise, numerous chimeric and transgenic preclinical candidates have been described. These include prophylactic vaccines against emerging viral infections (e.g. Lassa, Zika and SARS-CoV-2) and parasitic diseases (e.g. malaria), as well as therapeutic applications targeting persistent infections (e.g. HIV and chronic hepatitis), and cancer. Efforts to overcome historical safety concerns and manufacturing challenges are ongoing and pave the way for wider use of YF17D-based vaccines. In this review, we summarize recent insights regarding YF17D as vaccine platform, and how YF17D-based vaccines may complement as well as differentiate from other emerging modalities in response to unmet medical needs and for pandemic preparedness.
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Affiliation(s)
- Lorena Sanchez-Felipe
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium
| | - Yeranddy A Alpizar
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium
| | - Ji Ma
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium
| | - Lotte Coelmont
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium
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4
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Wu G, Li Q, Dai J, Mao G, Ma Y. Design and Application of Biosafe Coronavirus Engineering Systems without Virulence. Viruses 2024; 16:659. [PMID: 38793541 PMCID: PMC11126016 DOI: 10.3390/v16050659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
In the last twenty years, three deadly zoonotic coronaviruses (CoVs)-namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2-have emerged. They are considered highly pathogenic for humans, particularly SARS-CoV-2, which caused the 2019 CoV disease pandemic (COVID-19), endangering the lives and health of people globally and causing unpredictable economic losses. Experiments on wild-type viruses require biosafety level 3 or 4 laboratories (BSL-3 or BSL-4), which significantly hinders basic virological research. Therefore, the development of various biosafe CoV systems without virulence is urgently needed to meet the requirements of different research fields, such as antiviral and vaccine evaluation. This review aimed to comprehensively summarize the biosafety of CoV engineering systems. These systems combine virological foundations with synthetic genomics techniques, enabling the development of efficient tools for attenuated or non-virulent vaccines, the screening of antiviral drugs, and the investigation of the pathogenic mechanisms of novel microorganisms.
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Affiliation(s)
- Guoqiang Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Qiaoyu Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
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Fiacre L, Nougairède A, Migné C, Bayet M, Cochin M, Dumarest M, Helle T, Exbrayat A, Pagès N, Vitour D, Richardson JP, Failloux AB, Vazeille M, Albina E, Lecollinet S, Gonzalez G. Different viral genes modulate virulence in model mammal hosts and Culex pipiens vector competence in Mediterranean basin lineage 1 West Nile virus strains. Front Microbiol 2024; 14:1324069. [PMID: 38298539 PMCID: PMC10828019 DOI: 10.3389/fmicb.2023.1324069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024] Open
Abstract
West Nile virus (WNV) is a single-stranded positive-sense RNA virus (+ssRNA) belonging to the genus Orthoflavivirus. Its enzootic cycle involves mosquito vectors, mainly Culex, and wild birds as reservoir hosts, while mammals, such as humans and equids, are incidental dead-end hosts. It was first discovered in 1934 in Uganda, and since 1999 has been responsible for frequent outbreaks in humans, horses and wild birds, mostly in America and in Europe. Virus spread, as well as outbreak severity, can be influenced by many ecological factors, such as reservoir host availability, biodiversity, movements and competence, mosquito abundance, distribution and vector competence, by environmental factors such as temperature, land use and precipitation, as well as by virus genetic factors influencing virulence or transmission. Former studies have investigated WNV factors of virulence, but few have compared viral genetic determinants of pathogenicity in different host species, and even fewer have considered the genetic drivers of virus invasiveness and excretion in Culex vector. In this study, we characterized WNV genetic factors implicated in the difference in virulence observed in two lineage 1 WNV strains from the Mediterranean Basin, the first isolated during a significant outbreak reported in Israel in 1998, and the second from a milder outbreak in Italy in 2008. We used an innovative and powerful reverse genetic tool, e.g., ISA (infectious subgenomic amplicons) to generate chimeras between Israel 1998 and Italy 2008 strains, focusing on non-structural (NS) proteins and the 3'UTR non-coding region. We analyzed the replication of these chimeras and their progenitors in mammals, in BALB/cByJ mice, and vector competence in Culex (Cx.) pipiens mosquitoes. Results obtained in BALB/cByJ mice suggest a role of the NS2B/NS3/NS4B/NS5 genomic region in viral attenuation in mammals, while NS4B/NS5/3'UTR regions are important in Cx. pipiens infection and possibly in vector competence.
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Affiliation(s)
- Lise Fiacre
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
- UMR ASTRE, CIRAD, Petit-Bourg, Guadeloupe
| | - Antoine Nougairède
- Unité Des Virus Emergents (UVE), Aix-Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Camille Migné
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
| | | | - Maxime Cochin
- Unité Des Virus Emergents (UVE), Aix-Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Marine Dumarest
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Teheipuaura Helle
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Antoni Exbrayat
- ASTRE, CIRAD, INRAe, Université de Montpellier, Montpellier, France
| | | | - Damien Vitour
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Jennifer P. Richardson
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Anna-Bella Failloux
- Institut Pasteur, Université Paris Cité, Arboviruses and Insects Vectors, Paris, France
| | - Marie Vazeille
- Institut Pasteur, Université Paris Cité, Arboviruses and Insects Vectors, Paris, France
| | - Emmanuel Albina
- ASTRE, CIRAD, INRAe, Université de Montpellier, Montpellier, France
| | | | - Gaëlle Gonzalez
- UMR VIRO, ANSES, ENVA, INRAE Virologie, Laboratoire de Santé Animale, Maisons-Alfort, France
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6
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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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7
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Nogales A, Martínez-Sobrido L, Almazán F. Reverse Genetics of Zika Virus Using a Bacterial Artificial Chromosome. Methods Mol Biol 2024; 2733:185-206. [PMID: 38064034 DOI: 10.1007/978-1-0716-3533-9_12] [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
Zika virus (ZIKV) is a mosquito-borne member of the Flaviviridae family that has become a global threat to human health. Although ZIKV has been known to circulate for decades causing mild febrile illness, the more recent ZIKV outbreaks in the Americas and the Caribbean have been associated with severe neurological disorders and congenital abnormalities. The development of ZIKV reverse genetics approaches have allowed researchers to address key questions on the biology of ZIKV by genetically engineering infectious recombinant (r)ZIKV. This has resulted in a better understanding of the biology of ZIKV infections, including viral pathogenesis, molecular mechanisms of viral replication and transcription, or the interaction of viral and host factors, among others aspects. In addition, reverse genetics systems have facilitated the identification of anti-ZIKV compounds and the development of new prophylactic approaches to combat ZIKV infections. Different reverse genetics strategies have been implemented for the recovery of rZIKV. All these reverse genetics systems have faced and overcome multiple challenges, including the viral genome size, the toxicity of viral sequences in bacteria, etc. In this chapter we describe the generation of a ZIKV full-length complementary (c)DNA infectious clone based on the use of a bacterial artificial chromosome (BAC) and the experimental procedures for the successful recovery of rZIKV. Importantly, the protocol described in this chapter provides a powerful method for the generation of infectious clones of other flaviviruses with genomes that have stability problems during bacterial propagation.
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Affiliation(s)
- Aitor Nogales
- Centro de Investigación en Sanidad Animal (CISA-INIA/CSIC), Madrid, Spain
| | | | - Fernando Almazán
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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Comes JDG, Poniman M, van Oosten L, Doets K, de Cloe S, Geertsema C, Pijlman GP. Infectious clone of a contemporary Tembusu virus and replicons expressing reporter genes or heterologous antigens from poultry viruses. Biotechnol J 2024; 19:e2300254. [PMID: 37750498 DOI: 10.1002/biot.202300254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/30/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
The novel mosquito-borne Tembusu virus (TMUV, family Flaviviridae) was discovered as the cause of a severe outbreak of egg-drop syndrome affecting ducks in Southeast Asia in 2010. TMUV infection can also lead to high mortality in various additional avian species such as geese, pigeons, and chickens. This study describes the construction of an infectious cDNA clone of a contemporary duck-isolate (TMUV WU2016). The virus recovered after transfection of BHK-21 cells shows enhanced virus replication compared to the mosquito-derived MM1775 strain. Next, the WU2016 cDNA clone was modified to create a SP6 promoter-driven, self-amplifying mRNA (replicon) capable of expressing a range of different reporter genes (Renilla luciferase, mScarlet, mCherry, and GFP) and viral (glyco)proteins of avian influenza virus (AIV; family Orthomyxoviridae), infectious bursal disease virus (IDBV; family Bunyaviridae) and infectious bronchitis virus (IBV; family Coronaviridae). The current study demonstrates the flexibility of the TMUV replicon system, to produce different heterologous proteins over an extended period of time and its potential use as a platform technology for novel poultry vaccines.
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Affiliation(s)
- Jerome D G Comes
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Meliawati Poniman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Linda van Oosten
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Kristel Doets
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Sjoerd de Cloe
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Corinne Geertsema
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
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9
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Cai HL, Huang YW. Reverse genetics systems for SARS-CoV-2: Development and applications. Virol Sin 2023; 38:837-850. [PMID: 37832720 PMCID: PMC10786661 DOI: 10.1016/j.virs.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.
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Affiliation(s)
- Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Cherkashchenko L, Gros N, Trausch A, Neyret A, Hénaut M, Dubois G, Villeneuve M, Chable-Bessia C, Lyonnais S, Merits A, Muriaux D. Validation of flavivirus infectious clones carrying fluorescent markers for antiviral drug screening and replication studies. Front Microbiol 2023; 14:1201640. [PMID: 37779700 PMCID: PMC10541152 DOI: 10.3389/fmicb.2023.1201640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
Flaviviruses have emerged as major arthropod-transmitted pathogens and represent an increasing public health problem worldwide. High-throughput screening can be facilitated using viruses that easily express detectable marker proteins. Therefore, developing molecular tools, such as reporter-carrying versions of flaviviruses, for studying viral replication and screening antiviral compounds represents a top priority. However, the engineering of flaviviruses carrying either fluorescent or luminescent reporters remains challenging due to the genetic instability caused by marker insertion; therefore, new approaches to overcome these limitations are needed. Here, we describe reverse genetic methods that include the design and validation of infectious clones of Zika, Kunjin, and Dengue viruses harboring different reporter genes for infection, rescue, imaging, and morphology using super-resolution microscopy. It was observed that different flavivirus constructs with identical designs displayed strikingly different genetic stabilities, and corresponding virions resembled wild-type virus particles in shape and size. A successful strategy was assessed to increase the stability of rescued reporter virus and permit antiviral drug screening based on quantitative automated fluorescence microscopy and replication studies.
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Affiliation(s)
- Liubov Cherkashchenko
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Nathalie Gros
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
| | - Alice Trausch
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
| | - Aymeric Neyret
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
| | - Mathilde Hénaut
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
| | - Gregor Dubois
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
| | | | | | | | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Delphine Muriaux
- CEMIPAI UAR3725 CNRS, University of Montpellier, Montpellier, France
- IRIM UMR9004 CNRS, University of Montpellier, Montpellier, France
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Conde JN, Himmler GE, Mladinich MC, Setoh YX, Amarilla AA, Schutt WR, Saladino N, Gorbunova EE, Salamango DJ, Benach J, Kim HK, Mackow ER. Establishment of a CPER reverse genetics system for Powassan virus defines attenuating NS1 glycosylation sites and an infectious NS1-GFP11 reporter virus. mBio 2023; 14:e0138823. [PMID: 37489888 PMCID: PMC10470542 DOI: 10.1128/mbio.01388-23] [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: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/26/2023] Open
Abstract
Powassan virus (POWV) is an emerging tick-borne Flavivirus that causes lethal encephalitis and long-term neurologic damage. Currently, there are no POWV therapeutics, licensed vaccines, or reverse genetics systems for producing infectious POWVs from recombinant DNA. Using a circular polymerase extension reaction (CPER), we generated recombinant LI9 (recLI9) POWVs with attenuating NS1 protein mutations and a recLI9-split-eGFP reporter virus. NS1 proteins are highly conserved glycoproteins that regulate replication, spread, and neurovirulence. POWV NS1 contains three putative N-linked glycosylation sites that we modified individually in infectious recLI9 mutants (N85Q, N208Q, and N224Q). NS1 glycosylation site mutations reduced replication kinetics and were attenuated, with 1-2 log decreases in titer. Severely attenuated recLI9-N224Q exhibited a 2- to 3-day delay in focal cell-to-cell spread and reduced NS1 secretion but was lethal when intracranially inoculated into suckling mice. However, footpad inoculation of recLI9-N224Q resulted in the survival of 80% of mice and demonstrated that NS1-N224Q mutations reduce POWV neuroinvasion in vivo. To monitor NS1 trafficking, we CPER fused a split GFP11-tag to the NS1 C-terminus and generated an infectious reporter virus, recLI9-NS1-GFP11. Cells infected with recLI9-NS1-GFP11 revealed NS1 trafficking in live cells and the novel formation of large NS1-lined intracellular vesicles. An infectious recLI9-NS1-GFP11 reporter virus permits real-time analysis of NS1 functions in POWV replication, assembly, and secretion and provides a platform for evaluating antiviral compounds. Collectively, our robust POWV reverse genetics system permits analysis of viral spread and neurovirulence determinants in vitro and in vivo and enables the rational genetic design of live attenuated POWV vaccines. IMPORTANCE Our findings newly establish a mechanism for genetically modifying Powassan viruses (POWVs), systematically defining pathogenic determinants and rationally designing live attenuated POWV vaccines. This initial study demonstrates that mutating POWV NS1 glycosylation sites attenuates POWV spread and neurovirulence in vitro and in vivo. Our findings validate a robust circular polymerase extension reaction approach as a mechanism for developing, and evaluating, attenuated genetically modified POWVs. We further designed an infectious GFP-tagged reporter POWV that permits us to monitor secretory trafficking of POWV in live cells, which can be applied to screen potential POWV replication inhibitors. This robust system for modifying POWVs provides the ability to define attenuating POWV mutations and create genetically attenuated recPOWV vaccines.
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Affiliation(s)
- Jonas N. Conde
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Grace E. Himmler
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Megan C. Mladinich
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Yin Xiang Setoh
- Microbiology and Molecular Epidemiology Division, Environmental Health Institute, National Environmental Agency, Singapore, Singapore
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - William R. Schutt
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Nicholas Saladino
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Elena E. Gorbunova
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Daniel J. Salamango
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Jorge Benach
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Hwan Keun Kim
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
| | - Erich R. Mackow
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
- Molecular and Cell Biology Program, Stony Brook University, Stony Brook, New York, USA
- Center for Infectious Disease, Stony Brook University, Stony Brook, New York, USA
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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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Marano JM, Cereghino C, Finkielstein CV, Weger-Lucarelli J. An in vitro workflow to create and modify infectious clones using replication cycle reaction. Virology 2023; 585:109-116. [PMID: 37331111 PMCID: PMC10528026 DOI: 10.1016/j.virol.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/20/2023]
Abstract
Reverse genetics systems are critical tools in combating emerging viruses which enable a better understanding of the genetic mechanisms by which viruses cause disease. Traditional cloning approaches using bacteria are fraught with difficulties due to the bacterial toxicity of many viral sequences, resulting in unwanted mutations within the viral genome. Here, we describe a novel in vitro workflow that leverages gene synthesis and replication cycle reaction to produce a supercoiled infectious clone plasmid that is easy to distribute and manipulate. We developed two infectious clones as proof of concept: a low passage dengue virus serotype 2 isolate (PUO-218) and the USA-WA1/2020 strain of SARS-CoV-2, which replicated similarly to their respective parental viruses. Furthermore, we generated a medically relevant mutant of SARS-CoV-2, Spike D614G. Results indicate that our workflow is a viable method to generate and manipulate infectious clones for viruses that are notoriously difficult for traditional bacterial-based cloning methods.
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Affiliation(s)
- Jeffrey M Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
| | - Chelsea Cereghino
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
| | - Carla V Finkielstein
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA; Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
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14
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Park CJ, Lee YA, Yoo SM, Kim GA, Lee MS, Park C. Efficient reverse genetics approach involving infectious subgenomic amplicon for engineering dengue virus. J Med Virol 2023; 95:e28978. [PMID: 37515534 DOI: 10.1002/jmv.28978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
Dengue virus, which belongs to the Flaviviridae family, can induce a range of symptoms from mild to severe, including dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. While infectious cloning technology is a useful tool for understanding viral pathogenesis and symptoms, it exhibits limitations when constructing the entire Flavivirus genome. The instability and toxicity of the genome to bacteria make its full-length construction in bacterial vectors a time-consuming and laborious process. To address these challenges, we employed the modified infectious subgenomic amplicon (ISA) method in this study, which can potentially be a superior tool for reverse genetic studies on the dengue virus. Using ISA, we generated recombinant dengue viruses de novo and validated their robust replication in both human and insect cell lines, which was comparable to that of the original strains. Moreover, the efficiency of ISA in genetically modifying the dengue virus was elucidated by successfully inserting the gene for green fluorescence protein into the genome of dengue virus serotype 4. Overall, this study highlighted the effectiveness of ISA for genetically engineering the dengue virus and provided a technical basis for a convenient reverse genetics system that could expedite investigations into the dengue virus.
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Affiliation(s)
- Chang-Joo Park
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, Republic of Korea
| | - Yoon-A Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, Republic of Korea
| | - Seung-Min Yoo
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, Republic of Korea
| | - Geon A Kim
- Department of Biomedical Laboratory Science, School of Healthcare Science, Eulji University, Uijeongbu, Republic of Korea
| | - Myung-Shin Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, Republic of Korea
| | - Changhoon Park
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, Republic of Korea
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15
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Sion E, Ab-Rahim S, Muhamad M. Trends on Human Norovirus Virus-like Particles (HuNoV-VLPs) and Strategies for the Construction of Infectious Viral Clones toward In Vitro Replication. Life (Basel) 2023; 13:1447. [PMID: 37511822 PMCID: PMC10381778 DOI: 10.3390/life13071447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/30/2023] Open
Abstract
Most acute gastroenteritis (AGE) outbreaks and sporadic cases in developing countries are attributable to infection by human norovirus (HuNoV), the enteric virus mainly transmitted via fecal-contaminated water. However, it has been challenging to study HuNoV due to the lack of suitable systems to cultivate and replicate the virus, hindering the development of treatments and vaccines. Researchers have been using virus-like particles (VLPs) and infectious viral clones to overcome this challenge as alternatives to fresh virus isolates in various in vitro and ex vivo models. VLPs are multiprotein structures that mimic the wild-type virus but cannot replicate in host cells due to the lack of genetic materials for replication, limiting downstream analysis of the virus life cycle and pathogenesis. The development of in vitro cloning systems has shown promise for HuNoV replication studies. This review discusses the approaches for constructing HuNoV-VLPs and infectious viral clones, the techniques involved, and the challenges faced. It also highlights the relationship between viral genes and their protein products and provides a perspective on technical considerations for producing efficient HuNoV-VLPs and infectious viral clones, which could substitute for native human noroviruses in future studies.
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Affiliation(s)
- Emilly Sion
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Selangor Branch, Sungai Buloh Campus, Sungai Buloh 47000, Selangor, Malaysia
| | - Sharaniza Ab-Rahim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Selangor Branch, Sungai Buloh Campus, Sungai Buloh 47000, Selangor, Malaysia
| | - Mudiana Muhamad
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Selangor Branch, Sungai Buloh Campus, Sungai Buloh 47000, Selangor, Malaysia
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16
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Li C, Zhang L, Chen X, Jiang D, Hu J, Guo J, Ding J, Jiao X, Bao W, Li Y. Evaluation of the genotype I Japanese encephalitis virus as a stable viral vector for foreign gene expression. Antiviral Res 2023:105652. [PMID: 37301446 DOI: 10.1016/j.antiviral.2023.105652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Manipulation of the flavivirus genome to accommodate and express a heterologous gene of interest has become an attractive approach for gene delivery and the development of viral-vectored vaccines. However, due to the inherent genetic instability of the flavivirus genomes, the construction of recombinant viruses carrying a foreign gene could be problematic and heavily resistant. In this study, the possibility of the Japanese encephalitis virus (JEV) as a stable flavivirus vector for the expression of a foreign gene was assessed using reverse genetics. The full-length cDNA genome of genotype I (GI) JEV inherently possessed excellent stability and manipulability in a bacterial host, while mutations and deletions accumulated in the cDNA genomes of genotype Ⅲ (GⅢ) JEV strains. Using the GI JEV as backbones, we generate a panel of recombinant viruses expressing various foreign genes. All recombinant viruses exhibited excellent genetic stability and efficiently express foreign genes for at least ten serial passages in vitro. In application, a convenient, rapid and reliable image-based assay for neutralizing antibody testing and antiviral drug discovery was established with a mCherry-reporter recombinant virus (rBJ-mCherry). Meanwhile, the recombinant viruses expressing the antigens of the African swine fever virus (ASFV) or Classical swine fever virus (CSFV) could effectively induce antibody responses to the JEV vector and foreign antigens in a mouse vaccination model. Therefore, GI JEV strains could serve as viral vectors accommodating the expression of large foreign genes.
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Affiliation(s)
- Chenxi Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Linjie Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Xuan Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Daoyuan Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Jingbo Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Jinyao Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Jingjing Ding
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Xue Jiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yanhua Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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17
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Lin SC, Bai GH, Lin PC, Chen CY, Hsu YH, Lee YC, Chen SY. Molecular and Genetics-Based Systems for Tracing the Evolution and Exploring the Mechanisms of Human Norovirus Infections. Int J Mol Sci 2023; 24:ijms24109093. [PMID: 37240438 DOI: 10.3390/ijms24109093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Human noroviruses (HuNoV) are major causes of acute gastroenteritis around the world. The high mutation rate and recombination potential of noroviruses are significant challenges in studying the genetic diversity and evolution pattern of novel strains. In this review, we describe recent advances in the development of technologies for not only the detection but also the analysis of complete genome sequences of noroviruses and the future prospects of detection methods for tracing the evolution and genetic diversity of human noroviruses. The mechanisms of HuNoV infection and the development of antiviral drugs have been hampered by failure to develop the infectious virus in a cell model. However, recent studies have demonstrated the potential of reverse genetics for the recovery and generation of infectious viral particles, suggesting the utility of this genetics-based system as an alternative for studying the mechanisms of viral infection, such as cell entry and replication.
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Affiliation(s)
- Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Division of Allergy, Asthma, and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Geng-Hao Bai
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei City 10002, Taiwan
| | - Pei-Chun Lin
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
- Center for Nanotechnology, Institute of Biomedical Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuan-Chang Lee
- Department of Infectious Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Department of Infectious Diseases, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei City 11031, Taiwan
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Liu G, Gack MU. An optimized circular polymerase extension reaction-based method for functional analysis of SARS-CoV-2. Virol J 2023; 20:63. [PMID: 37029393 PMCID: PMC10080526 DOI: 10.1186/s12985-023-02025-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Reverse genetics systems have been crucial for studying specific viral genes and their relevance in the virus lifecycle, and become important tools for the rational attenuation of viruses and thereby for vaccine design. Recent rapid progress has been made in the establishment of reverse genetics systems for functional analysis of SARS-CoV-2, a coronavirus that causes the ongoing COVID-19 pandemic that has resulted in detrimental public health and economic burden. Among the different reverse genetics approaches, circular polymerase extension reaction (CPER) has become one of the leading methodologies to generate recombinant SARS-CoV-2 infectious clones. Although CPER has greatly facilitated SARS-CoV-2 analysis, it still has certain intrinsic limitations that impede the efficiency and robustness of virus rescue. RESULTS We developed an optimized CPER methodology which, through the use of a modified linker plasmid and by performing DNA nick ligation and direct transfection of permissive cells, overcomes certain intrinsic limitations of the 'traditional' CPER approaches for SARS-CoV-2, allowing for efficient virus rescue. CONCLUSIONS The herein described optimized CPER system may facilitate research studies to assess the contribution of SARS-CoV-2 genes and individual motifs or residues to virus replication, pathogenesis and immune escape, and may also be adapted to other viruses.
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Affiliation(s)
- GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
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Guo J, He Y, Wang X, Merits A, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Gao Q, Sun D, Tian B, Cheng A, Chen S. Attenuation of Avian Flavivirus by Rewiring the Leucine and Serine Codons of Its E-NS1 Protein toward Stop Mutation To Redirect Virus Evolution. Microbiol Spectr 2023; 11:e0292122. [PMID: 36625643 PMCID: PMC9927255 DOI: 10.1128/spectrum.02921-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/21/2022] [Indexed: 01/11/2023] Open
Abstract
Recently, a new strategy for attenuating RNA viruses by redirecting their evolution in sequence space was confirmed for Enterovirus and Influenza viruses. Using avian flavivirus as a model, the 69 serine and 53 leucine codons on the E-NS1 genes were modified to change evolutionary direction of the viral sequence space. This means that all codons encoding serine or leucine residues were substituted with codons that are only one base different from the three stop codons, resulting in the initial position of the virus genome in sequence space being closer to the detrimental areas to achieve attenuation by reducing viral adaptability. The growth curve and plaque size of CQW1-one-to-stop (CQW1-OTS) were similar to those of CQW1-wild type (CQW1-WT) in vitro, but attenuated proliferation was detected when treated with a mutagenic reagent (ribavirin). However, comparably high CQW1-OTS and CQW1-WT lethality rates were detected in 9-day-old duck embryos and 5-day-old ducklings, suggesting that this strategy works but with limitations. With that in mind, homologous hosts in nonsensitive age (25-day-old ducks) and heterologous hosts (3-week-old Kunming mice) were employed to investigate if CQW1-OTS was attenuated under host selection pressure. Minimal attenuation of CQW1-OTS in elder ducks and apparent attenuation in mice were reported, providing reduced viral titers, mild clinical signs, and lower specific infectivity. Collectively, we experimentally demonstrate that the attenuation strategy of redirecting virus evolution in sequence space works for flavivirus. Redirection of the virus is attenuated only under some outside pressure, such as heterologous hosts or antiviral drugs treatment, limiting its usage in flaviviruses. IMPORTANCE Flaviviruses are medically important arboviruses that threaten public health, but no approved treatments are currently available. Vaccines prevent flavivirus infection. We employed duck Tembusu virus (TMUV), a mosquito-borne flavivirus, to evaluate virus redirection. TMUV is native to birds and could infect mice by intracerebral injection, making it an experimental animal model to study flavivirus characteristics in vivo. The 69 serine and 53 leucine codons on the E-NS1 proteins of CQW1 were synonymously substituted to change evolutionary direction of the virus in sequence space. In vitro mutagen reagent treatment suppressed CQW1-OTS viral multiplication, but in vivo attenuation depended on host selective pressure. CQW1-OTS viral attenuation was observed in older ducks but not sensitive ducklings; considerable attenuation was also observed in heterogenous host (mice), which provides more selective pressure on viruses. Collectively, these data indicated that there are very important preconditions for application of evaluating whether this strategy shows application prospects in novel flavivirus vaccine development.
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Affiliation(s)
- Jiaqi Guo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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Kurhade C, Xie X, Shi PY. Reverse genetic systems of SARS-CoV-2 for antiviral research. Antiviral Res 2023; 210:105486. [PMID: 36657881 PMCID: PMC9776485 DOI: 10.1016/j.antiviral.2022.105486] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Reverse genetic systems are widely used to engineer recombinant viruses with desired mutations. In response to the COVID-19 pandemic, four types of reverse genetic systems have been developed for SARS-CoV-2: (i) a full-length infectious clone that can be used to prepare recombinant SARS-CoV-2 at biosafety level 3 (BSL3), (ii) a trans-complementation system that can be used to produce single-round infectious SARS-CoV-2 at BSL2, (iii) an attenuated SARS-CoV-2 vaccine candidate (with deletions of viral accessory genes) that may be developed for veterinary use as well as for antiviral screening at BSL2, and (iv) replicon systems with deletions of viral structural genes that can be used at BSL2. Each of these genetic systems has its advantages and disadvantages that can be used to address different questions for basic and translational research. Due to the long genomic size and bacteria-toxic sequences of SARS-CoV-2, several experimental approaches have been established to rescue recombinant viruses and replicons, including (i) in vitro DNA ligation, (ii) bacterial artificial chromosome (BAC) system, (iii) yeast artificial chromosome (YAC) system, and (iv) circular polymerase extension reaction (CPER). This review summarizes the current status of SARS-CoV-2 genetic systems and their applications for studying viral replication, pathogenesis, vaccines, and therapeutics.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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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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Accidental acquisition of a rescued Japanese encephalitis virus with unspliced introns in the viral genome when using an intron-based stabilization approach. Arch Virol 2023; 168:60. [PMID: 36629974 PMCID: PMC9833022 DOI: 10.1007/s00705-022-05697-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/28/2022] [Indexed: 01/12/2023]
Abstract
The intron-based stabilization approach is a very useful strategy for construction of stable flavivirus infectious clones. SA14-14-2 is a highly attenuated Japanese encephalitis (JE) live vaccine strain that has been widely used in China since 1989. To develop safe and effective recombinant vaccines with SA14-14-2 as a backbone vector, we constructed the DNA-based infectious clone pCMW-JEV of SA14-14-2 using the intron-based stabilization approach and acquired the rescued virus rDJEV, which retained the biological properties of the parental virus. Unexpectedly, a rescued virus strain with altered virulence, designated rHV-DJEV, was accidentally acquired in one of the transfection experiments. rHV-DJEV showed up to 105-fold increased neurovirulence compared with the SA14-14-2 parental strain. Genome sequencing showed that the inserted introns were still present in the genome of rHV-DJEV. Therefore, we think that the intron-based stabilization approach should be used with caution in vaccine development and direct iDNA immunization.
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23
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Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies. Pathogens 2022; 11:pathogens11121502. [PMID: 36558837 PMCID: PMC9781818 DOI: 10.3390/pathogens11121502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the effectiveness of the nonspecific sequencing technique sequence-independent single primer amplification (SISPA) on third-generation sequencing techniques (MinION sequencing, Oxford Nanopore Technologies, Oxford, UK) by comparing the sequencing results from six different samples of arboviruses known to be circulating in Africa (Crimean-Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), Dugbe virus (DUGV), Nairobi sheep disease virus (NSDV), Middleburg virus (MIDV) and Wesselsbron virus (WSLV)). All sequenced samples were derived either from previous field studies or animal infection trials. Using this approach, we were able to generate complete genomes for all six viruses without the need for virus-specific whole-genome PCRs. Higher Cq values in diagnostic RT-qPCRs and the origin of the samples (from cell culture or animal origin) along with their quality were found to be factors affecting the success of the sequencing run. The results of this study may stimulate the use of metagenomic sequencing approaches, contributing to a better understanding of the genetic diversity of neglected arboviruses.
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Liu G, Gack MU. An Optimized Circular Polymerase Extension Reaction-based Method for Functional Analysis of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.26.518005. [PMID: 36482966 PMCID: PMC9727755 DOI: 10.1101/2022.11.26.518005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Reverse genetics systems have been crucial for studying specific viral genes and their relevance in the virus lifecycle, and become important tools for the rational attenuation of viruses and thereby for vaccine design. Recent rapid progress has been made in the establishment of reverse genetics systems for functional analysis of SARS-CoV-2, a coronavirus that causes the ongoing COVID-19 pandemic that has resulted in detrimental public health and economic burden. Among the different reverse genetics approaches, CPER (circular polymerase extension reaction) has become one of the leading methodologies to generate recombinant SARS-CoV-2 infectious clones due to its accuracy, efficiency, and flexibility. Here, we report an optimized CPER methodology which, through the use of a modified linker plasmid and by performing DNA nick ligation and direct transfection of permissive cells, overcomes certain intrinsic limitations of the 'traditional' CPER approaches for SARS-CoV-2, allowing for efficient virus rescue. This optimized CPER system may facilitate research studies to assess the contribution of SARS-CoV-2 genes and individual motifs or residues to virus replication, pathogenesis and immune escape, and may also be adapted to other viruses.
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Huang Y, Zhang H, Li X, Zhao L, Cai D, Wang S, Ren N, Ma H, Huang D, Wang F, Yuan Z, Zhang B, Xia H. In Vitro and In Vivo Characterization of a New Strain of Mosquito Flavivirus Derived from Culicoides. Viruses 2022; 14:v14061298. [PMID: 35746769 PMCID: PMC9229015 DOI: 10.3390/v14061298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
Mosquito-specific flaviviruses comprise a group of insect-specific viruses with a single positive RNA, which can affect the duplication of mosquito-borne viruses and the life growth of mosquitoes, and which have the potential to be developed as a vaccine platform for mosquito-borne viruses. In this study, a strain of mosquito flavivirus (MFV) YN15-283-02 was detected in Culicoides collected from Yunnan, China. The isolation of the purified MFV YN15-283-02 from cell culture failed, and the virus was then rescued by an infectious clone. To study the biological features of MFV YN15-283-02 in vitro and in vivo, electron microscopy, phylogenetic tree, and viral growth kinetic analyses were performed in both cell lines and mosquitoes. The rescued MFV (rMFV) YN15-283-02 duplicated and reached a peak in C6/36 cells at 6 d.p.i. with approximately 2 × 106 RNA copies/μL (RNA to cell ratio of 0.1), but without displaying a cytopathic effect. In addition, the infection rate for the rMFV in Ae.aegypti show a low level in both larvae (≤15%) and adult mosquitoes (≤12%).
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Affiliation(s)
- Yi Huang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaodan Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
| | - Lu Zhao
- Westlake Disease Modeling Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China;
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Dirui Cai
- School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Shunlong Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nanjie Ren
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Ma
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
| | - Doudou Huang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
| | - Fei Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (B.Z.); (H.X.); Tel.: +86-27-87197607 (B.Z.); +86-27-87198120 (H.X.)
| | - Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (Y.H.); (H.Z.); (X.L.); (S.W.); (N.R.); (H.M.); (D.H.); (F.W.); (Z.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (B.Z.); (H.X.); Tel.: +86-27-87197607 (B.Z.); +86-27-87198120 (H.X.)
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Fang E, Liu X, Li M, Liu J, Zhang Z, Liu X, Li X, Li W, Peng Q, Yu Y, Li Y. Construction of a Dengue NanoLuc Reporter Virus for In Vivo Live Imaging in Mice. Viruses 2022; 14:v14061253. [PMID: 35746724 PMCID: PMC9230669 DOI: 10.3390/v14061253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Since the first isolation in 1943, the dengue virus (DENV) has spread throughout the world, but effective antiviral drugs or vaccines are still not available. To provide a more stable reporter DENV for vaccine development and antiviral drug screening, we constructed a reporter DENV containing the NanoLuc reporter gene, which was inserted into the 5′ untranslated region and capsid junction region, enabling rapid virus rescue by in vitro ligation. In addition, we established a live imaging mouse model and found that the reporter virus maintained the neurovirulence of prototype DENV before engineering. DENV-4 exhibited dramatically increased neurovirulence following a glycosylation site-defective mutation in the envelope protein. Significant mice mortality with neurological onset symptoms was observed after intracranial infection of wild-type (WT) mice, thus providing a visualization tool for DENV virulence assessment. Using this model, DENV was detected in the intestinal tissues of WT mice after infection, suggesting that intestinal lymphoid tissues play an essential role in DENV pathogenesis.
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Affiliation(s)
- Enyue Fang
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
- Wuhan Institute of Biological Products, Co., Ltd., Wuhan 430207, China
| | - Xiaohui Liu
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Miao Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Jingjing Liu
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Zelun Zhang
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Xinyu Liu
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Xingxing Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Wenjuan Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Qinhua Peng
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
| | - Yongxin Yu
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
- Correspondence: (Y.Y.); (Y.L.); Tel.: +86-010-5385-2137 (Y.Y.); +86-010-5385-2128 (Y.L.)
| | - Yuhua Li
- Department of Arbovirus Vaccine, National Institutes for Food and Drug Control, Beijing 102629, China; (E.F.); (X.L.); (M.L.); (J.L.); (Z.Z.); (X.L.); (X.L.); (W.L.); (Q.P.)
- Correspondence: (Y.Y.); (Y.L.); Tel.: +86-010-5385-2137 (Y.Y.); +86-010-5385-2128 (Y.L.)
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Construction and characterization of a full-length infectious clone of Getah virus in vivo. Virol Sin 2022; 37:348-357. [PMID: 35288349 PMCID: PMC9243596 DOI: 10.1016/j.virs.2022.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Getah virus (GETV) is a mosquito-borne virus of the genus Alphavirus in the family Togaviridae and, in recent years, it has caused several outbreaks in animals. The molecular basis for GETV pathogenicity is not well understood. Therefore, a reverse genetic system of GETV is needed to produce genetically modified viruses for the study of the viral replication and its pathogenic mechanism. Here, we generated a CMV-driven infectious cDNA clone based on a previously isolated GETV strain, GX201808 (pGETV-GX). Transfection of pGETV-GX into BHK-21 cells resulted in the recovery of a recombinant virus (rGETV-GX) which showed similar growth characteristics to its parental virus. Then three-day-old mice were experimentally infected with either the parental or recombinant virus. The recombinant virus showed milder pathogenicity than the parental virus in the mice. Based on the established CMV-driven cDNA clone, subgenomic promoter and two restriction enzyme sites (BamHI and EcoRI) were introduced into the region between E1 protein and 3′UTR. Then the green fluorescent protein (GFP), red fluorescent protein (RFP) and improved light-oxygen-voltage (iLOV) genes were inserted into the restriction enzyme sites. Transfection of the constructs carrying the reporter genes into BHK-21 cells proved the rescue of the recombinant reporter viruses. Taken together, the establishment of a reverse genetic system for GETV provides a valuable tool for the study of the virus life cycle, and to aid the development of genetically engineered GETVs as vectors for foreign gene expression. Generation and recovery of a CMV-driven infectious cDNA clone of GETV isolate, GX201808 (pGETV-GX). The recombinant virus showed milder pathogenicity than the parental virus in a mouse model. The Getah virus infectious clone can be used as a vector for expressing reporter genes.
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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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Novel reverse genetics of genotype I and III Japanese encephalitis viruses assembled through transformation associated recombination in yeast: The reporter viruses expressing a green fluorescent protein for the antiviral screening assay. Antiviral Res 2022; 197:105233. [DOI: 10.1016/j.antiviral.2021.105233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/24/2022]
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Qin Z, Chen Y, Yu J, He X, Liu X, Zhu L, Wu Q, Wan C, Zhang B, Zhao W. Rapid Construction of an Infectious Clone of the Zika Virus, Strain ZKC2. Front Microbiol 2021; 12:752578. [PMID: 34745057 PMCID: PMC8567171 DOI: 10.3389/fmicb.2021.752578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 11/26/2022] Open
Abstract
Zika virus (ZIKV) has had detrimental effects on global public health in recent years. This is because the management of the disease has been limited, in part because its pathogenic mechanisms are not yet completely understood. Infectious clones are an important tool that utilize reverse genetics; these can be used to modify the ZIKV genomic RNA at the DNA level. A homologous recombination clone was used to construct pWSK29, a low copy plasmid that contained sequences for a T7 promoter, the whole genome of ZIKV ZKC2 strain, and a hepatitis delta virus ribozyme. High fidelity PCR was then used to amplify the T7 transcription template. The transcript was then transfected into susceptible cells via lipofection to recover the ZIKV ZKC2 strain. Finally, the virulence of rZKC2 was evaluated both in vitro and in vivo. The rZKC2 was successfully obtained and it showed the same virulence as its parent, the ZIKV ZKC2 strain (pZKC2), both in vitro and in vivo. The 3730 (NS2A-D62G) mutation site was identified as being important, since it had significant impacts on rZKC2 recovery. The 4015 (NS2A, A157V) mutation may reduce virus production by increasing the interferon type I response. In this study, one of the earliest strains of ZIKV that was imported into China was used for infectious clone construction and one possible site for antiviral medication development was discovered. The use of homologous recombination clones, of PCR products as templates for T7 transcription, and of lipofection for large RNA transfection could increase the efficiency of infectious clone construction. Our infectious clone provides an effective tool which can be used to explore the life cycle and medical treatment of ZIKV.
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Affiliation(s)
- Zhiran Qin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yangyang Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jianhai Yu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xiaoen He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xuling Liu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Li Zhu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qinghua Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Chengsong Wan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Bao Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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Recovery of a Far-Eastern Strain of Tick-Borne Encephalitis Virus with a Full-Length Infectious cDNA Clone. Virol Sin 2021; 36:1375-1386. [PMID: 34191223 DOI: 10.1007/s12250-021-00396-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a pathogenic virus known to cause central nervous system (CNS) diseases in humans, and has become an increasing public health threat nowadays. The rates of TBEV infection in the endemic countries are increasing. However, there is no effective antiviral against the disease. This underscores the urgent need for tools to study the emergence and pathogenesis of TBEV and to accelerate the development of vaccines and antivirals. In this study, we reported an infectious cDNA clone of TBEV that was isolated in China (the WH2012 strain). A beta-globin intron was inserted in the coding region of nonstructural protein 1 (NS1) gene to improve the stability of viral genome in bacteria. In mammalian cells, the inserted intron was excised and spliced precisely, which did not lead to the generation of inserted mutants. High titers of infectious progeny viruses were generated after the transfection of the infectious clone. The cDNA-derived TBEV replicated efficiently, and caused typical cytopathic effect (CPE) and plaques in BHK-21 cells. In addition, the CPE and growth curve of cDNA-derived virus were similar to that of its parental isolate in cells. Together, we have constructed the first infectious TBEV cDNA clone in China, and the clone can be used to investigate the genetic determinants of TBEV virulence and disease pathogenesis, and to develop countermeasures against the virus.
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Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications. BIOLOGY 2021; 10:biology10070604. [PMID: 34209952 PMCID: PMC8301103 DOI: 10.3390/biology10070604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary Begomovirus has a wide host range and threatens a significant amount of economic damage to many important crops such as tomatoes, beans, cassava, squash and cotton. There are many efforts directed at controlling this disease including the use of insecticides to control the insect vector as well as screening the resistant varieties. The use of synthetic virus or infectious clones approaches has allowed plant virologists to characterize and exploit the genome virus at the molecular and biological levels. By exploiting the DNA of the virus using the infectious clones strategy, the viral genome can be manipulated at specific regions to study functional genes for host–virus interactions. Thus, this review will provide an overview of the strategy to construct infectious clones of Begomovirus. The significance of established infectious clones in Begomovirus study will also be discussed. Abstract Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.
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33
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Facile method for delivering chikungunya viral replicons into mosquitoes and mammalian cells. Sci Rep 2021; 11:12321. [PMID: 34112897 PMCID: PMC8192953 DOI: 10.1038/s41598-021-91830-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022] Open
Abstract
Reverse genetics is an important tool in the elucidation of viral replication and the development of countermeasures; however, these methods are impeded by laborious and inefficient replicon delivery methods. This paper demonstrates the use of a baculovirus to facilitate the efficient delivery of autonomous CHIKV replicons into mosquito and mammalian cells in vitro as well as adult mosquitoes in vivo. The efficacy of this approach was verified via co-localization among an eGFP reporter, nsP1, and dsRNA as well as through the inhibition of an RNA-dependent RNA polymerase (RdRp) null mutation (DDAA) in nsP4, or the treatment of a known antiviral compound (6-azauridine). We also investigated the correlation between CHIKV replicon-launched eGFP expression and the effectiveness of CHIKV replicon variants in inducing IFN-β expression in human cell lines. This delivery method based on a single vector is applicable to mosquito and mammalian cells in seeking to decipher the mechanisms underlying CHIKV replication, elucidate virus-host interactions, and develop antivirals. This study presents an effective alternative to overcome many of the technological issues related to the study and utilization of autonomous arbovirus replicons.
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Amarilla AA, Sng JDJ, Parry R, Deerain JM, Potter JR, Setoh YX, Rawle DJ, Le TT, Modhiran N, Wang X, Peng NYG, Torres FJ, Pyke A, Harrison JJ, Freney ME, Liang B, McMillan CLD, Cheung STM, Guevara DJDC, Hardy JM, Bettington M, Muller DA, Coulibaly F, Moore F, Hall RA, Young PR, Mackenzie JM, Hobson-Peters J, Suhrbier A, Watterson D, Khromykh AA. A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses. Nat Commun 2021; 12:3431. [PMID: 34103499 PMCID: PMC8187723 DOI: 10.1038/s41467-021-23779-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We demonstrate that despite the large size of the viral RNA genome (~30 kb), infectious full-length cDNA is readily assembled in vitro by a circular polymerase extension reaction (CPER) methodology without the need for technically demanding intermediate steps. Overlapping cDNA fragments are generated from viral RNA and assembled together with a linker fragment containing CMV promoter into a circular full-length viral cDNA in a single reaction. Transfection of the circular cDNA into mammalian cells results in the recovery of infectious SARS-CoV-2 virus that exhibits properties comparable to the parental virus in vitro and in vivo. CPER is also used to generate insect-specific Casuarina virus with ~20 kb genome and the human pathogens Ross River virus (Alphavirus) and Norovirus (Calicivirus), with the latter from a clinical sample. Additionally, reporter and mutant viruses are generated and employed to study virus replication and virus-receptor interactions. Here the authors describe a simple reverse genetics method that relies on overlapping cDNA fragments for generation of positive-strand viruses including SARS-CoV-2 and characterize them in vitro and in vivo.
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Affiliation(s)
- Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Julian D J Sng
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Joshua M Deerain
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - James R Potter
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Yin Xiang Setoh
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,Microbiology and Molecular Epidemiology Division, Environmental Health Institute, National Environmental Agency, Singapore, Singapore
| | - Daniel J Rawle
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Thuy T Le
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Xiaohui Wang
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Nias Y G Peng
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Francisco J Torres
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Alyssa Pyke
- Queensland Health Forensic & Scientific Services, Queensland Department of Health, Coopers Plains, QLD, Australia
| | - Jessica J Harrison
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Morgan E Freney
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Benjamin Liang
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Christopher L D McMillan
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Stacey T M Cheung
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | | | - Joshua M Hardy
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Mark Bettington
- School of Medicine, University of Queensland, Kelvin Grove, QLD, Australia
| | - David A Muller
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Fasséli Coulibaly
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Frederick Moore
- Queensland Health Forensic & Scientific Services, Queensland Department of Health, Coopers Plains, QLD, Australia
| | - Roy A Hall
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Paul R Young
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
| | - Alexander A Khromykh
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
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35
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Burton TD, Eyre NS. Applications of Deep Mutational Scanning in Virology. Viruses 2021; 13:1020. [PMID: 34071591 PMCID: PMC8227372 DOI: 10.3390/v13061020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Several recently developed high-throughput techniques have changed the field of molecular virology. For example, proteomics studies reveal complete interactomes of a viral protein, genome-wide CRISPR knockout and activation screens probe the importance of every single human gene in aiding or fighting a virus, and ChIP-seq experiments reveal genome-wide epigenetic changes in response to infection. Deep mutational scanning is a relatively novel form of protein science which allows the in-depth functional analysis of every nucleotide within a viral gene or genome, revealing regions of importance, flexibility, and mutational potential. In this review, we discuss the application of this technique to RNA viruses including members of the Flaviviridae family, Influenza A Virus and Severe Acute Respiratory Syndrome Coronavirus 2. We also briefly discuss the reverse genetics systems which allow for analysis of viral replication cycles, next-generation sequencing technologies and the bioinformatics tools that facilitate this research.
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Affiliation(s)
| | - Nicholas S. Eyre
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia;
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36
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Tangudu CS, Charles J, Nunez-Avellaneda D, Hargett AM, Brault AC, Blitvich BJ. Chimeric Zika viruses containing structural protein genes of insect-specific flaviviruses cannot replicate in vertebrate cells due to entry and post-translational restrictions. Virology 2021; 559:30-39. [PMID: 33812340 DOI: 10.1016/j.virol.2021.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/04/2021] [Accepted: 03/21/2021] [Indexed: 02/06/2023]
Abstract
Long Pine Key virus (LPKV) and Lammi virus are insect-specific flaviviruses that phylogenetically affiliate with dual-host flaviviruses. The goal of this study was to provide insight into the genetic determinants that condition this host range restriction. Chimeras were initially created by replacing select regions of the Zika virus genome, including the premembrane and envelope protein (prM-E) genes, with the corresponding regions of the LPKV genome. Of the four chimeras produced, one (the prM-E swap) yielded virus that replicated in mosquito cells. Another chimeric virus with a mosquito replication-competent phenotype was created by inserting the prM-E genes of Lammi virus into a Zika virus genetic background. Vertebrate cells did not support the replication of either chimeric virus although trace to modest amounts of viral antigen were produced, consistent with suboptimal viral entry. These data suggest that dual-host affiliated insect-specific flaviviruses cannot replicate in vertebrate cells due to entry and post-translational restrictions.
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Affiliation(s)
- Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Daniel Nunez-Avellaneda
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Alissa M Hargett
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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cDNA-Derived RNA Phage Assembly Reveals Critical Residues in the Maturation Protein of the Pseudomonas aeruginosa Leviphage PP7. J Virol 2021; 95:JVI.01643-20. [PMID: 33177196 DOI: 10.1128/jvi.01643-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/30/2020] [Indexed: 11/20/2022] Open
Abstract
PP7 is a leviphage, with a single-stranded RNA genome, that infects Pseudomonas aeruginosa PAO1. A reverse genetic system for PP7 was previously created by using reverse-transcribed cDNA (PP7O) from a virion-derived RNA genome. Here, we have found that the PP7O cDNA contained 20 nucleotide differences from the PP7 genome sequence deposited in the database. We created another reverse genetic system exploiting chemically synthesized cDNA (PP7S) based on the database sequence. Unlike PP7O, which yielded infectious PP7 virions, PP7S-derived particles were incapable of plaque formation on PAO1 cells, which was restored in the PAO1 cells expressing the maturation protein (MP) from PP7O Using this reverse genetic system, we revealed two amino acid residues involved in the known roles of MP (i.e., adsorption and genome replication), fortuitously providing a lesson that the viral RNA genome sequencing needs functional verification, possibly by a reverse genetic system.IMPORTANCE The biological significance of RNA phages has been largely ignored, ironically, because few studies have focused on RNA phages. As an initial attempt to properly represent RNA phages in the phageome, we previously created, by using reverse-transcribed cDNA, a reverse genetic system for the small RNA phage PP7, which infects the opportunistic human pathogen Pseudomonas aeruginosa We report another system by using chemically synthesized cDNA based on the database genome that has 20 nucleotide differences from the previous cDNA. Investigation of those cDNA-derived phage virions revealed that two amino acids of the maturation protein are crucial for the normal phage lifecycle at different steps. Our study provides insight into the molecular basis for the RNA phage lifecycle and a lesson that the RNA genome sequencing needs to be carefully validated by cDNA-based phage assembly systems.
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38
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Bates TA, Chuong C, Hawks SA, Rai P, Duggal NK, Weger-Lucarelli J. Development and characterization of infectious clones of two strains of Usutu virus. Virology 2020; 554:28-36. [PMID: 33352463 DOI: 10.1016/j.virol.2020.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022]
Abstract
Usutu virus (USUV; genus Flavivirus; family Flaviviridae) is a mosquito-borne, positive-sense RNA virus that is currently causing significant die-offs in numerous bird species throughout Europe and has caused infections in humans. Currently, there are no molecular clones for USUV, hence, hindering studies on the pathogenesis and transmission of USUV. Here, we demonstrate the development and characterization of infectious clones for two modern strains of USUV isolated from Europe and Africa. We show that the infectious clone-derived viruses replicated similarly to the parental strains in mammalian and insect cells. Additionally, we observed similar levels of replication and disease in two mouse models. These clones will aid the study of USUV infection, transmission, diagnostics, and vaccines.
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Affiliation(s)
- Tyler A Bates
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA
| | - Christina Chuong
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA
| | - Seth A Hawks
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA
| | - Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA
| | - Nisha K Duggal
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA.
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39
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Fiacre L, Pagès N, Albina E, Richardson J, Lecollinet S, Gonzalez G. Molecular Determinants of West Nile Virus Virulence and Pathogenesis in Vertebrate and Invertebrate Hosts. Int J Mol Sci 2020; 21:ijms21239117. [PMID: 33266206 PMCID: PMC7731113 DOI: 10.3390/ijms21239117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
West Nile virus (WNV), like the dengue virus (DENV) and yellow fever virus (YFV), are major arboviruses belonging to the Flavivirus genus. WNV is emerging or endemic in many countries around the world, affecting humans and other vertebrates. Since 1999, it has been considered to be a major public and veterinary health problem, causing diverse pathologies, ranging from a mild febrile state to severe neurological damage and death. WNV is transmitted in a bird–mosquito–bird cycle, and can occasionally infect humans and horses, both highly susceptible to the virus but considered dead-end hosts. Many studies have investigated the molecular determinants of WNV virulence, mainly with the ultimate objective of guiding vaccine development. Several vaccines are used in horses in different parts of the world, but there are no licensed WNV vaccines for humans, suggesting the need for greater understanding of the molecular determinants of virulence and antigenicity in different hosts. Owing to technical and economic considerations, WNV virulence factors have essentially been studied in rodent models, and the results cannot always be transported to mosquito vectors or to avian hosts. In this review, the known molecular determinants of WNV virulence, according to invertebrate (mosquitoes) or vertebrate hosts (mammalian and avian), are presented and discussed. This overview will highlight the differences and similarities found between WNV hosts and models, to provide a foundation for the prediction and anticipation of WNV re-emergence and its risk of global spread.
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Affiliation(s)
- Lise Fiacre
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Nonito Pagès
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Jennifer Richardson
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
| | - Sylvie Lecollinet
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
- Correspondence: ; Tel.: +33-1-43967376
| | - Gaëlle Gonzalez
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
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Klenov A, Hudak KA. Facile method of curing toxicity in large viral genomes by high-throughput identification and removal of cryptic promoters. J Virol Methods 2020; 287:113993. [PMID: 33068704 DOI: 10.1016/j.jviromet.2020.113993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
Infectious plant virus clones are challenging to construct and manipulate due to the presence of cryptic promoter sequences that induce toxicity in bacteria. Common methods to overcome toxicity include intron insertion to interrupt toxic open reading frames and the use of Rhizobium or yeast species that do not recognize the same cryptic promoters. Unfortunately, intron insertion must be attempted on a trial and error basis within full-length clones and may change the infection characteristics of the virus. We have developed a facile method that can detect multiple cryptic bacterial promoters within large virus genomes. These promoters can then be silenced to obtain infectious clones that can be manipulated in E. coli. Our strategy relies on the generation of a viral library which is cloned upstream of either an eGFP open reading frame for low-throughput analysis or chloramphenicol for next generation sequencing. Pokeweed mosaic virus (PkMV), a 9.5 Kb ssRNA potyvirus, was used as a proof of concept. We found 16 putative promoter regions within 150-250 bp library fragments throughout the PkMV genome. 5'RACE allowed identification of the promoter sequence within each fragment, and subsequent silencing produced infectious clones. Our results indicate that cryptic promoters are ubiquitous within large viral genomes and that promoter screening is a desirable first step when constructing a viral clone. Our method can be applied to large plant and animal viruses as well as any DNA sequence for which low level of background transcriptional activity is required.
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Suzuki Y, Tanaka A, Maeda Y, Emi A, Fujioka Y, Sakaguchi S, Vasudevan SG, Kobayashi T, Lim CK, Takasaki T, Wu H, Nakano T. Construction and characterization of an infectious clone generated from Chikungunya virus SL11131 strain. Virology 2020; 552:52-62. [PMID: 33059320 DOI: 10.1016/j.virol.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/08/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes Chikungunya fever in humans. In this study, we generated two DNA-based CHIKV infectious clones derived from an Indian Ocean Lineage SL11131 strain and a prototype Ross strain. When the replication capabilities of the infectious CHIKV in various cell lines were evaluated, the SL11131 strain was found to replicate more efficiently than the Ross strain in Aedes albopictus C6/36 cells, whereas SL11131 underwent limited replication in a BHK-21-derivative cell line named BHK-DRV. Infection experiments using chimeric CHIKV between SL11131 and Ross revealed that these different replication activities of SL11131 in C6/36 and BHK-DRV cells were determined by structural and nonstructural genes, respectively. Therefore, the infectious clones created in this study will be a useful tool for investigating the virological features of a recent epidemic strain of CHIKV and benefit the development of effective prevention and treatment of CHIKV infection.
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Affiliation(s)
- Youichi Suzuki
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan.
| | - Atsushi Tanaka
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Resilience Research Unit, Kyoto University, Kyoto, Japan
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akino Emi
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | | | - Takeshi Kobayashi
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Chang-Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hong Wu
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan
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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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Kannan M, Zainal Z, Ismail I, Baharum SN, Bunawan H. Application of Reverse Genetics in Functional Genomics of Potyvirus. Viruses 2020; 12:v12080803. [PMID: 32722532 PMCID: PMC7472138 DOI: 10.3390/v12080803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022] Open
Abstract
Numerous potyvirus studies, including virus biology, transmission, viral protein function, as well as virus–host interaction, have greatly benefited from the utilization of reverse genetic techniques. Reverse genetics of RNA viruses refers to the manipulation of viral genomes, transfection of the modified cDNAs into cells, and the production of live infectious progenies, either wild-type or mutated. Reverse genetic technology provides an opportunity of developing potyviruses into vectors for improving agronomic traits in plants, as a reporter system for tracking virus infection in hosts or a production system for target proteins. Therefore, this review provides an overview on the breakthroughs achieved in potyvirus research through the implementation of reverse genetic systems.
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Affiliation(s)
- Maathavi Kannan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (M.K.); (Z.Z.); (I.I.); (S.N.B.)
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (M.K.); (Z.Z.); (I.I.); (S.N.B.)
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (M.K.); (Z.Z.); (I.I.); (S.N.B.)
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (M.K.); (Z.Z.); (I.I.); (S.N.B.)
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (M.K.); (Z.Z.); (I.I.); (S.N.B.)
- Correspondence: ; Tel.: +60-3-8921-4554
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Guo Y, Wang H, Xu S, Zhou H, Zhou C, Fu S, Cheng M, Li F, Deng Y, Li X, Wang H, Qin CF. Recovery and Genetic Characterization of a West Nile Virus Isolate from China. Virol Sin 2020; 36:113-121. [PMID: 32632819 DOI: 10.1007/s12250-020-00246-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/25/2020] [Indexed: 11/27/2022] Open
Abstract
West Nile virus (WNV) is an important neurotropic flavivirus that is widely distributed globally. WNV strain XJ11129 was first isolated in Xinjiang, China, and its genetic and biological characteristics remain largely unknown. In this study, phylogenetic and sequence analyses revealed that XJ11129 belongs to lineage 1a and shares high genetic identity with the highly pathogenic strain NY99. Then, the full-length genomic cDNA of XJ11129 was amplified and assembled using a modified Gibson assembly (GA) method. The virus (named rXJ11129) was successfully rescued in days following this method. Compared with other wild-type WNV isolates, rXJ11129 exhibited virulence indistinguishable from that of the NY99 strain in vivo. In summary, the genomic and virulence phenotypes of rXJ11129 were characterized in vivo and in vitro, and these data will improve the understanding of the spread and pathogenesis of this reemerging virus.
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Affiliation(s)
- Yan Guo
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Hongjiang Wang
- PLA Strategic Support Force Characteristic Medical Center, Beijing, 100071, China
| | - Songtao Xu
- Department of Arbovirus, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hangyu Zhou
- Suzhou Institute of System Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, 215000, China
| | - Chao Zhou
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease, Nanjing Medical University, Nanjing, 211166, China
| | - Shihong Fu
- Department of Arbovirus, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Mengli Cheng
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Fan Li
- Department of Arbovirus, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yongqiang Deng
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xiaofeng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Huanyu Wang
- Department of Arbovirus, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
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Guo J, He Y, Wang X, Jiang B, Lin X, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Chen S, Cheng A. Stabilization of a full-length infectious cDNA clone for duck Tembusu virus by insertion of an intron. J Virol Methods 2020; 283:113922. [PMID: 32598895 DOI: 10.1016/j.jviromet.2020.113922] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
Duck Tembusu virus (DTMUV) belongs to the genus Flavivirus, family Flaviviridae. In our previously study, a full-length cDNA clone of DTMUV was constructed, however, it is prone to mutation during genetic engineering due to the prokaryotic toxicity of viral protein, which is also a common feature for flavivirus. In this study, we reported an intron-containing full-length cDNA clone for a clinical strain CQW1, the intro (133bp) was inserted into nonstructural protein 1 of DTMUV at 192 site. This intron-containing full-length cDNA clone was stably propagated in Escherichia coli without prokaryotic toxicity, and recombinant virus was produced by direct transfection of plasmids. Besides, this cDNA clone-derived recombinant virus showed similar properties in comparison with parent virus both in vitro and in vivo. It's convenient and efficient, making it a useful platform for the subsequent research of reverse genetics of flavivirus.
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Affiliation(s)
- Jiaqi Guo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaoli Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Bowen Jiang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiao Lin
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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Yun SI, Song BH, Woolley ME, Frank JC, Julander JG, Lee YM. Development, Characterization, and Application of Two Reporter-Expressing Recombinant Zika Viruses. Viruses 2020; 12:v12050572. [PMID: 32456014 PMCID: PMC7290298 DOI: 10.3390/v12050572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Zika virus (ZIKV), a mosquito-borne transplacentally transmissible flavivirus, is an enveloped virus with an ~10.8 kb plus-strand RNA genome that can cause neurological disease. To facilitate the identification of potential antivirals, we developed two reporter-expressing ZIKVs, each capable of expressing an enhanced green fluorescent protein or an improved luminescent NanoLuc luciferase. First, a full-length functional ZIKV cDNA clone was engineered as a bacterial artificial chromosome, with each reporter gene under the cap-independent translational control of a cardiovirus-derived internal ribosome entry site inserted downstream of the single open reading frame of the viral genome. Two reporter-expressing ZIKVs were then generated by transfection of ZIKV-susceptible BHK-21 cells with infectious RNAs derived by in vitro run-off transcription from the respective cDNAs. As compared to the parental virus, the two reporter-expressing ZIKVs grew to lower titers with slower growth kinetics and formed smaller foci; however, they displayed a genome-wide viral protein expression profile identical to that of the parental virus, except for two previously unrecognized larger forms of the C and NS1 proteins. We then used the NanoLuc-expressing ZIKV to assess the in vitro antiviral activity of three inhibitors (T-705, NITD-008, and ribavirin). Altogether, our reporter-expressing ZIKVs represent an excellent molecular tool for the discovery of novel antivirals.
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Affiliation(s)
- Sang-Im Yun
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Byung-Hak Song
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Michael E. Woolley
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Jordan C. Frank
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Justin G. Julander
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
- Veterinary Diagnostics and Infectious Diseases, Utah Science Technology and Research, Utah State University, Logan, UT 84341, USA
- Correspondence: ; Tel.: +1-435-797-9667
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Liu J, Ren X, Li H, Yu X, Zhao B, Liu B, Ning Z. Development of the reverse genetics system for emerging atypical porcine pestivirus using in vitro and intracellular transcription systems. Virus Res 2020; 283:197975. [PMID: 32311384 DOI: 10.1016/j.virusres.2020.197975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/31/2023]
Abstract
Atypical porcine pestivirus (APPV) is a novel pestivirus causing congenital tremor (CT) type AII in piglets and exhibiting a broad geographical distribution. Lack of an operating system for the viral genome is one of bottlenecks which restrict further research on pathogenesis and gene functions of APPV. Reverse genetics system (RGS) is a feasible solution to this bottleneck problem, but, to-date, no RGSs have been developed for APPV. Here, for the first time, recombinant APPV CH-GD2017 were rescued using in vitro and intracellular transcription systems and the virons were observed via transmission electron microscopy. As the process of in vitro transcription is time-consuming and inefficient, a full-length cDNA clone in an intracellular transcription was further constructed using an RNA polymerase II system. Then, the rescued virus was identified via RT-PCR detection, indirect immunofluorescent assay, and transmission electron microscopy. Development of the RGS for APPV will provide an important tool for further research on this newly emerging pathogen.
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Affiliation(s)
- Jianxin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Xujiao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Huizi Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Xianglong Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Bingqian Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Boyang Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Zhangyong Ning
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642.
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48
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The discovery of segmented flaviviruses: implications for viral emergence. Curr Opin Virol 2020; 40:11-18. [DOI: 10.1016/j.coviro.2020.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/01/2020] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
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49
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Ávila-Pérez G, Nogales A, Park JG, Vasquez DM, Dean DA, Barravecchia M, Perez DR, Almazán F, Martínez-Sobrido L. In vivo rescue of recombinant Zika virus from an infectious cDNA clone and its implications in vaccine development. Sci Rep 2020; 10:512. [PMID: 31949262 PMCID: PMC6965646 DOI: 10.1038/s41598-020-57545-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne member of the Flaviviridae family that has been known to circulate for decades causing mild febrile illness. The more recent ZIKV outbreaks in the Americas and the Caribbean associated with congenital malformations and Guillain-Barré syndrome in adults have placed public health officials in high alert and highlight the significant impact of ZIKV on human health. New technologies to study the biology of ZIKV and to develop more effective prevention options are highly desired. In this study we demonstrate that direct delivery in mice of an infectious ZIKV cDNA clone allows the rescue of recombinant (r)ZIKV in vivo. A bacterial artificial chromosome containing the sequence of ZIKV strain Paraiba/2015 under the control of the cytomegalovirus promoter was complexed with a commercial transfection reagent and administrated using different routes in type-I interferon receptor deficient A129 mice. Clinical signs and death associated with ZIKV viremia were observed in mice. The rZIKV recovered from these mice remained fully virulent in a second passage in mice. Interestingly, infectious rZIKV was also recovered after intraperitoneal inoculation of the rZIKV cDNA in the absence of transfection reagent. Further expanding these studies, we demonstrate that a single intraperitoneal inoculation of a cDNA clone encoding an attenuated rZIKV was safe, highly immunogenic, and provided full protection against lethal ZIKV challenge. This novel in vivo reverse genetics method is a potentially suitable delivery platform for the study of wild-type and live-attenuated ZIKV devoid of confounding factors typical associated with in vitro systems. Moreover, our results open the possibility of employing similar in vivo reverse genetic approaches for the generation of other viruses and, therefore, change the way we will use reverse genetics in the future.
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MESH Headings
- Animals
- Chlorocebus aethiops
- Chromosomes, Artificial, Bacterial/genetics
- DNA, Complementary/genetics
- DNA, Complementary/immunology
- DNA, Viral/genetics
- DNA, Viral/immunology
- Disease Models, Animal
- Female
- Genetic Vectors/administration & dosage
- Male
- Mice
- Receptor, Interferon alpha-beta/genetics
- Reverse Genetics
- Vaccines, Attenuated/administration & dosage
- Vaccines, Attenuated/immunology
- Vero Cells
- Viral Vaccines/administration & dosage
- Viral Vaccines/immunology
- Viremia/genetics
- Viremia/immunology
- Viremia/prevention & control
- Zika Virus/genetics
- Zika Virus/immunology
- Zika Virus Infection/genetics
- Zika Virus Infection/immunology
- Zika Virus Infection/prevention & control
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Affiliation(s)
- Gines Ávila-Pérez
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
- Center for Animal Health Research, INIA-CISA, 28130, Valdeolmos, Madrid, Spain
| | - Jun-Gyu Park
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - Desarey Morales Vasquez
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - David A Dean
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - Michael Barravecchia
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - Daniel R Perez
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Georgia, USA
| | - Fernando Almazán
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), 3 Darwin street, 28049, Madrid, Spain.
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA.
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Ávila-Pérez G, Nogales A, Park JG, Márquez-Jurado S, Iborra FJ, Almazan F, Martínez-Sobrido L. A natural polymorphism in Zika virus NS2A protein responsible of virulence in mice. Sci Rep 2019; 9:19968. [PMID: 31882898 PMCID: PMC6934710 DOI: 10.1038/s41598-019-56291-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV) infection is currently one of the major concerns in human public health due to its association with neurological disorders. Intensive effort has been implemented for the treatment of ZIKV, however there are not currently approved vaccines or antivirals available to combat ZIKV infection. In this sense, the identification of virulence factors associated with changes in ZIKV virulence could help to develop safe and effective countermeasures to treat ZIKV or to prevent future outbreaks. Here, we have compared the virulence of two related ZIKV strains from the recent outbreak in Brazil (2015), Rio Grande do Norte Natal (RGN) and Paraiba. In spite of both viruses being identified in the same period of time and region, significant differences in virulence and replication were observed using a validated mouse model of ZIKV infection. While ZIKV-RGN has a 50% mouse lethal dose (MLD50) of ~105 focus forming units (FFUs), ZIKV-Paraiba infection resulted in 100% of lethality with less than 10 FFUs. Combining deep-sequencing analysis and our previously described infectious ZIKV-RGN cDNA clone, we identified a natural polymorphism in the non-structural protein 2 A (NS2A) that increase the virulence of ZIKV. Moreover, results demonstrate that the single amino acid alanine to valine substitution at position 117 (A117V) in the NS2A was sufficient to convert the attenuated rZIKV-RGN in a virulent Paraiba-like virus (MLD50 < 10 FFU). The mechanism of action was also evaluated and data indicate that substitution A117V in ZIKV NS2A protein reduces host innate immune responses and viral-induced apoptosis in vitro. Therefore, amino acid substitution A117V in ZIKV NS2A could be used as a genetic risk-assessment marker for future ZIKV outbreaks.
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Affiliation(s)
- Gines Ávila-Pérez
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
- Center for Animal Health Research, INIA-CISA, 28130, Valdeolmos, Madrid, Spain
| | - Jun-Gyu Park
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA
| | - Silvia Márquez-Jurado
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autonóma de Madrid, 3 Darwin Street, 28049, Madrid, Spain
| | - Francisco J Iborra
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autonóma de Madrid, 3 Darwin Street, 28049, Madrid, Spain
| | - Fernando Almazan
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autonóma de Madrid, 3 Darwin Street, 28049, Madrid, Spain.
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York, 14642, USA.
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