1
|
Bilotti K, Keep S, Sikkema AP, Pryor JM, Kirk J, Foldes K, Doyle N, Wu G, Freimanis G, Dowgier G, Adeyemi O, Tabatabaei SK, Lohman GJS, Bickerton E. One-pot Golden Gate Assembly of an avian infectious bronchitis virus reverse genetics system. PLoS One 2024; 19:e0307655. [PMID: 39052682 PMCID: PMC11271894 DOI: 10.1371/journal.pone.0307655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Avian infectious bronchitis is an acute respiratory disease of poultry of particular concern for global food security. Investigation of infectious bronchitis virus (IBV), the causative agent of avian infectious bronchitis, via reverse genetics enables deeper understanding of virus biology and a rapid response to emerging variants. Classic methods of reverse genetics for IBV can be time consuming, rely on recombination for the introduction of mutations, and, depending on the system, can be subject to genome instability and unreliable success rates. In this study, we have applied data-optimized Golden Gate Assembly design to create a rapidly executable, flexible, and faithful reverse genetics system for IBV. The IBV genome was divided into 12 fragments at high-fidelity fusion site breakpoints. All fragments were synthetically produced and propagated in E. coli plasmids, amenable to standard molecular biology techniques for DNA manipulation. The assembly can be carried out in a single reaction, with the products used directly in subsequent viral rescue steps. We demonstrate the use of this system for generation of point mutants and gene replacements. This Golden Gate Assembly-based reverse genetics system will enable rapid response to emerging variants of IBV, particularly important to vaccine development for controlling spread within poultry populations.
Collapse
Affiliation(s)
- Katharina Bilotti
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Sarah Keep
- The Pirbright Institute, Woking, United Kingdom
| | - Andrew P. Sikkema
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - John M. Pryor
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - James Kirk
- The Pirbright Institute, Woking, United Kingdom
| | | | | | - Ge Wu
- The Pirbright Institute, Woking, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
2
|
Ujike M, Suzuki T. Progress of research on coronaviruses and toroviruses in large domestic animals using reverse genetics systems. Vet J 2024; 305:106122. [PMID: 38641200 DOI: 10.1016/j.tvjl.2024.106122] [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: 12/12/2023] [Revised: 03/24/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The generation of genetically engineered recombinant viruses from modified DNA/RNA is commonly referred to as reverse genetics, which allows the introduction of desired mutations into the viral genome. Reverse genetics systems (RGSs) are powerful tools for studying fundamental viral processes, mechanisms of infection, pathogenesis and vaccine development. However, establishing RGS for coronaviruses (CoVs) and toroviruses (ToVs), which have the largest genomes among vertebrate RNA viruses, is laborious and hampered by technical constraints. Hence, little research has focused on animal CoVs and ToVs using RGSs, especially in large domestic animals such as pigs and cattle. In the last decade, however, studies of porcine CoVs and bovine ToVs using RGSs have been reported. In addition, the coronavirus disease-2019 pandemic has prompted the development of new and simple CoV RGSs, which will accelerate RGS-based research on animal CoVs and ToVs. In this review, we summarise the general characteristics of CoVs and ToVs, the RGSs available for CoVs and ToVs and the progress made in the last decade in RGS-based research on porcine CoVs and bovine ToVs.
Collapse
Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan; Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.
| | - Tohru Suzuki
- Division of Zoonosis Research, Sapporo Research Station, National Institute of Animal Health, NARO, Sapporo, Hokkaido 062-0045, Japan
| |
Collapse
|
3
|
Álvarez ÁL, Arboleya A, Abade dos Santos FA, García-Manso A, Nicieza I, Dalton KP, Parra F, Martín-Alonso JM. Highs and Lows in Calicivirus Reverse Genetics. Viruses 2024; 16:866. [PMID: 38932159 PMCID: PMC11209508 DOI: 10.3390/v16060866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an "infectious clone". This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones.
Collapse
Affiliation(s)
- Ángel L. Álvarez
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Aroa Arboleya
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Fábio A. Abade dos Santos
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Nacional de Investigação Agrária e Veterinária, 2780-157 Oeiras, Portugal
| | - Alberto García-Manso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Inés Nicieza
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Kevin P. Dalton
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José M. Martín-Alonso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| |
Collapse
|
4
|
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.
Collapse
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.)
| |
Collapse
|
5
|
Kubinski HC, Despres HW, Johnson BA, Schmidt MM, Jaffrani SA, Mills MG, Lokugamage K, Dumas CM, Shirley DJ, Estes LK, Pekosz A, Crothers JW, Roychoudhury P, Greninger AL, Jerome KR, Di Genova BM, Walker DH, Ballif BA, Ladinsky MS, Bjorkman PJ, Menachery VD, Bruce EA. Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584120. [PMID: 38559000 PMCID: PMC10979914 DOI: 10.1101/2024.03.08.584120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Finally, we demonstrate that the N:G215C virus packages more nucleocapsid per virion and that individual virions are larger, with elongated morphologies.
Collapse
Affiliation(s)
- Hannah C. Kubinski
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Sara A. Jaffrani
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Caroline M. Dumas
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department. Burlington VT, 05405, USA
| | - Leah K. Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, MD College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pavitra Roychoudhury
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A. Ballif
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| |
Collapse
|
6
|
Keep S, Stevenson-Leggett P, Webb I, Fones A, Kirk J, Britton P, Bickerton E. The spike protein of the apathogenic Beaudette strain of avian coronavirus can elicit a protective immune response against a virulent M41 challenge. PLoS One 2024; 19:e0297516. [PMID: 38265985 PMCID: PMC10807761 DOI: 10.1371/journal.pone.0297516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/07/2024] [Indexed: 01/26/2024] Open
Abstract
The avian Gammacoronavirus infectious bronchitis virus (IBV) causes major economic losses in the poultry industry as the aetiological agent of infectious bronchitis, a highly contagious respiratory disease in chickens. IBV causes major economic losses to poultry industries across the globe and is a concern for global food security. IBV vaccines are currently produced by serial passage, typically 80 to 100 times in chicken embryonated eggs (CEE) to achieve attenuation by unknown molecular mechanisms. Vaccines produced in this manner present a risk of reversion as often few consensus level changes are acquired. The process of serial passage is cumbersome, time consuming, solely dependent on the supply of CEE and does not allow for rapid vaccine development in response to newly emerging IBV strains. Both alternative rational attenuation and cell culture-based propagation methods would therefore be highly beneficial. The majority of IBV strains are however unable to be propagated in cell culture proving a significant barrier to the development of cell-based vaccines. In this study we demonstrate the incorporation of a heterologous Spike (S) gene derived from the apathogenic Beaudette strain of IBV into a pathogenic M41 genomic backbone generated a recombinant IBV denoted M41K-Beau(S) that exhibits Beaudette's unique ability to replicate in Vero cells, a cell line licenced for vaccine production. The rIBV M41K-Beau(S) additionally exhibited an attenuated in vivo phenotype which was not the consequence of the presence of a large heterologous gene demonstrating that the Beaudette S not only offers a method for virus propagation in cell culture but also a mechanism for rational attenuation. Although historical research suggested that Beaudette, and by extension the Beaudette S protein was poorly immunogenic, vaccination of chickens with M41K-Beau(S) induced a complete cross protective immune response in terms of clinical disease and tracheal ciliary activity against challenge with a virulent IBV, M41-CK, belonging to the same serogroup as Beaudette. This implies that the amino acid sequence differences between the Beaudette and M41 S proteins have not distorted important protective epitopes. The Beaudette S protein therefore offers a significant avenue for vaccine development, with the advantage of a propagation platform less reliant on CEE.
Collapse
Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Surrey, United Kingdom
| | | | - Isobel Webb
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, The University of Bristol, Bristol, United Kingdom
| | | | - James Kirk
- The Pirbright Institute, Surrey, United Kingdom
| | | | | |
Collapse
|
7
|
Meyers G, Tews BA. Self-Replicating RNA Derived from the Genomes of Positive-Strand RNA Viruses. Methods Mol Biol 2024; 2786:25-49. [PMID: 38814389 DOI: 10.1007/978-1-0716-3770-8_2] [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: 05/31/2024]
Abstract
Self-replicating RNA derived from the genomes of positive-strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. The following chapter summarizes the principles how such RNAs can be established and used for design of vaccines. Due to the large variety of strategies needed to circumvent specific pitfalls in the design of such constructs the technical details of the experiments are not described here but can be found in the cited literature.
Collapse
Affiliation(s)
- Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Birke Andrea Tews
- Institut für Infektionsmedizin, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
| |
Collapse
|
8
|
Borah Slater K, Ahmad M, Poirier A, Stott A, Siedler BS, Brownsword M, Mehat J, Urbaniec J, Locker N, Zhao Y, La Ragione R, Silva SRP, McFadden J. Development of a loop-mediated isothermal amplification (LAMP)-based electrochemical test for rapid detection of SARS-CoV-2. iScience 2023; 26:107570. [PMID: 37664622 PMCID: PMC10470312 DOI: 10.1016/j.isci.2023.107570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Rapid, reliable, sensitive, portable, and accurate diagnostics are required to control disease outbreaks such as COVID-19 that pose an immense burden on human health and the global economy. Here we developed a loop-mediated isothermal amplification (LAMP)-based electrochemical test for the detection of SARS-CoV-2 that causes COVID-19. The test is based on the oxidation-reduction reaction between pyrophosphates (generated from positive LAMP reaction) and molybdate that is detected by cyclic voltammetry using inexpensive and disposable carbon screen printed electrodes. Our test showed higher sensitivity (detecting as low as 5.29 RNA copies/μL) compared to the conventional fluorescent reverse transcriptase (RT)-LAMP. We validated our tests using human serum and saliva spiked with SARS-CoV-2 RNA and clinical (saliva and nasal-pharyngeal) swab samples demonstrating 100% specificity and 93.33% sensitivity. Our assay provides a rapid, specific, and sensitive test with an electrochemical readout in less than 45 min that could be adapted for point-of-care settings.
Collapse
Affiliation(s)
- Khushboo Borah Slater
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Muhammad Ahmad
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Aurore Poirier
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Ash Stott
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Bianca Sica Siedler
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Matthew Brownsword
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Jai Mehat
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Joanna Urbaniec
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicolas Locker
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Yunlong Zhao
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Roberto La Ragione
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - S. Ravi P. Silva
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Johnjoe McFadden
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| |
Collapse
|
9
|
Keep S, Dowgier G, Lulla V, Britton P, Oade M, Freimanis G, Tennakoon C, Jonassen CM, Tengs T, Bickerton E. Deletion of the s2m RNA Structure in the Avian Coronavirus Infectious Bronchitis Virus and Human Astrovirus Results in Sequence Insertions. J Virol 2023; 97:e0003823. [PMID: 36779761 PMCID: PMC10062133 DOI: 10.1128/jvi.00038-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/25/2023] [Indexed: 02/14/2023] Open
Abstract
Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large positive-sense single-stranded molecule of RNA containing many RNA structures. One structure, denoted s2m and consisting of 41 nucleotides, is located within the 3' untranslated region (3' UTR) and is shared between some coronavirus species, including infectious bronchitis virus (IBV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2, as well as other pathogens, including human astrovirus. Using a reverse genetic system to generate recombinant viruses, we investigated the requirement of the s2m structure in the replication of IBV, a globally distributed economically important Gammacoronavirus that infects poultry causing respiratory disease. Deletion of three nucleotides predicted to destabilize the canonical structure of the s2m or the deletion of the nucleotides corresponding to s2m impacted viral replication in vitro. In vitro passaging of the recombinant IBV with the s2m sequence deleted resulted in a 36-nucleotide insertion in place of the deletion, which was identified to be composed of a duplication of flanking sequences. A similar result was observed following serial passage of human astrovirus with a deleted s2m sequence. RNA modeling indicated that deletion of the nucleotides corresponding to the s2m impacted other RNA structures present in the IBV 3' UTR. Our results indicated for both IBV and human astrovirus a preference for nucleotide occupation in the genome location corresponding to the s2m, which is independent of the specific s2m sequence. IMPORTANCE Coronaviruses infect many species, including humans and animals, with substantial effects on livestock, particularly with respect to poultry. The coronavirus RNA genome consists of structural elements involved in viral replication whose roles are poorly understood. We investigated the requirement of the RNA structural element s2m in the replication of the Gammacoronavirus infectious bronchitis virus, an economically important viral pathogen of poultry. Using reverse genetics to generate recombinant IBVs with either a disrupted or deleted s2m, we showed that the s2m is not required for viral replication in cell culture; however, replication is decreased in tracheal tissue, suggesting a role for the s2m in the natural host. Passaging of these viruses as well as human astrovirus lacking the s2m sequence demonstrated a preference for nucleotide occupation, independent of the s2m sequence. RNA modeling suggested deletion of the s2m may negatively impact other essential RNA structures.
Collapse
Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Woking, United Kingdom
| | | | - Valeria Lulla
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | | | - Michael Oade
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | |
Collapse
|
10
|
Shiaelis N, Tometzki A, Peto L, McMahon A, Hepp C, Bickerton E, Favard C, Muriaux D, Andersson M, Oakley S, Vaughan A, Matthews PC, Stoesser N, Crook DW, Kapanidis AN, Robb NC. Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning. ACS NANO 2023; 17:697-710. [PMID: 36541630 PMCID: PMC9836350 DOI: 10.1021/acsnano.2c10159] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The increasing frequency and magnitude of viral outbreaks in recent decades, epitomized by the COVID-19 pandemic, has resulted in an urgent need for rapid and sensitive diagnostic methods. Here, we present a methodology for virus detection and identification that uses a convolutional neural network to distinguish between microscopy images of fluorescently labeled intact particles of different viruses. Our assay achieves labeling, imaging, and virus identification in less than 5 min and does not require any lysis, purification, or amplification steps. The trained neural network was able to differentiate SARS-CoV-2 from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses. We were also able to differentiate closely related strains of influenza, as well as SARS-CoV-2 variants. Additional and novel pathogens can easily be incorporated into the test through software updates, offering the potential to rapidly utilize the technology in future infectious disease outbreaks or pandemics. Single-particle imaging combined with deep learning therefore offers a promising alternative to traditional viral diagnostic and genomic sequencing methods and has the potential for significant impact.
Collapse
Affiliation(s)
- Nicolas Shiaelis
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Alexander Tometzki
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Leon Peto
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Andrew McMahon
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Christof Hepp
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Erica Bickerton
- The
Pirbright Institute, Ash Road, Pirbright, Woking, SurreyGU24 0NF, United
Kingdom
| | - Cyril Favard
- Membrane
Domains and Viral Assembly, IRIM, UMR 9004 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
| | - Delphine Muriaux
- Membrane
Domains and Viral Assembly, IRIM, UMR 9004 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
- CEMIPAI, UMS 3725 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
| | - Monique Andersson
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Sarah Oakley
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Ali Vaughan
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Oxford Biomedical Research Centre, University
of Oxford, OxfordOX3 9DU, United
Kingdom
| | - Philippa C. Matthews
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Nicole Stoesser
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Health Protection Research Unit in Healthcare Associated Infections
and Antimicrobial Resistance, in partnership with Public Health England, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Derrick W. Crook
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Oxford Biomedical Research Centre, University
of Oxford, OxfordOX3 9DU, United
Kingdom
- NIHR
Health Protection Research Unit in Healthcare Associated Infections
and Antimicrobial Resistance, in partnership with Public Health England, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Achillefs N. Kapanidis
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, OxfordOX1 3QU, United Kingdom
| | - Nicole C. Robb
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
- Warwick
Medical School, University of Warwick, CoventryCV4 7AL, United Kingdom
| |
Collapse
|
11
|
Väisänen E, Jiang M, Laine L, Waris M, Julkunen I, Österlund P. Infectious viruses from transfected SARS-CoV-2 genomic RNA. Front Bioeng Biotechnol 2023; 11:1129111. [PMID: 37064222 PMCID: PMC10098207 DOI: 10.3389/fbioe.2023.1129111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
SARS-CoV-2 emerged at the end of 2019, and like other novel pathogens causing severe symptoms, WHO recommended heightened biosafety measures for laboratories working with the virus. The positive-stranded genomic RNA of coronaviruses has been known to be infectious since the 1970s, and overall, all experiments with the possibility of SARS-CoV-2 propagation are carried out in higher containment level laboratories. However, as SARS-CoV-2 RNA has been routinely handled in BSL-2 laboratories, the question of the true nature of RNA infectiousness has risen along with discussion of appropriate biosafety measures. Here, we studied the ability of native SARS-CoV-2 genomic RNA to produce infectious viruses when transfected into permissive cells and discussed the biosafety control measures related to these assays. In transfection assays large quantities of genomic vRNA of SARS-CoV-2 was required for a successful production of infectious viruses. However, the quantity of vRNA alone was not the only factor, and especially when the transfected RNA was derived from infected cells, even small amounts of genomic vRNA was enough for an infection. Virus replication was found to start rapidly after transfection, and infectious viruses were detected in the cell culture media at 24 h post-transfection. In addition, silica membrane-based kits were shown to be as good as traditional TRI-reagent based methods in extracting high-quality, 30 kb-long genomic vRNA. Taken together, our data indicates that all transfection experiments with samples containing genomic SARS-CoV-2 RNA should be categorized as a propagative work and the work should be conducted only in a higher containment BSL-3 laboratory.
Collapse
Affiliation(s)
- Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Elina Väisänen,
| | - Miao Jiang
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matti Waris
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| |
Collapse
|
12
|
Advances in Molecular Genetics Enabling Studies of Highly Pathogenic RNA Viruses. Viruses 2022; 14:v14122682. [PMID: 36560685 PMCID: PMC9784166 DOI: 10.3390/v14122682] [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: 10/24/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Experimental work with viruses that are highly pathogenic for humans and animals requires specialized Biosafety Level 3 or 4 facilities. Such pathogens include some spectacular but also rather seldomly studied examples such as Ebola virus (requiring BSL-4), more wide-spread and commonly studied viruses such as HIV, and the most recent example, SARS-CoV-2, which causes COVID-19. A common characteristic of these virus examples is that their genomes consist of single-stranded RNA, which requires the conversion of their genomes into a DNA copy for easy manipulation; this can be performed to study the viral life cycle in detail, develop novel therapies and vaccines, and monitor the disease course over time for chronic virus infections. We summarize the recent advances in such new genetic applications for RNA viruses in Switzerland over the last 25 years, from the early days of the HIV/AIDS epidemic to the most recent developments in research on the SARS-CoV-2 coronavirus. We highlight game-changing collaborative efforts between clinical and molecular disciplines in HIV research on the path to optimal clinical disease management. Moreover, we summarize how the modern technical evolution enabled the molecular studies of emerging RNA viruses, confirming that Switzerland is at the forefront of SARS-CoV-2 research and potentially other newly emerging viruses.
Collapse
|
13
|
A Temperature-Sensitive Recombinant of Avian Coronavirus Infectious Bronchitis Virus Provides Complete Protection against Homologous Challenge. J Virol 2022; 96:e0110022. [PMID: 35972294 PMCID: PMC9472628 DOI: 10.1128/jvi.01100-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Avian coronavirus infectious bronchitis virus (IBV) is the etiological agent of infectious bronchitis, an acute highly contagious economically relevant respiratory disease of poultry. Vaccination is used to control IBV infections, with live-attenuated vaccines generated via serial passage of a virulent field isolate through embryonated hens' eggs. A fine balance must be achieved between attenuation and the retention of immunogenicity. The exact molecular mechanism of attenuation is unknown, and vaccines produced in this manner present a risk of reversion to virulence as few consensus level changes are acquired. Our previous research resulted in the generation of a recombinant IBV (rIBV) known as M41-R, based on a pathogenic strain M41-CK. M41-R was attenuated in vivo by two amino acid changes, Nsp10-Pro85Leu and Nsp14-Val393Leu; however, the mechanism of attenuation was not determined. Pro85 and Val393 were found to be conserved among not only IBV strains but members of the wider coronavirus family. This study demonstrates that the same changes are associated with a temperature-sensitive (ts) replication phenotype at 41°C in vitro, suggesting that the two phenotypes may be linked. Vaccination of specific-pathogen-free chickens with M41-R induced 100% protection against clinical disease, tracheal ciliary damage, and challenge virus replication following homologous challenge with virulent M41-CK. Temperature sensitivity has been used to rationally attenuate other viral pathogens, including influenza, and the identification of amino acid changes that impart both a ts and an attenuated phenotype may therefore offer an avenue for future coronavirus vaccine development. IMPORTANCE Infectious bronchitis virus is a pathogen of economic and welfare concern for the global poultry industry. Live-attenuated vaccines against are generated by serial passage of a virulent isolate in embryonated eggs until attenuation is achieved. The exact mechanisms of attenuation are unknown, and vaccines produced have a risk of reversion to virulence. Reverse genetics provides a method to generate vaccines that are rationally attenuated and are more stable with respect to back selection due to their clonal origin. Genetic populations resulting from molecular clones are more homogeneous and lack the presence of parental pathogenic viruses, which generation by multiple passage does not. In this study, we identified two amino acids that impart a temperature-sensitive replication phenotype. Immunogenicity is retained and vaccination results in 100% protection against homologous challenge. Temperature sensitivity, used for the development of vaccines against other viruses, presents a method for the development of coronavirus vaccines.
Collapse
|
14
|
The Genetic Stability, Replication Kinetics and Cytopathogenicity of Recombinant Avian Coronaviruses with a T16A or an A26F Mutation within the E Protein Is Cell-Type Dependent. Viruses 2022; 14:v14081784. [PMID: 36016406 PMCID: PMC9415719 DOI: 10.3390/v14081784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
The envelope (E) protein of the avian coronavirus infectious bronchitis virus (IBV) is a small-membrane protein present in two forms during infection: a monomer and a pentameric ion channel. Each form has an independent role during replication; the monomer disrupts the secretory pathway, and the pentamer facilitates virion production. The presence of a T16A or A26F mutation within E exclusively generates the pentameric or monomeric form, respectively. We generated two recombinant IBVs (rIBVs) based on the apathogenic molecular clone Beau-R, containing either a T16A or A26F mutation, denoted as BeauR-T16A and BeauR-A26F. The replication and genetic stability of the rIBVs were assessed in several different cell types, including primary and continuous cells, ex vivo tracheal organ cultures (TOCs) and in ovo. Different replication profiles were observed between cell cultures of different origins. BeauR-A26F replicated to a lower level than Beau-R in Vero cells and in ovo but not in DF1, primary chicken kidney (CK) cells or TOCs. Genetic stability and cytopathic effects were found to differ depending on the cell system. The effect of the T16A and A26F mutations appear to be cell-type dependent, which, therefore, highlights the importance of cell type in the investigation of the IBV E protein.
Collapse
|
15
|
Reverse genetics in virology: A double edged sword. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
16
|
Engineering and Characterization of Avian Coronavirus Mutants Expressing Fluorescent Reporter Proteins from the Replicase Gene. J Virol 2022; 96:e0065322. [PMID: 35862676 PMCID: PMC9327687 DOI: 10.1128/jvi.00653-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an avian coronavirus that causes infectious bronchitis, an acute and highly contagious respiratory disease of chickens. IBV evolution under the pressure of comprehensive and widespread vaccination requires surveillance for vaccine resistance, as well as periodic vaccine updates. Reverse genetics systems are very valuable tools in virology, as they facilitate rapid genetic manipulation of viral genomes, thereby advancing basic and applied research. We report here the construction of an infectious clone of IBV strain Beaudette as a bacterial artificial chromosome (BAC). The engineered full-length IBV clone allowed the rescue of an infectious virus that was phenotypically indistinguishable from the parental virus. We used the infectious IBV clone and examined whether an enhanced green fluorescent protein (EGFP) can be produced by the replicase gene ORF1 and autocatalytically released from the replicase polyprotein through cleavage by the main coronavirus protease. We show that IBV tolerates insertion of the EGFP ORF at the 3' end of the replicase gene, between the sequences encoding nsp13 and nsp16 (helicase, RNA exonuclease, RNA endonuclease, and RNA methyltransferase). We further show that EGFP is efficiently cleaved from the replicase polyprotein and can be localized in double-membrane vesicles along with viral RNA polymerase and double-stranded RNA, an intermediate of IBV genome replication. One of the engineered reporter EGFP viruses were genetically stable during passage in cultured cells. We demonstrate that the reporter EGFP viruses can be used to study virus replication in host cells and for antiviral drug discovery and development of diagnostic assays. IMPORTANCE Reverse genetics systems based on bacterial artificial chromosomes (BACs) are the most valuable systems in coronavirus research. Here, we describe the establishment of a reverse genetics system for the avian coronavirus strain Beaudette, the most intensively studied strain. We cloned a copy of the avian coronavirus genome into a BAC vector and recovered infectious virus in permissive cells. We used the new system to construct reporter viruses that produce enhanced green fluorescent protein (EGFP). The EGFP coding sequence was inserted into 11 known cleavage sites of the major coronavirus protease in the replicase gene ORF1. Avian coronavirus tolerated the insertion of the EGFP coding sequence at three sites. The engineered reporter viruses replicated with parental efficiency in cultured cells and were sufficiently genetically stable. The new system facilitates functional genomics of the avian coronavirus genome but can also be used for the development of novel vaccines and anticoronaviral drugs.
Collapse
|
17
|
Ting X, Xiang C, Liu DX, Chen R. Establishment and Cross-Protection Efficacy of a Recombinant Avian Gammacoronavirus Infectious Bronchitis Virus Harboring a Chimeric S1 Subunit. Front Microbiol 2022; 13:897560. [PMID: 35935229 PMCID: PMC9354458 DOI: 10.3389/fmicb.2022.897560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a gammacoronavirus that causes a highly contagious disease in chickens and seriously endangers the poultry industry. A diversity of serotypes and genotypes of IBV have been identified worldwide, and the currently available vaccines do not cross-protect. In the present study, an efficient reverse genetics technology based on Beaudette-p65 has been used to construct a recombinant IBV, rIBV-Beaudette-KC(S1), by replacing the nucleotides 21,704–22,411 with the corresponding sequence from an isolate of QX-like genotype KC strain. Continuous passage of this recombinant virus in chicken embryos resulted in the accumulation of two point mutations (G21556C and C22077T) in the S1 region. Further studies showed that the T248S (G21556C) substitution may be essential for the adaptation of the recombinant virus to cell culture. Immunization of chicks with the recombinant IBV elicited strong antibody responses and showed high cross-protection against challenges with virulent M41 and a QX-like genotype IBV. This study reveals the potential of developing rIBV-Beau-KC(S1) as a cell-based vaccine with a broad protective immunity against two different genotypes of IBV.
Collapse
Affiliation(s)
- Xiong Ting
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chengwei Xiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ding Xiang Liu
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Ding Xiang Liu ;
| | - Ruiai Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
- *Correspondence: Ruiai Chen
| |
Collapse
|
18
|
Weng W, Liu Q, Xue W, Wang H, Fang S, Sun Y, Tan L, Song C, Qiu X, Liu W, Ding C, Liao Y. Characterization of the Protective Efficacy Against QX Strain of a Recombinant Infectious Bronchitis Virus With H120 Backbone and QX Spike Gene. Front Microbiol 2022; 13:883642. [PMID: 35783402 PMCID: PMC9247577 DOI: 10.3389/fmicb.2022.883642] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Infectious bronchitis virus (IBV) has been prevalent in chicken farms for many years, and its control relies on extensive vaccine administration. The continuous emergence of new variants and the low cross-protection efficiency prompt the development of new vaccines. In this study, we develop a reverse genetics technique based on the classical vaccine strain H120 genome, via in vitro ligation method. Using the H120 genome as the backbone, we constructed the recombinant virus rH120-QX(S) by replacing the H120 S gene with the QX S gene, a prevalent strain in China. Biological characteristics of the rH120-QX(S) virus, such as 50% egg lethal dose (ELD50), 50% egg infectious dose (EID50), dwarf embryo, growth curve, and genetic stability, are measured, which are comparable to the parental virus H120. There are no clinical symptoms and tissue lesions in the trachea and kidney in the rH120-QX(S)-infected specific-pathogen-free (SPF) chickens, demonstrating that this recombinant virus does not confer pathogenicity. Furthermore, protection studies show that there is 100% homologous protection of rH120-QX(S) to the virulent QX strain, as shown by the absence of clinical signs and no lethality. Taken together, our results demonstrate that swapping the S gene onto the H120 genetic backbone is a precise and effective way to produce genetically defined IBV vaccine candidates.
Collapse
Affiliation(s)
- Wenlian Weng
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Qingyan Liu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- College of Agriculture, College of Animal Sciences, Yangtze University, Jingzhou, China
| | - Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shouguo Fang
- College of Agriculture, College of Animal Sciences, Yangtze University, Jingzhou, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Weiwei Liu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao
| |
Collapse
|
19
|
Li S, Fan S, Li N, Shen Y, Xiang X, Chen W, Xia J, Han X, Cui M, Huang Y. The N1038S Substitution and 1153EQTRPKKSV 1162 Deletion of the S2 Subunit of QX-Type Avian Infectious Bronchitis Virus Can Synergistically Enhance Viral Proliferation. Front Microbiol 2022; 13:829218. [PMID: 35432239 PMCID: PMC9006875 DOI: 10.3389/fmicb.2022.829218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The S2 subunit of infectious bronchitis virus (IBV) plays a critical role in the process of IBV infection. A comparison between the S2 subunit sequence of chicken embryo kidney cell (CEK) adapted virulent QX-like IBV strain SczyC30 (hereafter referred to as zy30) and its CEK-attenuated strain, SczyC100, revealed an N1038S substitution in S2 subunit and a 1154EQTRPKKSV1162 residue deletion in the C-terminus of the S2 subunit. In order to explore whether these two mutations are related to changes in the biological characteristics of IBV, we firstly constructed an infectious clone of zy30 using a bacterial artificial chromosome (BAC), which combines the transcription of infectious IBV genomic RNA in non-susceptible BHK-21 cells with the amplification of rescued virus rzy30 in CEK cells. Then, three recombinant viruses, including an rzy30S2-N1038S strain that contained the N1038S substitution, an rzy30S2-CT9△ strain that contained the 1154EQTRPKKSV1162 deletion, and an rzy30S2-N1038S-CT9△ strain that contained both mutations, were constructed using rescued virus rzy30 as the backbone. The results showed that each mutation did not significantly affect the replication titer in CEK cells but reduced pathogenicity in chickens, while in combination, the N1038S substitution and 1154EQTRPKKSV1162 deletion improved the proliferation efficiency in CEK cells and reduced pathogenicity, compared to rzy30 strain. The contribution made by the 1154EQTRPKKSV1162 deletion in reducing pathogenicity was higher than that of N1038S substitution. Our results revealed that the N1038S substitution and 1154EQTRPKKSV1162 deletion in S2 subunit were deeply involved in the replication efficiency of IBV and contributed to reduction of viral pathogenicity.
Collapse
Affiliation(s)
- Shuyun Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shunyi Fan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Nianning Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuxi Shen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xuelian Xiang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wen Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Xia
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinfeng Han
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Min Cui
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
20
|
Genetic Analysis of the Complete S1 Gene in Japanese Infectious Bronchitis Virus Strains. Viruses 2022; 14:v14040716. [PMID: 35458447 PMCID: PMC9029843 DOI: 10.3390/v14040716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
The complete nucleotide sequence of the S1 glycoprotein gene of the Japanese infectious bronchitis virus (IBV) strains was determined and genetically analyzed. A total of 61 Japanese IBV strains were classified into seven genotypes, namely GI-1, 3, 7, 13, 18, 19, and GVI-1 using the classification scheme that was proposed by Valastro et al, with three exceptions. These genotypes practically corresponded to those defined in Japan, namely Mass, Gray, JP-II, 4/91, JP-I, JP-III, and JP-IV, which have been identified through their partial nucleotide sequences containing hypervariable regions 1 and 2. In addition, three exceptive strains were considered to be derived from recombination within the S1 gene of IBV strains G1-13 and GI-19. By analyzing the amino acid polymorphism of the S1 glycoprotein among Japanese genotypes, a diversity was observed based on the genotype-specific amino acid residue, the proteolytic cleavage motif at the S1/S2 cleavage site, and the position of the potential N-glycosylation sites.
Collapse
|
21
|
Identification of Amino Acids within Nonstructural Proteins 10 and 14 of the Avian Coronavirus Infectious Bronchitis Virus That Result in Attenuation In Vivo and In Ovo. J Virol 2022; 96:e0205921. [PMID: 35044208 PMCID: PMC8941869 DOI: 10.1128/jvi.02059-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gammacoronavirus infectious bronchitis virus (IBV) is a highly contagious global pathogen prevalent in all types of poultry flocks. IBV is responsible for economic losses and welfare issues in domestic poultry, resulting in a significant risk to food security. IBV vaccines are currently generated by serial passage of virulent IBV field isolates through embryonated hens' eggs. The different patterns of genomic variation accumulated during this process means that the exact mechanism of attenuation is unknown and presents a risk of reversion to virulence. Additionally, the passaging process adapts the virus to replicate in chicken embryos, increasing embryo lethality. Vaccines produced in this manner are therefore unsuitable for in ovo application. We have developed a reverse genetics system, based on the pathogenic IBV strain M41, to identify genes which can be targeted for rational attenuation. During the development of this reverse genetics system, we identified four amino acids, located in nonstructural proteins (nsps) 10, 14, 15, and 16, which resulted in attenuation both in vivo and in ovo. Further investigation highlighted a role of amino acid changes, Pro85Leu in nsp 10 and Val393Leu in nsp 14, in the attenuated in vivo phenotype observed. This study provides evidence that mutations in nsps offer a promising mechanism for the development of rationally attenuated live vaccines against IBV, which have the potential for in ovo application. IMPORTANCE The Gammacoronavirus infectious bronchitis virus (IBV) is the etiological agent of infectious bronchitis, an acute, highly contagious, economically important disease of poultry. Vaccination is achieved using a mixture of live attenuated vaccines for young chicks and inactivated vaccines as boosters for laying hens. Live attenuated vaccines are generated through serial passage in embryonated hens' eggs, an empirical process which achieves attenuation but retains immunogenicity. However, these vaccines have a risk of reversion to virulence, and they are lethal to the embryo. In this study, we identified amino acids in the replicase gene which attenuated IBV strain M41, both in vivo and in ovo. Stability assays indicate that the attenuating amino acids are stable and unlikely to revert. The data in this study provide evidence that specific modifications in the replicase gene offer a promising direction for IBV live attenuated vaccine development, with the potential for in ovo application.
Collapse
|
22
|
Inayoshi Y, Oguro S, Tanahashi E, Lin Z, Kawaguchi Y, Kodama T, Sasakawa C. Bacterial artificial chromosome-based reverse genetics system for cloning and manipulation of the full-length genome of infectious bronchitis virus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100155. [PMID: 35909616 PMCID: PMC9325906 DOI: 10.1016/j.crmicr.2022.100155] [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: 12/01/2022] Open
Abstract
Reverse genetics system to clone attenuated IBV C-78 full-length genome in a BAC. Rescued virus from BAC-cloned C-78 show parental virus properties. Genetic manipulation of BAC-cloned C-78 using Red-mediated recombination in E. coli. Construction of S gene recombinant C-78 by swapping with the S gene of virulent IBV. S gene determines neutralization specificity but not virulence and tissue-tropism.
Avian infectious bronchitis virus (IBV) causes highly contagious respiratory reproductive and renal system diseases in chickens, and emergence of serotypic variants resulting from mutations in the viral S gene hampers vaccine management for IBV infection. In this study, to facilitate the molecular analysis of IBV pathogenesis and the development of a new-generation IBV vaccine, we established a reverse genetics system (RGS) for cloning the full-length cDNA of the IBV C-78E128 attenuated strain in a bacterial artificial chromosome (BAC). The BAC-cloned C-78E128 cDNA generated infectious viruses with biological properties of the parental C-78E128 strain with regard to an avirulent phenotype, tissue tropism and induction of virus neutralizing (VN) antibody in vivo. To assess the feasibility of genetic manipulation of the IBV genome using the BAC-based RGS, the S gene of the BAC-cloned C-78E128 cDNA was replaced with that of the IBV S95E4 virulent strain, which differs from the C-78E128 strain in serotype and tissue tropism, by bacteriophage lambda Red-mediated homologous recombination in Escherichia coli (E. coli). The resultant S gene recombinant virus was found to be avirulent and fully competent to induce a serotype-specific VN antibody against the S95 strain; however, the S gene recombinant virus did not fully recapitulate the tissue tropism of the S95E4 strain. These data imply that serotype-specific VN immunogenicity, but not tissue-tropism and pathogenicity, of IBV is determined by the viral S gene. The IBV BAC-based RGS that enables cloning and manipulation of the IBV virus genome entirely in E. coli provides a useful platform for the molecular analyses of IBV pathogenesis and the development of rationally designed IBV recombinant vaccines.
Collapse
|
23
|
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.
Collapse
|
24
|
Coronavirus RNA Synthesis Takes Place within Membrane-Bound Sites. Viruses 2021; 13:v13122540. [PMID: 34960809 PMCID: PMC8708976 DOI: 10.3390/v13122540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
Infectious bronchitis virus (IBV), a gammacoronavirus, is an economically important virus to the poultry industry, as well as a significant welfare issue for chickens. As for all positive strand RNA viruses, IBV infection causes rearrangements of the host cell intracellular membranes to form replication organelles. Replication organelle formation is a highly conserved and vital step in the viral life cycle. Here, we investigate the localization of viral RNA synthesis and the link with replication organelles in host cells. We have shown that sites of viral RNA synthesis and virus-related dsRNA are associated with one another and, significantly, that they are located within a membrane-bound compartment within the cell. We have also shown that some viral RNA produced early in infection remains within these membranes throughout infection, while a proportion is trafficked to the cytoplasm. Importantly, we demonstrate conservation across all four coronavirus genera, including SARS-CoV-2. Understanding more about the replication of these viruses is imperative in order to effectively find ways to control them.
Collapse
|
25
|
Koetzner CA, Hurst-Hess KR, Kuo L, Masters PS. Analysis of a crucial interaction between the coronavirus nucleocapsid protein and the major membrane-bound subunit of the viral replicase-transcriptase complex. Virology 2021; 567:1-14. [PMID: 34933176 PMCID: PMC8669624 DOI: 10.1016/j.virol.2021.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022]
Abstract
The coronavirus nucleocapsid (N) protein comprises two RNA-binding domains connected by a central spacer, which contains a serine- and arginine-rich (SR) region. The SR region engages the largest subunit of the viral replicase-transcriptase, nonstructural protein 3 (nsp3), in an interaction that is essential for efficient initiation of infection by genomic RNA. We carried out an extensive genetic analysis of the SR region of the N protein of mouse hepatitis virus in order to more precisely define its role in RNA synthesis. We further examined the N-nsp3 interaction through construction of nsp3 mutants and by creation of an interspecies N protein chimera. Our results indicate a role for the central spacer as an interaction hub of the N molecule that is partially regulated by phosphorylation. These findings are discussed in relation to the recent discovery that nsp3 forms a molecular pore in the double-membrane vesicles that sequester the coronavirus replicase-transcriptase.
Collapse
Affiliation(s)
- Cheri A Koetzner
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Kelley R Hurst-Hess
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Lili Kuo
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Paul S Masters
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA; Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY, 12208, USA.
| |
Collapse
|
26
|
Abstract
Historically part of the coronavirus (CoV) family, torovirus (ToV) was recently classified into the new family Tobaniviridae. While reverse genetics systems have been established for various CoVs, none exist for ToVs. Herein, we developed a reverse genetics system using an infectious full-length cDNA clone of bovine ToV (BToV) in a bacterial artificial chromosome (BAC). Recombinant BToV harboring genetic markers had the same phenotype as wild-type (wt) BToV. To generate two types of recombinant virus, the hemagglutinin-esterase (HE) gene was edited, as cell-adapted wtBToV generally loses full-length HE (HEf), resulting in soluble HE (HEs). First, recombinant viruses with HEf and HA-tagged HEf or HEs genes were rescued. These exhibited no significant differences in their effect on virus growth in HRT18 cells, suggesting that HE is not essential for viral replication in these cells. Thereafter, we generated recombinant virus (rEGFP), wherein HE was replaced by the enhanced green fluorescent protein (EGFP) gene. The rEGFP expressed EGFP in infected cells, but showed significantly lower viral growth compared to wtBToV. Moreover, the rEGFP readily deleted the EGFP gene after one passage. Interestingly, rEGFP variants with two mutations (C1442F and I3562T) in non-structural proteins (NSPs) that emerged during passages exhibited improved EGFP expression, EGFP gene retention, and viral replication. An rEGFP into which both mutations were introduced displayed a similar phenotype to these variants, suggesting that the mutations contributed to EGFP gene acceptance. The current findings provide new insights into BToV, and reverse genetics will help advance the current understanding of this neglected pathogen. Importance ToVs are diarrhea-causing pathogens detected in various species, including humans. Through the development of a BAC-based BToV, we introduced the first reverse genetics system for Tobaniviridae. Utilizing this system, recombinant BToVs with a full-length HE gene were generated. Remarkably, although clinical BToVs generally lose the HE gene after a few passages, some recombinant viruses generated in the current study retained the HE gene for up to 20 passages while accumulating mutations in NSPs, which suggested that these mutations may be involved in HE gene retention. The EGFP gene of recombinant viruses was unstable, but rEGFP into which two NSP mutations were introduced exhibited improved EGFP expression, gene retention, and viral replication. These data suggested the existence of an NSP-based acceptance or retention mechanism for exogenous RNA or HE genes. Recombinant BToVs and reverse genetics are powerful tools for understanding fundamental viral processes, infection pathogenesis, and BToV vaccine development.
Collapse
|
27
|
Hepp C, Shiaelis N, Robb NC, Vaughan A, Matthews PC, Stoesser N, Crook D, Kapanidis AN. Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA. Sci Rep 2021; 11:19579. [PMID: 34599242 PMCID: PMC8486776 DOI: 10.1038/s41598-021-98972-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 min, in virus cultures, combined nasal and throat swabs with added virus and likely patient samples without previous purification. This fast and facile workflow can be adapted both as a lab technique and a future diagnostic tool in enveloped viruses with an accessible genome.
Collapse
Affiliation(s)
- Christof Hepp
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
| | - Nicolas Shiaelis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Nicole C Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Vaughan
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicole Stoesser
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
| |
Collapse
|
28
|
Kanai Y, Kobayashi T. FAST Proteins: Development and Use of Reverse Genetics Systems for Reoviridae Viruses. Annu Rev Virol 2021; 8:515-536. [PMID: 34586868 DOI: 10.1146/annurev-virology-091919-070225] [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] [Indexed: 11/09/2022]
Abstract
Reverse genetics systems for viruses, the technology used to generate gene-engineered recombinant viruses from artificial genes, enable the study of the roles of the individual nucleotides and amino acids of viral genes and proteins in infectivity, replication, and pathogenicity. The successful development of a reverse genetics system for poliovirus in 1981 accelerated the establishment of protocols for other RNA viruses important for human health. Despite multiple efforts, rotavirus (RV), which causes severe gastroenteritis in infants, was refractory to reverse genetics analysis, and the first complete reverse genetics system for RV was established in 2017. This novel technique involves use of the fusogenic protein FAST (fusion-associated small transmembrane) derived from the bat-borne Nelson Bay orthoreovirus, which induces massive syncytium formation. Co-transfection of a FAST-expressing plasmid with complementary DNAs encoding RV genes enables rescue of recombinant RV. This review focuses on methodological insights into the reverse genetics system for RV and discusses applications and potential improvements to this system.
Collapse
Affiliation(s)
- Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; ,
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; ,
| |
Collapse
|
29
|
Tanhaei M, Mohebbi SR, Hosseini SM, Rafieepoor M, Kazemian S, Ghaemi A, Shamloei S, Mirjalali H, Asadzadeh Aghdaei H, Zali MR. The first detection of SARS-CoV-2 RNA in the wastewater of Tehran, Iran. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:38629-38636. [PMID: 33738744 PMCID: PMC7972808 DOI: 10.1007/s11356-021-13393-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/08/2021] [Indexed: 05/03/2023]
Abstract
Following the official announcement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide pandemic spread by WHO on March 11, 2020, more than 300,000 COVID-19 cases reported in Iran resulting in approximately 17,000 deaths as of August 2, 2020. In the present survey, we investigated the presence of SARS-CoV-2 RNA in raw and treated wastewater samples in Tehran, Iran. Untreated and treated wastewater samples were gathered from four wastewater treatment plants over a month period from June to July 2020. Firstly, an adsorption-elution concentration method was tested using an avian coronavirus (infectious bronchitis virus, IBV). Then, the method was effectively employed to survey the presence of SARS-CoV-2 genome in influent and effluent wastewater samples. SARS-CoV-2 RNA was found in 8 out of 10 treated wastewater samples utilizing a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) test to detect ORF1ab and N genes. Moreover, the rate of positivity in wastewater samples increased in last sample collection that shows circulation of SARS-CoV-2 was increased among the population. In addition, the high values detected in effluent wastewater from local wastewater treatment plants have several implications in health and ecology that should be further assessed.
Collapse
Affiliation(s)
- Mohammad Tanhaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Arabi str., Yaman Ave., Velenjak, Tehran, Iran.
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Maedeh Rafieepoor
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Kazemian
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Arabi str., Yaman Ave., Velenjak, Tehran, Iran
| | - Amir Ghaemi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Sharareh Shamloei
- Department of Water and Wastewater Quality Control Laboratory, Water and Wastewater Company, Tehran, Iran
| | - Hamed Mirjalali
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Arabi str., Yaman Ave., Velenjak, Tehran, Iran
| |
Collapse
|
30
|
Kumar D T, Shaikh N, Kumar S U, Doss C GP, Zayed H. Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Front Mol Biosci 2021; 8:645216. [PMID: 33898520 PMCID: PMC8062963 DOI: 10.3389/fmolb.2021.645216] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 01/18/2023] Open
Abstract
The number of confirmed COVID-19 cases is rapidly increasing with no direct treatment for the disease. Few repurposed drugs, such as Remdesivir, Chloroquine, Hydroxychloroquine, Lopinavir, and Ritonavir, are being tested against SARS-CoV-2. Remdesivir is the drug of choice for Ebola virus disease and has been authorized for emergency use. This drug acts against SARS-CoV-2 by inhibiting the RNA-dependent-RNA-polymerase (RdRp) of SARS-CoV-2. RdRp of viruses is prone to mutations that confer drug resistance. A recent study by Pachetti et al. in 2020 identified the P323L mutation in the RdRp protein of SARS-CoV-2. In this study, we aimed to determine the potency of lead compounds similar to Remdesivir, which can be used as an alternative when variants of SARS-CoV-2 develop resistance due to RdRp mutations. The initial screening yielded 704 compounds that were 90% similar to the control drug, Remdesivir. On further evaluation through drugability and antiviral inhibition percentage analyses, we shortlisted 32 and seven compounds, respectively. These seven compounds were further analyzed for their molecular interactions, which revealed that all seven compounds interacted with RdRp with higher affinity than Remdesivir under native conditions. However, three compounds failed to interact with the mutant protein with higher affinity than Remdesivir. Dynamic cross-correlation matrix (DCCM) and vector field collective motions analyses were performed to identify the precise movements of docked complexes' residues. Furthermore, the compound SCHEMBL20144212 showed a high affinity for native and mutant proteins and might provide an alternative against SARS-CoV-2 variants that might confer resistance to Remdesivir. Further validations by in vitro and in vivo studies are needed to confirm the efficacy of our lead compounds for their inhibition against SARS-CoV-2.
Collapse
Affiliation(s)
- Thirumal Kumar D
- Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Nishaat Shaikh
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Udhaya Kumar S
- Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - George Priya Doss C
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| |
Collapse
|
31
|
Benzigar MR, Bhattacharjee R, Baharfar M, Liu G. Current methods for diagnosis of human coronaviruses: pros and cons. Anal Bioanal Chem 2021; 413:2311-2330. [PMID: 33219449 PMCID: PMC7679240 DOI: 10.1007/s00216-020-03046-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/14/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
The current global fight against coronavirus disease (COVID-19) to flatten the transmission curve is put forth by the World Health Organization (WHO) as there is no immediate diagnosis or cure for COVID-19 so far. In order to stop the spread, researchers worldwide are working around the clock aiming to develop reliable tools for early diagnosis of severe acute respiratory syndrome (SARS-CoV-2) understanding the infection path and mechanisms. Currently, nucleic acid-based molecular diagnosis (real-time reverse transcription polymerase chain reaction (RT-PCR) test) is considered the gold standard for early diagnosis of SARS-CoV-2. Antibody-based serology detection is ineffective for the purpose of early diagnosis, but a potential tool for serosurveys, providing people with immune certificates for clearance from COVID-19 infection. Meanwhile, there are various blooming methods developed these days. In this review, we summarise different types of coronavirus discovered which can be transmitted between human beings. Methods used for diagnosis of the discovered human coronavirus (SARS, MERS, COVID-19) including nucleic acid detection, gene sequencing, antibody detection, antigen detection, and clinical diagnosis are presented. Their merits, demerits and prospects are discussed which can help the researchers to develop new generation of advanced diagnostic tools for accurate and effective control of human coronavirus transmission in the communities and hospitals.
Collapse
Affiliation(s)
- Mercy R Benzigar
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ripon Bhattacharjee
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mahroo Baharfar
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Guozhen Liu
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia.
| |
Collapse
|
32
|
Sun X, Li L, Pan L, Wang Z, Chen H, Shao C, Yu J, Ren Y, Wang X, Huang X, Zhang R, Li G. Infectious bronchitis virus: Identification of Gallus gallus APN high-affinity ligands with antiviral effects. Antiviral Res 2020; 186:104998. [PMID: 33340637 DOI: 10.1016/j.antiviral.2020.104998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
Infectious bronchitis virus (IBV) is a coronavirus, causes infectious bronchitis (IB) with high morbidity and mortality, and gives rise to huge economic losses for the poultry industry. Aminopeptidase N (APN) may be one of the IBV functional receptors. In this study, Gallus gallus APN (gAPN) protein was screened by phage-displayed 12-mer peptide library. Two high-affinity peptides H (HDYLYYTFTGNP) and T (TKFSPPSFWYLH) to gAPN protein were selected for in depth characterization of their anti-IBV effects. In vitro, indirect ELISA showed that these two high-affinity ligands could bind IBV S1 antibodies. Quantitative real-time PCR (qRT-PCR) assay, virus yield reduction assay and indirect immunofluorescence assay results revealed 3.125-50 μg/ml of peptide H and 6.25-50 μg/ml of peptide T reduced IBV proliferation in chicken embryo kidney cells (CEKs). In vivo, high-affinity phage-vaccinated chickens were able to induce specific IBV S1 antibodies and IBV neutralizing antibodies. QRT-PCR results confirmed that high-affinity phages reduced virus proliferation in chicken tracheas, lungs and kidneys, and alleviated IBV-induced lesions. By multiple sequence alignment, motif 'YxYY' and 'FxPPxxWxLH' of high-affinity peptides were identified in IBV S1-NTD, while another motif 'YxFxGN' located in S2. These results indicated that high affinity peptides of gAPN could present an alternative approach to IB prevention or treatment.
Collapse
Affiliation(s)
- Xiaoqi Sun
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Lanlan Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Long Pan
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zheng Wang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Huijie Chen
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Changhao Shao
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jia Yu
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yudong Ren
- College of Electrical and Information Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiurong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, 150069, China
| | - Xiaodan Huang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ruili Zhang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Guangxing Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
33
|
Keep S, Oade MS, Lidzbarski-Silvestre F, Bentley K, Stevenson-Leggett P, Freimanis GL, Tennakoon C, Sanderson N, Hammond JA, Jones RC, Britton P, Bickerton E. Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus. J Gen Virol 2020; 101:1103-1118. [PMID: 32720890 PMCID: PMC7660457 DOI: 10.1099/jgv.0.001474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus sub-genomic mRNA (sgmRNA) synthesis occurs via a process of discontinuous transcription involving complementary transcription regulatory sequences (TRSs), one (TRS-L) encompassing the leader sequence of the 5' untranslated region (UTR), and the other upstream of each structural and accessory gene (TRS-B). Several coronaviruses have an ORF located between the N gene and the 3'-UTR, an area previously thought to be non-coding in the Gammacoronavirus infectious bronchitis virus (IBV) due to a lack of a canonical TRS-B. Here, we identify a non-canonical TRS-B allowing for a novel sgmRNA relating to this ORF to be produced in several strains of IBV: Beaudette, CR88, H120, D1466, Italy-02 and QX. Interestingly, the potential protein produced by this ORF is prematurely truncated in the Beaudette strain. A single nucleotide deletion was made in the Beaudette strain allowing for the generation of a recombinant IBV (rIBV) that had the potential to express a full-length protein. Assessment of this rIBV in vitro demonstrated that restoration of the full-length potential protein had no effect on viral replication. Further assessment of the Beaudette-derived RNA identified a second non-canonically transcribed sgmRNA located within gene 2. Deep sequencing analysis of allantoic fluid from Beaudette-infected embryonated eggs confirmed the presence of both the newly identified non-canonically transcribed sgmRNAs and highlighted the potential for further yet unidentified sgmRNAs. This HiSeq data, alongside the confirmation of non-canonically transcribed sgmRNAs, indicates the potential of the coronavirus genome to encode a larger repertoire of genes than has currently been identified.
Collapse
Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
| | | | - Filip Lidzbarski-Silvestre
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Kirsten Bentley
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- School of Biology, University of St Andrews, St Andrews, UK
| | | | | | | | - Nicholas Sanderson
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Richard C. Jones
- School of Veterinary Science, University of Liverpool, Neston, UK
| | - Paul Britton
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
| | | |
Collapse
|
34
|
Stevenson-Leggett P, Keep S, Bickerton E. Treatment with Exogenous Trypsin Expands In Vitro Cellular Tropism of the Avian Coronavirus Infectious Bronchitis Virus. Viruses 2020; 12:E1102. [PMID: 33003350 PMCID: PMC7600076 DOI: 10.3390/v12101102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
The Gammacoronavirus infectious bronchitis virus (IBV) causes a highly contagious and economically important respiratory disease in poultry. In the laboratory, most IBV strains are restricted to replication in ex vivo organ cultures or in ovo and do not replicate in cell culture, making the study of their basic virology difficult. Entry of IBV into cells is facilitated by the large glycoprotein on the surface of the virion, the spike (S) protein, comprised of S1 and S2 subunits. Previous research showed that the S2' cleavage site is responsible for the extended tropism of the IBV Beaudette strain. This study aims to investigate whether protease treatment can extend the tropism of other IBV strains. Here we demonstrate that the addition of exogenous trypsin during IBV propagation in cell culture results in significantly increased viral titres. Using a panel of IBV strains, exhibiting varied tropisms, the effects of spike cleavage on entry and replication were assessed by serial passage cell culture in the presence of trypsin. Replication could be maintained over serial passages, indicating that the addition of exogenous protease is sufficient to overcome the barrier to infection. Mutations were identified in both S1 and S2 subunits following serial passage in cell culture. This work provides a proof of concept that exogenous proteases can remove the barrier to IBV replication in otherwise non-permissive cells, providing a platform for further study of elusive field strains and enabling sustainable vaccine production in vitro.
Collapse
Affiliation(s)
| | | | - Erica Bickerton
- The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK; (P.S.-L.); (S.K.)
| |
Collapse
|
35
|
Keep S, Britton P, Bickerton E. Transient Dominant Selection for the Modification and Generation of Recombinant Infectious Bronchitis Coronaviruses. Methods Mol Biol 2020; 2203:147-165. [PMID: 32833211 DOI: 10.1007/978-1-0716-0900-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have developed a reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) in which a full-length cDNA corresponding to the IBV genome is inserted into the vaccinia virus genome under the control of a T7 promoter sequence. Vaccinia virus as a vector for the full-length IBV cDNA has the advantage that modifications can be introduced into the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. Here, we describe the use of transient dominant selection as a method for introducing modifications into the IBV cDNA that has been successfully used for the substitution of specific nucleotides, deletion of genomic regions, and the exchange of complete genes. Infectious recombinant IBVs are generated in situ following the transfection of vaccinia virus DNA, containing the modified IBV cDNA, into cells infected with a recombinant fowlpox virus expressing T7 DNA-dependent RNA polymerase.
Collapse
|
36
|
Lv C, Shi T, Zhu P, Peng X, Cao S, Yan Y, Ojha NK, Liao M, Zhou J. Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis. Appl Microbiol Biotechnol 2020; 104:8427-8437. [PMID: 32813067 PMCID: PMC7434845 DOI: 10.1007/s00253-020-10834-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 01/08/2023]
Abstract
Abstract Infectious bronchitis virus (IBV) is a member of genus gamma-coronavirus in the family Coronaviridae, causing serious economic losses to the poultry industry. Reverse genetics is a common technique to study the biological characteristics of viruses. So far, there is no BAC reverse genetic system available for rescue of IBV infectious clone. In the present study, a new strategy for the construction of IBV infectious cDNA clone was established. The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. Subsequently, using the same technique, another plasmid pBAC-H120/SCS1 was also constructed, in which S1 gene from IBV H120 strain was replaced with that of a virulent SC021202 strain. Recombinant virus rH120 and rH120/SCS1 were rescued by transfecting the plasmids into BHK cells and passaged in embryonated chicken eggs. Finally, the pathogenicity of both the recombinant virus strains rH120 and rH120/SCS1 was evaluated in SPF chickens. The results showed that the chimeric rH120/SCS1 strain was not pathogenic compared with the wild-type IBV SC021202 strain and the chickens inoculated with rH120/SCS1 could resist challenge infection by IBV SC021202. Taken together, our results indicate that BAC reverse genetic system could be used to rescue IBV in vitro and IBV S1 protein alone might not be the key factor for IBV pathogenicity. Key points • BAC vector was used to construct IBV full-length cDNA by homologous recombination. • Based on four subcloning vectors, a recombinant chimeric IBV H120/SCS1 was constructed and rescued. • Pathogenicity of H120/SCS1 was similar to that of H120, but different to that of SC021202.
Collapse
Affiliation(s)
- Chenfei Lv
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Tingting Shi
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Pengpeng Zhu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Xing Peng
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Shangshang Cao
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Yan Yan
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Nishant Kumar Ojha
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Min Liao
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China.
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| |
Collapse
|
37
|
The Characterization of chIFITMs in Avian Coronavirus Infection In Vivo, Ex Vivo and In Vitro. Genes (Basel) 2020; 11:genes11080918. [PMID: 32785186 PMCID: PMC7464837 DOI: 10.3390/genes11080918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 01/11/2023] Open
Abstract
The coronaviruses are a large family of enveloped RNA viruses that commonly cause gastrointestinal or respiratory illnesses in the infected host. Avian coronavirus infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of chickens that can affect the kidneys and reproductive systems resulting in bird mortality and decreased reproductivity. The interferon-inducible transmembrane (IFITM) proteins are activated in response to viral infections and represent a class of cellular restriction factors that restrict the replication of many viral pathogens. Here, we characterize the relative mRNA expression of the chicken IFITM genes in response to IBV infection, in vivo, ex vivo and in vitro using the pathogenic M41-CK strain, the nephropathogenic QX strain and the nonpathogenic Beaudette strain. In vivo we demonstrate a significant upregulation of chIFITM1, 2, 3 and 5 in M41-CK- and QX-infected trachea two days post-infection. In vitro infection with Beaudette, M41-CK and QX results in a significant upregulation of chIFITM1, 2 and 3 at 24 h post-infection. We confirmed a differential innate response following infection with distinct IBV strains and believe that our data provide new insights into the possible role of chIFITMs in early IBV infection.
Collapse
|
38
|
Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, Kato T, Lee RE, Yount BL, Mascenik TM, Chen G, Olivier KN, Ghio A, Tse LV, Leist SR, Gralinski LE, Schäfer A, Dang H, Gilmore R, Nakano S, Sun L, Fulcher ML, Livraghi-Butrico A, Nicely NI, Cameron M, Cameron C, Kelvin DJ, de Silva A, Margolis DM, Markmann A, Bartelt L, Zumwalt R, Martinez FJ, Salvatore SP, Borczuk A, Tata PR, Sontake V, Kimple A, Jaspers I, O'Neal WK, Randell SH, Boucher RC, Baric RS. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell 2020; 182:429-446.e14. [PMID: 32526206 DOI: 10.1016/j.cell.2020.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 05/26/2023]
Abstract
The mode of acquisition and causes for the variable clinical spectrum of coronavirus disease 2019 (COVID-19) remain unknown. We utilized a reverse genetics system to generate a GFP reporter virus to explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and a luciferase reporter virus to demonstrate sera collected from SARS and COVID-19 patients exhibited limited cross-CoV neutralization. High-sensitivity RNA in situ mapping revealed the highest angiotensin-converting enzyme 2 (ACE2) expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) versus distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. These findings highlight the nasal susceptibility to SARS-CoV-2 with likely subsequent aspiration-mediated virus seeding to the lung in SARS-CoV-2 pathogenesis. These reagents provide a foundation for investigations into virus-host interactions in protective immunity, host susceptibility, and virus pathogenesis.
Collapse
Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takafumi Kato
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa M Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gang Chen
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Ghio
- National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rodney Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ling Sun
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Leslie Fulcher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Nathan I Nicely
- Protein Expression and Purification Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark Cameron
- Department of Population and Quantitative Health Science, Case Western Reserve University, Cleveland, OH, USA
| | - Cheryl Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunology, Shantou University Medical College, Shantou, Guangdong, China
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Markmann
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luther Bartelt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ross Zumwalt
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Steven P Salvatore
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Adam Kimple
- Department of Otolaryngology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ilona Jaspers
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
39
|
Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, Kato T, Lee RE, Yount BL, Mascenik TM, Chen G, Olivier KN, Ghio A, Tse LV, Leist SR, Gralinski LE, Schäfer A, Dang H, Gilmore R, Nakano S, Sun L, Fulcher ML, Livraghi-Butrico A, Nicely NI, Cameron M, Cameron C, Kelvin DJ, de Silva A, Margolis DM, Markmann A, Bartelt L, Zumwalt R, Martinez FJ, Salvatore SP, Borczuk A, Tata PR, Sontake V, Kimple A, Jaspers I, O'Neal WK, Randell SH, Boucher RC, Baric RS. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell 2020; 182:429-446.e14. [PMID: 32526206 PMCID: PMC7250779 DOI: 10.1016/j.cell.2020.05.042] [Citation(s) in RCA: 1069] [Impact Index Per Article: 267.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
The mode of acquisition and causes for the variable clinical spectrum of coronavirus disease 2019 (COVID-19) remain unknown. We utilized a reverse genetics system to generate a GFP reporter virus to explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and a luciferase reporter virus to demonstrate sera collected from SARS and COVID-19 patients exhibited limited cross-CoV neutralization. High-sensitivity RNA in situ mapping revealed the highest angiotensin-converting enzyme 2 (ACE2) expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) versus distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. These findings highlight the nasal susceptibility to SARS-CoV-2 with likely subsequent aspiration-mediated virus seeding to the lung in SARS-CoV-2 pathogenesis. These reagents provide a foundation for investigations into virus-host interactions in protective immunity, host susceptibility, and virus pathogenesis.
Collapse
Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takafumi Kato
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa M Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gang Chen
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Ghio
- National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rodney Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ling Sun
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Leslie Fulcher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Nathan I Nicely
- Protein Expression and Purification Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark Cameron
- Department of Population and Quantitative Health Science, Case Western Reserve University, Cleveland, OH, USA
| | - Cheryl Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunology, Shantou University Medical College, Shantou, Guangdong, China
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Markmann
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luther Bartelt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ross Zumwalt
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Steven P Salvatore
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Adam Kimple
- Department of Otolaryngology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ilona Jaspers
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
40
|
Keep S, Stevenson-Leggett P, Steyn A, Oade MS, Webb I, Stuart J, Vervelde L, Britton P, Maier HJ, Bickerton E. Temperature Sensitivity: A Potential Method for the Generation of Vaccines against the Avian Coronavirus Infectious Bronchitis Virus. Viruses 2020; 12:E754. [PMID: 32674326 PMCID: PMC7412246 DOI: 10.3390/v12070754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022] Open
Abstract
The Gammacoronavirus infectious bronchitis virus (IBV) is a highly contagious economically important respiratory pathogen of domestic fowl. Reverse genetics allows for the molecular study of pathogenic determinants to enable rational vaccine design. The recombinant IBV (rIBV) Beau-R, a molecular clone of the apathogenic Beaudette strain, has previously been investigated as a vaccine platform. To determine tissues in which Beau-R could effectively deliver antigenic genes, an in vivo study in chickens, the natural host, was used to compare the pattern of viral dissemination of Beau-R to the pathogenic strain M41-CK. Replication of Beau-R was found to be restricted to soft tissue within the beak, whereas M41-CK was detected in beak tissue, trachea and eyelid up to seven days post infection. In vitro assays further identified that, unlike M41-CK, Beau-R could not replicate at 41 °C, the core body temperature of a chicken, but is able to replicate a 37 °C, a temperature relatable to the very upper respiratory tract. Using a panel of rIBVs with defined mutations in the structural and accessory genes, viral replication at permissive and non-permissive temperatures was investigated, identifying that the Beau-R replicase gene was a determinant of temperature sensitivity and that sub-genomic mRNA synthesis had been affected. The identification of temperature sensitive allelic lesions within the Beau-R replicase gene opens up the possibility of using this method of attenuation in other IBV strains for future vaccine development as well as a method to investigate the functions of the IBV replicase proteins.
Collapse
Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Phoebe Stevenson-Leggett
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Angela Steyn
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Michael S. Oade
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Isobel Webb
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Jamie Stuart
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Lonneke Vervelde
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK;
| | - Paul Britton
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Helena J. Maier
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| | - Erica Bickerton
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (A.S.); (M.S.O.); (I.W.); (J.S.); (P.B.); (H.J.M.)
| |
Collapse
|
41
|
Keep S, Sives S, Stevenson-Leggett P, Britton P, Vervelde L, Bickerton E. Limited Cross-Protection against Infectious Bronchitis Provided by Recombinant Infectious Bronchitis Viruses Expressing Heterologous Spike Glycoproteins. Vaccines (Basel) 2020; 8:E330. [PMID: 32580371 PMCID: PMC7350270 DOI: 10.3390/vaccines8020330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Gammacoronavirus infectious bronchitis virus (IBV) causes an economically important respiratory disease of poultry. Protective immunity is associated with the major structural protein, spike (S) glycoprotein, which induces neutralising antibodies and defines the serotype. Cross-protective immunity between serotypes is limited and can be difficult to predict. In this study, the ability of two recombinant IBV vaccine candidates, BeauR-M41(S) and BeauR-4/91(S), to induce cross-protection against a third serotype, QX, was assessed. Both rIBVs are genetically based on the Beaudette genome with only the S gene derived from either M41 or 4/91, two unrelated serotypes. The use of these rIBVs allowed for the assessment of the potential of M41 and 4/91 S glycoproteins to induce cross-protective immunity against a heterologous QX challenge. The impact of the order of vaccination was also assessed. Homologous primary and secondary vaccination with BeauR-M41(S) or BeauR-4/91(S) resulted in a significant reduction of infectious QX load in the trachea at four days post-challenge, whereas heterologous primary and secondary vaccination with BeauR-M41(S) and BeauR-4/91(S) reduced viral RNA load in the conjunctiva-associated lymphoid tissue (CALT). Both homologous and heterologous vaccination regimes reduced clinical signs and birds recovered more rapidly as compared with an unvaccinated/challenge control group. Despite both rIBV BeauR-M41(S) and BeauR-4/91(S) displaying limited replication in vivo, serum titres in these vaccinated groups were higher as compared with the unvaccinated/challenge control group. This suggests that vaccination with rIBV primed the birds for a boosted humoral response to heterologous QX challenge. Collectively, vaccination with the rIBV elicited limited protection against challenge, with failure to protect against tracheal ciliostasis, clinical manifestations, and viral replication. The use of a less attenuated recombinant vector that replicates throughout the respiratory tract could be required to elicit a stronger and prolonged protective immune response.
Collapse
Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (P.B.)
| | - Samantha Sives
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; (S.S.); (L.V.)
| | | | - Paul Britton
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (P.B.)
| | - Lonneke Vervelde
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; (S.S.); (L.V.)
| | - Erica Bickerton
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (P.B.)
| |
Collapse
|
42
|
Snijder EJ, Limpens RWAL, de Wilde AH, de Jong AWM, Zevenhoven-Dobbe JC, Maier HJ, Faas FFGA, Koster AJ, Bárcena M. A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis. PLoS Biol 2020; 18:e3000715. [PMID: 32511245 PMCID: PMC7302735 DOI: 10.1371/journal.pbio.3000715] [Citation(s) in RCA: 304] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/18/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Abstract
Zoonotic coronavirus (CoV) infections, such as those responsible for the current severe acute respiratory syndrome-CoV 2 (SARS-CoV-2) pandemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). Although double-membrane vesicles (DMVs) appear to be a pan-CoV RO element, studies to date describe an assortment of additional CoV-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labeling of newly synthesized viral RNA followed by quantitative electron microscopy (EM) autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs Middle East respiratory syndrome-CoV (MERS-CoV) and SARS-CoV and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in CoV infection.
Collapse
Affiliation(s)
- Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ronald W. A. L. Limpens
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Adriaan H. de Wilde
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Anja W. M. de Jong
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jessika C. Zevenhoven-Dobbe
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Frank F. G. A. Faas
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Abraham J. Koster
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
43
|
Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity. Vaccine 2020; 38:3157-3168. [PMID: 32057575 PMCID: PMC7115396 DOI: 10.1016/j.vaccine.2020.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/28/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
Infectious bronchitis (IB) is a highly infectious viral disease responsible for major economic losses in the poultry industry. A reverse genetic vaccine is a safe, rapid, and effective method of achieving IB prevention and control. In this study, we constructed the recombinant strain, rH120-S1/YZ, using a reverse genetic system, based on the backbone of the H120 vaccine strain, with the S1 gene replaced with that of the QX-like nephropathogenic strain, ck/CH/IBYZ/2011, isolated in China. The results of dwarf chicken embryos, growth kinetics, and viral titration in the embryos demonstrated that the biological characteristics of the recombinant virus remained unchanged. Like the rH120-infected group and in contrast to the rIBYZ-infected group, no mortality, clinical signs, or lesions were observed in the lungs or kidneys of young chickens inoculated with rH120-S1/YZ. The viral loads in various tissues, cloacal, and oral swabs was lower in most types of samples, indicating that the rH120-S1/YZ strain was highly safe in chicks. Compared to rH120 vaccination group, when the efficacy of this strain was evaluated against the QX-like IBV strain, better protection, with 100% survival rate and no disease symptom or gross lesion was observed in the chickens vaccinated with rH120-S1/YZ. Increased levels of IBV-specific antibodies were detected in the serum of the rH120-S1/YZ-vaccinated animals 14 days post-vaccination. Collectively, our results suggest that the recombinant strain, rH120-S1/YZ, may represent a promising vaccine candidate against QX-like IBVs.
Collapse
|
44
|
In-Yeast Assembly of Coronavirus Infectious cDNA Clones Using a Synthetic Genomics Pipeline. Methods Mol Biol 2020; 2203:167-184. [PMID: 32833212 DOI: 10.1007/978-1-0716-0900-2_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Escherichia coli and vaccinia virus-based reverse genetics systems have been widely applied for the manipulation and engineering of coronavirus genomes. These systems, however, present several limitations and are sometimes difficult to establish in a timely manner for (re-)emerging viruses. In this chapter, we present a new universal reverse genetics platform for the assembly and engineering of infectious full-length cDNAs using yeast-based transformation-associated recombination cloning. This novel assembly method not only results in stable coronavirus infectious full-length cDNAs cloned in the yeast Saccharomyces cerevisiae but also fosters and accelerates the manipulation of their genomes. Such a platform is widely applicable for the scientific community, as it requires no specific equipment and can be performed in a standard laboratory setting. The protocol described can be easily adapted to virtually all known or emerging coronaviruses, such as Middle East respiratory syndrome coronavirus (MERS-CoV).
Collapse
|
45
|
Zhao X, Jiang Y, Cheng X, Yu Y, Gao M, Zhou S. Pathogenicity of a QX-like strain of infectious bronchitis virus and effects of accessory proteins 3a and 3b in chickens. Vet Microbiol 2019; 239:108464. [PMID: 31767070 DOI: 10.1016/j.vetmic.2019.108464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/20/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022]
Abstract
QX-like genotype infectious bronchitis virus (IBV) has become prevalent in recent years. Few studies have reported the effects of accessory proteins 3a and 3b on pathogenicity in vivo. We developed a reverse genetics system to manipulate the genome of a QX-like IBV strain IBYZ. Recombinant viruses rIBYZ-ScAUG3a, rIBYZ-ScAUG3b and rIBYZ-ScAUG3ab were generated. These viruses do not express the accessory proteins 3a, 3b, or 3ab due to a mutation in the AUG start codons. In SPF embryonated eggs, the recombinant viruses grew to the same viral load as parental strain rIBYZ. The pathogenicity of rIBYZ and recombinant viruses was examined in 1-day-old SPF chickens. In SPF chickens, rIBYZ-ScAUG3a had a lower mortality than rIBYZ. The clinical signs, gross lesions and histopathological changes of rIBYZ-ScAUG3a group were comparable to those of rIBYZ group. However, viral distribution and viral shedding showed that the viral loads of rIBYZ-ScAUG3a were lower than those of rIBYZ in tissue samples and swab specimens. The rIBYZ-ScAUG3b and rIBYZ-ScAUG3ab strains showed attenuated pathogenicity compared to rIBYZ, as no chickens died and all the parameters tested were considerably low. This study indicates that the absence of accessory proteins 3a and 3b in IBV lead to attenuated pathogenicity in chickens. Protein 3b has a greater effect on pathogenicity than protein 3a. These findings may be used in vaccination trials for the development of a new live-attenuated vaccine.
Collapse
Affiliation(s)
- Xiumei Zhao
- Jiangsu Institute of Poultry Science, Yangzhou 225125, People's Republic of China
| | - Yi Jiang
- Jiangsu Institute of Poultry Science, Yangzhou 225125, People's Republic of China
| | - Xu Cheng
- Jiangsu Institute of Poultry Science, Yangzhou 225125, People's Republic of China
| | - Yan Yu
- Jiangsu Institute of Poultry Science, Yangzhou 225125, People's Republic of China
| | - Mingyan Gao
- Jiangsu Institute of Poultry Science, Yangzhou 225125, People's Republic of China
| | - Sheng Zhou
- Jiangsu Institute of Poultry Science, Yangzhou 225125, People's Republic of China.
| |
Collapse
|
46
|
The S2 Subunit of QX-type Infectious Bronchitis Coronavirus Spike Protein Is an Essential Determinant of Neurotropism. Viruses 2019; 11:v11100972. [PMID: 31652591 PMCID: PMC6832359 DOI: 10.3390/v11100972] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 01/23/2023] Open
Abstract
Some coronaviruses (CoVs) have an extra furin cleavage site (RRKR/S, furin-S2′ site) upstream of the fusion peptide in the spike protein, which plays roles in virion adsorption and fusion. Mutation of the S2′ site of QX genotype (QX-type) infectious bronchitis virus (IBV) spike protein (S) in a recombinant virus background results in higher pathogenicity, pronounced neural symptoms and neurotropism when compared with conditions in wild-type IBV (WT-IBV) infected chickens. In this study, we present evidence suggesting that recombinant IBV with a mutant S2′ site (furin-S2′ site) leads to higher mortality. Infection with mutant IBV induces severe encephalitis and breaks the blood–brain barrier. The results of a neutralization test and immunoprotection experiment show that an original serum and vaccine can still provide effective protection in vivo and in vitro. This is the first demonstration of IBV-induced neural symptoms in chickens with encephalitis and the furin-S2′ site as a determinant of neurotropism.
Collapse
|
47
|
Dinan AM, Keep S, Bickerton E, Britton P, Firth AE, Brierley I. Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution. J Virol 2019; 93:e00714-19. [PMID: 31243124 PMCID: PMC6714804 DOI: 10.1128/jvi.00714-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022] Open
Abstract
Like all coronaviruses, avian infectious bronchitis virus (IBV) possesses a long, single-stranded, positive-sense RNA genome (∼27 kb) and has a complex replication strategy that includes the production of a nested set of subgenomic mRNAs (sgmRNAs). Here, we used whole-transcriptome sequencing (RNASeq) and ribosome profiling (RiboSeq) to delineate gene expression in the IBV M41-CK and Beau-R strains at subcodon resolution. RNASeq facilitated a comparative analysis of viral RNA synthesis and revealed two novel transcription junction sites in the attenuated Beau-R strain, one of which would generate a sgmRNA encoding a ribosomally occupied open reading frame (dORF) located downstream of the nucleocapsid coding region. RiboSeq permitted quantification of the translational efficiency of virus gene expression and identified, for the first time, sites of ribosomal pausing on the genome. Quantification of reads flanking the programmed ribosomal frameshifting (PRF) signal at the genomic RNA ORF1a/ORF1b junction revealed that PRF in IBV is highly efficient (33 to 40%). Triplet phasing of RiboSeq data allowed precise determination of reading frames and revealed the translation of two ORFs (ORF4b and ORF4c on sgmRNA IR), which are widely conserved across IBV isolates. Analysis of differential gene expression in infected primary chick kidney cells indicated that the host cell response to IBV occurs primarily at the level of transcription, with global upregulation of immune-related mRNA transcripts following infection and comparatively modest changes in the translation efficiencies of host genes. Cellular genes and gene networks differentially expressed during virus infection were also identified, giving insights into the host cell response to IBV infection.IMPORTANCE IBV is a major avian pathogen and presents a substantial economic burden to the poultry industry. Improved vaccination strategies are urgently needed to curb the global spread of this virus, and the development of suitable vaccine candidates will be aided by an improved understanding of IBV molecular biology. Our high-resolution data have enabled a precise study of transcription and translation in cells infected with both pathogenic and attenuated forms of IBV and expand our understanding of gammacoronaviral gene expression. We demonstrate that gene expression shows considerable intraspecies variation, with single nucleotide polymorphisms being associated with altered production of sgmRNA transcripts, and our RiboSeq data sets enabled us to uncover novel ribosomally occupied ORFs in both strains. The numerous cellular genes and gene networks found to be differentially expressed during virus infection provide insights into the host cell response to IBV infection.
Collapse
Affiliation(s)
- Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Keep
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | - Paul Britton
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
48
|
Zhao Y, Cheng J, Xu G, Thiel V, Zhang G. Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure. Virus Res 2019; 272:197726. [PMID: 31430502 PMCID: PMC7114641 DOI: 10.1016/j.virusres.2019.197726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
A vaccinia virus-based IBV reverse genetics system was developed. BHK21/N cells and ECE were used to improve rescue efficiency. The improved rescue procedure is readily applicable to other IBVs.
In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. Ten fragments contiguously spanning the complete IBV genome were amplified and cloned into the vaccinia virus genome by homologous recombination. The full-length genomic cDNA was transcribed in vitro, and its transcript was transfected into BHK-21/N cells that could stably express IBV N protein. At 48 h post transfection, the culture medium was harvested and inoculated into 10-day-old specific-pathogen-free embryonated chicken eggs to replicate the rescued virus. This strategy was chosen to facilitate the rescue procedure and to ensure that the recombinant rYN virus will not require any cell culture adaptations. After only one in ovo passage, the recombinant YN virus (rYN) was successfully recovered and confirmed to possess the introduced silent marker mutation in its genome. Biological characteristics of rYN such as the EID50, TCID50, replication in ovo, and replication kinetcs in vitro were tested and all were similar to its parental strain YN. Our findings demonstrate the successful construction of highly-pathogenic QX-type IBV using a modified rescue procedure, allowing for future studies of the molecular biology and pathogenicity of IBV field strains.
Collapse
Affiliation(s)
- Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jinlong Cheng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Gang Xu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Volker Thiel
- Institute for Virology and Immunology, 3012, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty Bern, University of Bern, Switzerland.
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
49
|
Zhao Y, Cheng J, Yan S, Jia W, Zhang K, Zhang G. S gene and 5a accessory gene are responsible for the attenuation of virulent infectious bronchitis coronavirus. Virology 2019; 533:12-20. [PMID: 31078931 PMCID: PMC7112010 DOI: 10.1016/j.virol.2019.04.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/27/2019] [Accepted: 04/29/2019] [Indexed: 11/01/2022]
Abstract
To explore the critical genes associated with infectious bronchitis virus (IBV) virulence, we compared the genome sequences of virulent YN strain and its attenuated strain aYN. Accumulation of mutations in the S gene and the accessory gene 5a were observed, suggesting a potential role in the loss of viral pathogenicity. Two recombinant IBVs (rIBVs) with replacement of the S gene or 5a with corresponding regions from aYN were rescued to verify this speculation. Embryo mortality time/rate showed that rYN-S-aYN and rYN-5a-aYN had an attenuated phenotype in ovo. Replication assay in ovo and in vitro demonstrated the rIBVs had similar replication patterns with wild-type rIBV. Both rIBVs showed reduced mortality, tissue lesions and tissue virus titers in chicken. In conclusion, S gene and 5a accessory gene are responsible for the attenuation of virulent IBV. Insight into the genes responsible for virus attenuation will facilitate the development of future vaccines against IBV.
Collapse
Affiliation(s)
- Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jinlong Cheng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Shihong Yan
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Wenfeng Jia
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Keran Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
50
|
Wang G, Liang R, Liu Z, Shen Z, Shi J, Shi Y, Deng F, Xiao S, Fu ZF, Peng G. The N-Terminal Domain of Spike Protein Is Not the Enteric Tropism Determinant for Transmissible Gastroenteritis Virus in Piglets. Viruses 2019; 11:v11040313. [PMID: 30935078 PMCID: PMC6520731 DOI: 10.3390/v11040313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is the etiologic agent of transmissible gastroenteritis in pigs, and the N-terminal domain of TGEV spike protein is generally recognized as both the virulence determinant and enteric tropism determinant. Here, we assembled a full-length infectious cDNA clone of TGEV in a bacterial artificial chromosome. Using a novel approach, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems efficiently and rapidly rescued another recombinant virus with a 224-amino-acid deletion in the N-terminal domain of the TGEV Spike gene (S_NTD224), which is analogous to the N-terminal domain of porcine respiratory coronavirus. S_NTD224 notably affected the TGEV growth kinetics in PK-15 cells but was not essential for recombinant virus survival. In animal experiments with 13 two-day-old piglets, the TGEV recombinant viruses with/without S_NTD224 deletion induced obvious clinical signs and mortality. Together, our results directly demonstrated that S_NTD224 of TGEV mildly influenced TGEV virulence but was not the enteric tropism determinant and provide new insights for the development of a new attenuated vaccine against TGEV. Importantly, the optimized reverse genetics platform used in this study will simplify the construction of mutant infectious clones and help accelerate progress in coronavirus research.
Collapse
Affiliation(s)
- Gang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Rui Liang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Ziwei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Feng Deng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
- Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|