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Smits SL, Bodewes R, Ruiz-González A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Recovering full-length viral genomes from metagenomes. Front Microbiol 2015; 6:1069. [PMID: 26483782 PMCID: PMC4589665 DOI: 10.3389/fmicb.2015.01069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022] Open
Abstract
Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany
| | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
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102
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Uribe-Campero L, Monroy-García A, Durán-Meza AL, Villagrana-Escareño MV, Ruíz-García J, Hernández J, Núñez-Palenius HG, Gómez-Lim MA. Plant-based porcine reproductive and respiratory syndrome virus VLPs induce an immune response in mice. Res Vet Sci 2015; 102:59-66. [PMID: 26412521 DOI: 10.1016/j.rvsc.2015.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/10/2015] [Accepted: 07/19/2015] [Indexed: 01/14/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) significantly affects the swine industry worldwide. An efficient, protective vaccine is still lacking. Here, we report for the first time the generation and purification of PRRSV virus like particles (VLPs) by expressing GP5, M and N genes in Nicotiana silvestris plants. The particles were clearly visible by transmission electron microscopy (TEM) with a size of 60-70 nm. Hydrodynamic diameter of the particles was obtained and it was confirmed that the VLPs had the appropriate size for PRRS virions and that the VLPs were highly pure. By measuring the Z potential we described the electrophoretic mobility behavior of VLPs and the best conditions for stability of the VLPs were determined. The particles were immunogenic in mice. A western blot of purified particles allowed detection of three coexpressed genes. These VLPs may serve as a platform to develop efficient PRRSV vaccines.
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Affiliation(s)
- Laura Uribe-Campero
- Departamento de Ingeniería Genética, CINVESTAV-IPN, Km 9.6 Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, México.
| | - Alberto Monroy-García
- Unidad de Investigación Médica en Enfermedades Oncológicas, IMSS, CMN SXXI, México, D.F., México; Laboratorio de Inmunobiología, Lab, 3PB, Unidad de Investigación en Diferenciación Celular y Cáncer, Facultad de Estudios Superiores Zaragoza, UMIEZ, Campus II, UNAM, Batalla 5 de mayo s/n, Col. E. Oriente, Esquina Fuerte Loreto, Iztapalapa, CP 09230 México, D.F., México.
| | - Ana L Durán-Meza
- Laboratorio de Física Biológica, Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, México.
| | - María V Villagrana-Escareño
- Laboratorio de Física Biológica, Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, México.
| | - Jaime Ruíz-García
- Laboratorio de Física Biológica, Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, México.
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo A.C., Carretera a La Victoria km 0.6, Hermosillo, Sonora C.P. 83304, México.
| | - Héctor G Núñez-Palenius
- División de Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Exhacienda El Copal s/n, A.P. 311, Irapuato, Gto. C.P. 36500, México.
| | - Miguel A Gómez-Lim
- Departamento de Ingeniería Genética, CINVESTAV-IPN, Km 9.6 Carretera Irapuato-León, C.P. 36821 Irapuato, Guanajuato, México.
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103
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Lehmann KC, Hooghiemstra L, Gulyaeva A, Samborskiy DV, Zevenhoven-Dobbe JC, Snijder EJ, Gorbalenya AE, Posthuma CC. Arterivirus nsp12 versus the coronavirus nsp16 2'-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins. J Gen Virol 2015; 96:2643-2655. [PMID: 26041874 PMCID: PMC7081073 DOI: 10.1099/vir.0.000209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/02/2015] [Indexed: 01/19/2023] Open
Abstract
The 3'-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 2'-O-methyltransferase (2'-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 5' cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 5' cap although no candidate MTases have been identified thus far. To address this knowledge gap, we analysed the uncharacterized nsp12 of arteriviruses, which occupies the ORF1b position equivalent to that of the nidovirus 2'-O-MTase (coronavirus nsp16). In our in-depth bioinformatics analysis of nsp12, the protein was confirmed to be family specific whilst having diverged much further than other nidovirus ORF1b-encoded proteins, including those of the family Coronaviridae. Only one invariant and several partially conserved, predominantly aromatic residues were identified in nsp12, which may adopt a structure with alternating α-helices and β-strands, an organization also found in known MTases. However, no statistically significant similarity was found between nsp12 and the twofold larger coronavirus nsp16, nor could we detect MTase activity in biochemical assays using recombinant equine arteritis virus (EAV) nsp12. Our further analysis established that this subunit is essential for replication of this prototypic arterivirus. Using reverse genetics, we assessed the impact of 25 substitutions at 14 positions, yielding virus phenotypes ranging from WT-like to non-viable. Notably, replacement of the invariant phenylalanine 109 with tyrosine was lethal. We concluded that nsp12 plays an essential role during EAV replication, possibly by acting as a co-factor for another enzyme.
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Affiliation(s)
- Kathleen C. Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Lisa Hooghiemstra
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Anastasia Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Dmitry V. Samborskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | | | - Eric J. Snijder
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Clara C. Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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104
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Lehmann KC, Gulyaeva A, Zevenhoven-Dobbe JC, Janssen GMC, Ruben M, Overkleeft HS, van Veelen PA, Samborskiy DV, Kravchenko AA, Leontovich AM, Sidorov IA, Snijder EJ, Posthuma CC, Gorbalenya AE. Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. Nucleic Acids Res 2015; 43:8416-34. [PMID: 26304538 PMCID: PMC4787807 DOI: 10.1093/nar/gkv838] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/08/2015] [Indexed: 11/13/2022] Open
Abstract
RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that catalyzes the synthesis of their RNA(s). In the case of positive-stranded RNA viruses belonging to the order Nidovirales, the RdRp resides in a replicase subunit that is unusually large. Bioinformatics analysis of this non-structural protein has now revealed a nidoviral signature domain (genetic marker) that is N-terminally adjacent to the RdRp and has no apparent homologs elsewhere. Based on its conservation profile, this domain is proposed to have nucleotidylation activity. We used recombinant non-structural protein 9 of the arterivirus equine arteritis virus (EAV) and different biochemical assays, including irreversible labeling with a GTP analog followed by a proteomics analysis, to demonstrate the manganese-dependent covalent binding of guanosine and uridine phosphates to a lysine/histidine residue. Most likely this was the invariant lysine of the newly identified domain, named nidovirus RdRp-associated nucleotidyltransferase (NiRAN), whose substitution with alanine severely diminished the described binding. Furthermore, this mutation crippled EAV and prevented the replication of severe acute respiratory syndrome coronavirus (SARS-CoV) in cell culture, indicating that NiRAN is essential for nidoviruses. Potential functions supported by NiRAN may include nucleic acid ligation, mRNA capping and protein-primed RNA synthesis, possibilities that remain to be explored in future studies.
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Affiliation(s)
- Kathleen C Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Anastasia Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Mark Ruben
- Leiden Institute of Chemistry, Leiden University, 2300 CC, Leiden, The Netherlands
| | - Hermen S Overkleeft
- Leiden Institute of Chemistry, Leiden University, 2300 CC, Leiden, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Dmitry V Samborskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Alexander A Kravchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Andrey M Leontovich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Igor A Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia
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105
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of Potential RNAi (miRNA and siRNA) Molecules for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Gene Silencing by Computational Method. Interdiscip Sci 2015. [PMID: 26223545 PMCID: PMC7090891 DOI: 10.1007/s12539-015-0266-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF1ab replicase polyprotein may be used as a suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence-specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In the current study, four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Md Anayet Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.
| | - Mohammad Al Amin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Mehjabeen Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Tahmina Sharmin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
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106
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Wu CH, Chen PJ, Yeh SH. Nucleocapsid phosphorylation and RNA helicase DDX1 recruitment enables coronavirus transition from discontinuous to continuous transcription. Cell Host Microbe 2015; 16:462-72. [PMID: 25299332 PMCID: PMC7104987 DOI: 10.1016/j.chom.2014.09.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 07/11/2014] [Accepted: 08/22/2014] [Indexed: 11/27/2022]
Abstract
Coronaviruses contain a positive-sense single-stranded genomic (g) RNA, which encodes nonstructural proteins. Several subgenomic mRNAs (sgmRNAs) encoding structural proteins are generated by template switching from the body transcription regulatory sequence (TRS) to the leader TRS. The process preferentially generates shorter sgmRNA. Appropriate readthrough of body TRSs is required to produce longer sgmRNAs and full-length gRNA. We find that phosphorylation of the viral nucleocapsid (N) by host glycogen synthase kinase-3 (GSK-3) is required for template switching. GSK-3 inhibition selectively reduces the generation of gRNA and longer sgmRNAs, but not shorter sgmRNAs. N phosphorylation allows recruitment of the RNA helicase DDX1 to the phosphorylated-N-containing complex, which facilitates template readthrough and enables longer sgmRNA synthesis. DDX1 knockdown or loss of helicase activity markedly reduces the levels of longer sgmRNAs. Thus, coronaviruses employ a unique strategy for the transition from discontinuous to continuous transcription to ensure balanced sgmRNAs and full-length gRNA synthesis.
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Affiliation(s)
- Chia-Hsin Wu
- Department of Microbiology, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan
| | - Pei-Jer Chen
- Department of Microbiology, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan; National Taiwan University Research Center for Medical Excellence, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan
| | - Shiou-Hwei Yeh
- Department of Microbiology, National Taiwan University College of Medicine, No. 1, Jen-Ai Road, Section 1, Taipei 10051, Taiwan; National Taiwan University Research Center for Medical Excellence, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, No. 1, Changde Street, Taipei 10048, Taiwan.
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107
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Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging highly pathogenic respiratory virus. Although MERS-CoV only emerged in 2012, we and others have developed assays to grow and quantify infectious MERS-CoV and RNA products of replication in vitro. MERS-CoV is able to infect a range of cell types, but replicates to high titers in Vero E6 cells. Protocols for the propagation and quantification of MERS-CoV are presented.
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Affiliation(s)
- Christopher M Coleman
- University of Maryland School of Medicine, Microbiology and Immunology, Baltimore, Maryland
| | - Matthew B Frieman
- University of Maryland School of Medicine, Microbiology and Immunology, Baltimore, Maryland
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108
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Zhang T, Han Z, Xu Q, Wang Q, Gao M, Wu W, Shao Y, Li H, Kong X, Liu S. Serotype shift of a 793/B genotype infectious bronchitis coronavirus by natural recombination. INFECTION GENETICS AND EVOLUTION 2015; 32:377-87. [PMID: 25843651 PMCID: PMC7106108 DOI: 10.1016/j.meegid.2015.03.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 01/26/2023]
Abstract
Infectious bronchitis virus causes a respiratory disease in domestic chickens worldwide. Recombination is thought to contribute to the emergence of IBV variants. Strain ck/CH/LHLJ/140906 is originated from recombination events between 4/91- and H120-like strains. Recombination of the S1 domain resulted in the emergence of a novel serotype of IBV.
An infectious bronchitis coronavirus, designated as ck/CH/LHLJ/140906, was isolated from an infectious bronchitis virus (IBV) strain H120-vaccinated chicken flock, which presented with a suspected infectious bronchitis virus (IBV) infection. A phylogenetic analysis based on the S1 gene clustered ck/CH/LHLJ/140906 with the 793/B group; however, a pairwise comparison showed that the 5′ terminal of the S1 gene (containing hypervariable regions I and II) had high sequence identity with the H120 strain, while the 3′ terminal sequence was very similar to that of IBV 4/91 strain. A SimPlot analysis of the complete genomic sequence, which was confirmed by a phylogenetic analysis and nucleotide similarities using the corresponding gene fragments, suggested that isolate ck/CH/LHLJ/140906 emerged from multiple recombination events between parental IBV strains 4/91 and H120. Although the isolate ck/CH/LHLJ/140906 had slightly higher S1 amino acid sequence identity to strain 4/91 (88.2%) than to strain H120 (86%), the serotype of the virus was more closely related to that of the H120 strain (32% antigenic relatedness) than to the 4/91 strain (15% antigenic relatedness). Whereas, vaccination of specific pathogen-free chickens with the 4/91 vaccine provided better protection against challenge with ck/CH/LHLJ/140906 than did vaccination with the H120 strain according to the result of virus re-isolation. As the spike protein, especially in the hypervariable regions of the S1 domain, of IBVs contains viral neutralizing epitopes, the results of this study showed that recombination of the S1 domain resulted in the emergence of a new serotype.
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Affiliation(s)
- Tingting Zhang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Zongxi Han
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Qianqian Xu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Qiuling Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Mengying Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Wei Wu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Yuhao Shao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Huixin Li
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Xiangang Kong
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China
| | - Shengwang Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China.
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109
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Kappes MA, Faaberg KS. PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity. Virology 2015; 479-480:475-86. [PMID: 25759097 PMCID: PMC7111637 DOI: 10.1016/j.virol.2015.02.012] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/23/2015] [Accepted: 02/09/2015] [Indexed: 11/26/2022]
Abstract
Porcine reproductive and respiratory disease virus (PRRSV) has the intrinsic ability to adapt and evolve. After 25 years of study, this persistent pathogen has continued to frustrate efforts to eliminate infection of herds through vaccination or other elimination strategies. The purpose of this review is to summarize the research on the virion structure, replication and recombination properties of PRRSV that have led to the extraordinary phenotype and genotype diversity that exists worldwide. Review of structure, replication and recombination of porcine reproductive and respiratory syndrome virus. Homologous recombination to produce conventional subgenomic messenger RNA as well as heteroclite RNA. Discussion of structure, replication and recombination mechanisms that have yielded genotypic and phenotypic diversity.
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Affiliation(s)
- Matthew A Kappes
- Virus and Prion Research Unit, USDA-ARS-National Animal Disease Center, Ames, IA, USA
| | - Kay S Faaberg
- Virus and Prion Research Unit, USDA-ARS-National Animal Disease Center, Ames, IA, USA.
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110
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Franzo G, Cecchinato M, Martini M, Ceglie L, Gigli A, Drigo M. Observation of high recombination occurrence of Porcine Reproductive and Respiratory Syndrome Virus in field condition. Virus Res 2014; 194:159-66. [PMID: 25150757 PMCID: PMC7127771 DOI: 10.1016/j.virusres.2014.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/07/2014] [Accepted: 08/12/2014] [Indexed: 01/23/2023]
Abstract
Recombination in Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a well-documented phenomenon. A high recombination frequency has been reported in experimental conditions both in vitro and in vivo, and its role in driving viral evolution has been postulated by several authors. However field evidences are rare, mainly obtained from large-scale sampling and typically represented by single sequences rather than by groups of circulating "recombinant progenies". The present work was aimed to investigate the gray area between experimental studies and large-scale epidemiological investigations. The study was performed on ORF5, ORF7 and concatenated sequences obtained in our laboratory or available in GenBank collected between 2009 and 2012 in northern Italy. Six independent recombinant strains out of 66 concatenated sequences (∼9%) were found, demonstrating a high recombination frequency respect to previous field studies but comparable to in vitro experiments. In silico analysis let speculate that this new strain displayed physicochemical features diverse enough to potentially alter its immunological properties. Taken altogether, the results of our study support previous experimental evidences that depict PRRSV to be extremely prone to recombination. The limited temporal and geographical spread of recombinant strains however states in favor of a limited fitness of the recombinant progeny compared to parental strains and the marginal role of this phenomenon in PRRSV evolution.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), Viale dell'Università 16, 35020 Legnaro (PD), Italy.
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), Viale dell'Università 16, 35020 Legnaro (PD), Italy.
| | - Marco Martini
- Department of Animal Medicine, Production and Health (MAPS), Viale dell'Università 16, 35020 Legnaro (PD), Italy.
| | - Letizia Ceglie
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy.
| | - Alessandra Gigli
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy.
| | - Michele Drigo
- Department of Animal Medicine, Production and Health (MAPS), Viale dell'Università 16, 35020 Legnaro (PD), Italy.
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111
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Zhang Y, Li J, Xiao Y, Zhang J, Wang Y, Chen L, Paranhos-Baccalà G, Ren L, Wang J. Genotype shift in human coronavirus OC43 and emergence of a novel genotype by natural recombination. J Infect 2014; 70:641-50. [PMID: 25530469 PMCID: PMC7112537 DOI: 10.1016/j.jinf.2014.12.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/29/2014] [Accepted: 12/14/2014] [Indexed: 11/30/2022]
Abstract
Background Human coronavirus (HCoV) OC43 is the most prevalent HCoV in respiratory tract infections. Its molecular epidemiological characterization, particularly the genotyping, was poorly addressed. Methods The full-length spike (S), RNA-dependent RNA polymerase (RdRp), and nucleocapsid (N) genes were amplified from each respiratory sample collected from 65 HCoV-OC43-positive patients between 2005 and 2012. Genotypes were determined by phylogenetic analysis. Recombination was analyzed based on full-length viral genome sequences. Clinical manifestations of each HCoV genotype infection were compared by reviewing clinical records. Results Sixty of these 65 samples belong to genotypes B, C and D. The remaining five strains had incongruent positions in the phylogenetic trees of the S, RdRp and N genes, suggesting a novel genotype emerging, designated as genotype E. Whole genome sequencing and bootscan analysis indicated that genotype E is generated by recombination between genotypes B, C and D. Temporal analysis revealed a sequential genotype replacement of C, B, D and E over the study period with genotype D being the dominant genotype since 2007. The novel genotype E was only detected in children younger than three years suffering from lower respiratory tract infections. Conclusions Our results suggest that HCoV-OC43 genotypes are evolving. Such genotype shift may be an adapting mechanism for HCoV-OC43 maintaining its epidemic. Temporal shift of multiple human coronavirus OC43 genotypes. Emergence of a novel genotype E by natural recombination. Genotype D dominated HCoV-OC43 epidemic in China in recent years. Genotype evolving plays an important role in HCoV-OC43 epidemic.
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Affiliation(s)
- Yue Zhang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Jianguo Li
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Yan Xiao
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Jing Zhang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Ying Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Lan Chen
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | | | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China.
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China.
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112
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Lehmann KC, Snijder EJ, Posthuma CC, Gorbalenya AE. What we know but do not understand about nidovirus helicases. Virus Res 2014; 202:12-32. [PMID: 25497126 PMCID: PMC7114383 DOI: 10.1016/j.virusres.2014.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The ubiquitous nidovirus helicase is a multi-functional enzyme of superfamily 1. Its unique N-terminal domain is most similar to the Upf1 multinuclear zinc-binding domain. It has been implicated in replication, transcription, virion biogenesis, translation and post-transcriptional viral RNA processing. Four different classes of antiviral compounds targeting the helicase have been identified.
Helicases are versatile NTP-dependent motor proteins of monophyletic origin that are found in all kingdoms of life. Their functions range from nucleic acid duplex unwinding to protein displacement and double-strand translocation. This explains their participation in virtually every metabolic process that involves nucleic acids, including DNA replication, recombination and repair, transcription, translation, as well as RNA processing. Helicases are encoded by all plant and animal viruses with a positive-sense RNA genome that is larger than 7 kb, indicating a link to genome size evolution in this virus class. Viral helicases belong to three out of the six currently recognized superfamilies, SF1, SF2, and SF3. Despite being omnipresent, highly conserved and essential, only a few viral helicases, mostly from SF2, have been studied extensively. In general, their specific roles in the viral replication cycle remain poorly understood at present. The SF1 helicase protein of viruses classified in the order Nidovirales is encoded in replicase open reading frame 1b (ORF1b), which is translated to give rise to a large polyprotein following a ribosomal frameshift from the upstream ORF1a. Proteolytic processing of the replicase polyprotein yields a dozen or so mature proteins, one of which includes a helicase. Its hallmark is the presence of an N-terminal multi-nuclear zinc-binding domain, the nidoviral genetic marker and one of the most conserved domains across members of the order. This review summarizes biochemical, structural, and genetic data, including drug development studies, obtained using helicases originating from several mammalian nidoviruses, along with the results of the genomics characterization of a much larger number of (putative) helicases of vertebrate and invertebrate nidoviruses. In the context of our knowledge of related helicases of cellular and viral origin, it discusses the implications of these results for the protein's emerging critical function(s) in nidovirus evolution, genome replication and expression, virion biogenesis, and possibly also post-transcriptional processing of viral RNAs. Using our accumulated knowledge and highlighting gaps in our data, concepts and approaches, it concludes with a perspective on future research aimed at elucidating the role of helicases in the nidovirus replication cycle.
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Affiliation(s)
- Kathleen C Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.
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113
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Firth AE. Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses. Nucleic Acids Res 2014; 42:12425-39. [PMID: 25326325 PMCID: PMC4227794 DOI: 10.1093/nar/gku981] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 09/20/2014] [Accepted: 10/04/2014] [Indexed: 12/29/2022] Open
Abstract
Identification of the full complement of genes and other functional elements in any virus is crucial to fully understand its molecular biology and guide the development of effective control strategies. RNA viruses have compact multifunctional genomes that frequently contain overlapping genes and non-coding functional elements embedded within protein-coding sequences. Overlapping features often escape detection because it can be difficult to disentangle the multiple roles of the constituent nucleotides via mutational analyses, while high-throughput experimental techniques are often unable to distinguish functional elements from incidental features. However, RNA viruses evolve very rapidly so that, even within a single species, substitutions rapidly accumulate at neutral or near-neutral sites providing great potential for comparative genomics to distinguish the signature of purifying selection. Computationally identified features can then be efficiently targeted for experimental analysis. Here we analyze alignments of protein-coding virus sequences to identify regions where there is a statistically significant reduction in the degree of variability at synonymous sites, a characteristic signature of overlapping functional elements. Having previously tested this technique by experimental verification of discoveries in selected viruses, we now analyze sequence alignments for ∼700 RNA virus species to identify hundreds of such regions, many of which have not been previously described.
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Affiliation(s)
- Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
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114
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of potential RNAi (miRNA and siRNA) molecules for Middle East respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip Sci 2014. [PMID: 25373633 DOI: 10.1007/s12539-014-0208-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
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115
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of potential RNAi (miRNA and siRNA) molecules for Middle East respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip Sci 2014. [PMID: 25519155 DOI: 10.1007/s12539-014-0233-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
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116
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Han M, Yoo D. Engineering the PRRS virus genome: updates and perspectives. Vet Microbiol 2014; 174:279-295. [PMID: 25458419 PMCID: PMC7172560 DOI: 10.1016/j.vetmic.2014.10.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 12/03/2022]
Abstract
We review PRRSV infectious clones and their applications. 14 infectious clones are available so far for genotypes I and II. Genomic mutations, insertions, deletions, and replacements are successful. We discuss advances and utilization of PRRSV reverse genetics and future potential.
Porcine reproductive and respiratory syndrome virus (PRRSV) is endemic in most pig producing countries worldwide and causes enormous economic losses to the pork industry. Infectious clones for PRRSV have been constructed, and so far at least 14 different infectious clones are available representing both genotypes I and II. Two strategies have been taken for progeny reconstitution: RNA transfection and DNA transfection. Mutations, insertions, deletions, and replacements of the viral genome have been employed to study the structure function relationship, foreign gene expression, functional complementation, and virulence determinants. Essential regions and non-essential regions for viral replication have been identified in both the coding regions and non-encoding regions. Foreign sequences have successfully been inserted into the nsp2 and N regions and in the space between ORF1b and ORF2a. Chimeras between member viruses in the family Arteriviridae have also been constructed and utilized to study cell tropism and functional complementation. This review discusses the advances and utilization of PRRSV reverse genetics and its potential for future research.
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Affiliation(s)
- Mingyuan Han
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, United States
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, United States.
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117
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Sevajol M, Subissi L, Decroly E, Canard B, Imbert I. Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus. Virus Res 2014; 194:90-9. [PMID: 25451065 PMCID: PMC7114481 DOI: 10.1016/j.virusres.2014.10.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/06/2014] [Accepted: 10/06/2014] [Indexed: 10/30/2022]
Abstract
The successive emergence of highly pathogenic coronaviruses (CoVs) such as the Severe Acute Respiratory Syndrome (SARS-CoV) in 2003 and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 has stimulated a number of studies on the molecular biology. This research has provided significant new insight into functions and activities of the replication/transcription multi-protein complex. The latter directs both continuous and discontinuous RNA synthesis to replicate and transcribe the large coronavirus genome made of a single-stranded, positive-sense RNA of ∼30 kb. In this review, we summarize our current understanding of SARS-CoV enzymes involved in RNA biochemistry, such as the in vitro characterization of a highly active and processive RNA polymerase complex which can associate with methyltransferase and 3'-5' exoribonuclease activities involved in RNA capping, and RNA proofreading, respectively. The recent discoveries reveal fascinating RNA-synthesizing machinery, highlighting the unique position of coronaviruses in the RNA virus world.
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Affiliation(s)
- Marion Sevajol
- Centre National de la Recherche Scientifique, Aix-Marseille Université, UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Lorenzo Subissi
- Centre National de la Recherche Scientifique, Aix-Marseille Université, UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Etienne Decroly
- Centre National de la Recherche Scientifique, Aix-Marseille Université, UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université, UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Isabelle Imbert
- Centre National de la Recherche Scientifique, Aix-Marseille Université, UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France.
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118
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Madhugiri R, Fricke M, Marz M, Ziebuhr J. RNA structure analysis of alphacoronavirus terminal genome regions. Virus Res 2014; 194:76-89. [PMID: 25307890 PMCID: PMC7114417 DOI: 10.1016/j.virusres.2014.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/30/2014] [Accepted: 10/01/2014] [Indexed: 02/07/2023]
Abstract
Review of current knowledge of cis-acting RNA elements essential to coronavirus replication. Identification of RNA structural elements in alphacoronavirus terminal genome regions. Discussion of intra- and intergeneric conservation of genomic cis-acting RNA elements in alpha- and betacoronaviruses.
Coronavirus genome replication is mediated by a multi-subunit protein complex that is comprised of more than a dozen virally encoded and several cellular proteins. Interactions of the viral replicase complex with cis-acting RNA elements located in the 5′ and 3′-terminal genome regions ensure the specific replication of viral RNA. Over the past years, boundaries and structures of cis-acting RNA elements required for coronavirus genome replication have been extensively characterized in betacoronaviruses and, to a lesser extent, other coronavirus genera. Here, we review our current understanding of coronavirus cis-acting elements located in the terminal genome regions and use a combination of bioinformatic and RNA structure probing studies to identify and characterize putative cis-acting RNA elements in alphacoronaviruses. The study suggests significant RNA structure conservation among members of the genus Alphacoronavirus but also across genus boundaries. Overall, the conservation pattern identified for 5′ and 3′-terminal RNA structural elements in the genomes of alpha- and betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements.
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Affiliation(s)
- Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Markus Fricke
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany.
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119
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Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius. mBio 2014; 5:e01484-14. [PMID: 25205093 PMCID: PMC4173777 DOI: 10.1128/mbio.01484-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A severe, sometimes fatal respiratory disease has been observed in captive ball pythons (Python regius) since the late 1990s. In order to better understand this disease and its etiology, we collected case and control samples and performed pathological and diagnostic analyses. Electron micrographs revealed filamentous virus-like particles in lung epithelial cells of sick animals. Diagnostic testing for known pathogens did not identify an etiologic agent, so unbiased metagenomic sequencing was performed. Abundant nidovirus-like sequences were identified in cases and were used to assemble the genome of a previously unknown virus in the order Nidovirales. The nidoviruses, which were not previously known to infect nonavian reptiles, are a diverse order that includes important human and veterinary pathogens. The presence of the viral RNA was confirmed in all diseased animals (n = 8) but was not detected in healthy pythons or other snakes (n = 57). Viral RNA levels were generally highest in the lung and other respiratory tract tissues. The 33.5-kb viral genome is the largest RNA genome yet described and shares canonical characteristics with other nidovirus genomes, although several features distinguish this from related viruses. This virus, which we named ball python nidovirus (BPNV), will likely establish a new genus in Torovirinae subfamily. The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease. Ball pythons are popular pets because of their diverse coloration, generally nonaggressive behavior, and relatively small size. Since the 1990s, veterinarians have been aware of an infectious respiratory disease of unknown cause in ball pythons that can be fatal. We used unbiased shotgun sequencing to discover a novel virus in the order Nidovirales that was present in cases but not controls. While nidoviruses are known to infect a variety of animals, this is the first report of a nidovirus recovered from any reptile. This report will enable diagnostics that will assist in determining the role of this virus in the causation of disease, which would allow control of the disease in zoos and private collections. Given its evolutionary divergence from known nidoviruses and its unique host, the study of reptile nidoviruses may further our understanding of related diseases and the viruses that cause them in humans and other animals.
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120
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One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proc Natl Acad Sci U S A 2014; 111:E3900-9. [PMID: 25197083 DOI: 10.1073/pnas.1323705111] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In addition to members causing milder human infections, the Coronaviridae family includes potentially lethal zoonotic agents causing severe acute respiratory syndrome (SARS) and the recently emerged Middle East respiratory syndrome. The ∼30-kb positive-stranded RNA genome of coronaviruses encodes a replication/transcription machinery that is unusually complex and composed of 16 nonstructural proteins (nsps). SARS-CoV nsp12, the canonical RNA-dependent RNA polymerase (RdRp), exhibits poorly processive RNA synthesis in vitro, at odds with the efficient replication of a very large RNA genome in vivo. Here, we report that SARS-CoV nsp7 and nsp8 activate and confer processivity to the RNA-synthesizing activity of nsp12. Using biochemical assays and reverse genetics, the importance of conserved nsp7 and nsp8 residues was probed. Whereas several nsp7 mutations affected virus replication to a limited extent, the replacement of two nsp8 residues (P183 and R190) essential for interaction with nsp12 and a third (K58) critical for the interaction of the polymerase complex with RNA were all lethal to the virus. Without a loss of processivity, the nsp7/nsp8/nsp12 complex can associate with nsp14, a bifunctional enzyme bearing 3'-5' exoribonuclease and RNA cap N7-guanine methyltransferase activities involved in replication fidelity and 5'-RNA capping, respectively. The identification of this tripartite polymerase complex that in turn associates with the nsp14 proofreading enzyme sheds light on how coronaviruses assemble an RNA-synthesizing machinery to replicate the largest known RNA genomes. This protein complex is a fascinating example of the functional integration of RNA polymerase, capping, and proofreading activities.
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121
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Terada Y, Matsui N, Noguchi K, Kuwata R, Shimoda H, Soma T, Mochizuki M, Maeda K. Emergence of pathogenic coronaviruses in cats by homologous recombination between feline and canine coronaviruses. PLoS One 2014; 9:e106534. [PMID: 25180686 PMCID: PMC4152292 DOI: 10.1371/journal.pone.0106534] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022] Open
Abstract
Type II feline coronavirus (FCoV) emerged via double recombination between type I FCoV and type II canine coronavirus (CCoV). In this study, two type I FCoVs, three type II FCoVs and ten type II CCoVs were genetically compared. The results showed that three Japanese type II FCoVs, M91-267, KUK-H/L and Tokyo/cat/130627, also emerged by homologous recombination between type I FCoV and type II CCoV and their parent viruses were genetically different from one another. In addition, the 3'-terminal recombination sites of M91-267, KUK-H/L and Tokyo/cat/130627 were different from one another within the genes encoding membrane and spike proteins, and the 5'-terminal recombination sites were also located at different regions of ORF1. These results indicate that at least three Japanese type II FCoVs emerged independently. Sera from a cat experimentally infected with type I FCoV was unable to neutralize type II CCoV infection, indicating that cats persistently infected with type I FCoV may be superinfected with type II CCoV. Our previous study reported that few Japanese cats have antibody against type II FCoV. All of these observations suggest that type II FCoV emerged inside the cat body and is unable to readily spread among cats, indicating that these recombination events for emergence of pathogenic coronaviruses occur frequently.
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MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- Cat Diseases/virology
- Cats
- Coronavirus Infections/veterinary
- Coronavirus Infections/virology
- Coronavirus, Canine/classification
- Coronavirus, Canine/genetics
- Coronavirus, Canine/pathogenicity
- Coronavirus, Feline/classification
- Coronavirus, Feline/genetics
- Coronavirus, Feline/pathogenicity
- DNA, Viral/genetics
- Dogs
- Genes, Viral
- Homologous Recombination
- Japan
- Molecular Sequence Data
- Phylogeny
- Reassortant Viruses/genetics
- Reassortant Viruses/pathogenicity
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Yutaka Terada
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Nobutaka Matsui
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Keita Noguchi
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Takehisa Soma
- Veterinary Diagnostic Laboratory, Marupi Lifetech Co. Ltd., Osaka, Japan
| | - Masami Mochizuki
- Laboratory of Emerging Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
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122
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Zhao F, Han Z, Zhang T, Shao Y, Kong X, Ma H, Liu S. Genomic characteristics and changes of avian infectious bronchitis virus strain CK/CH/LDL/97I after serial passages in chicken embryos. Intervirology 2014; 57:319-30. [PMID: 25195733 PMCID: PMC7179551 DOI: 10.1159/000365193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 06/07/2014] [Indexed: 12/12/2022] Open
Abstract
Background We previously attenuated the infectious bronchitis virus (IBV) strain CK/CH/LDL/97I and found that it can convey protection against the homologous pathogenic virus. Objective To compare the full-length genome sequences of the Chinese IBV strain CK/CH/LDL/97I and its embryo-passaged, attenuated level to identify sequence substitutions responsible for the attenuation and define markers of attenuation. Methods The full-length genomes of CK/CH/LDL/97I P5 and P115 were amplified and sequenced. The sequences were assembled and compared using the MEGALIGN program (DNAStar) and a phylogenetic tree was constructed using MEGA4 software. Results The CK/CH/LDL/97I virus population contained subpopulations with a mixture of genetic mutants. Changes were observed in nsp4, nsp9, nsp11/12, nsp14, nsp15, nsp16, and ORF3a, but these did not result in amino acid substitutions or did not show functional variations. Amino acid substitutions occurred in the remaining genes between P5 and P115; most were found in the S region, and some of the nucleotide mutations resulted in amino acid substitutions. Among the 9 nsps in the ORF1 region, nsp3 contained the most nucleotide substitutions. Conclusions Sequence variations in different genes, especially the S gene and nsp3, in the genomes of CK/CH/LDL/97I viruses might contribute to differences in viral replication, pathogenicity, antigenicity, immunogenicity, and tissue tropism.
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Affiliation(s)
- Fei Zhao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, PR China
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Wang L, Hou J, Gao L, Guo XK, Yu Z, Zhu Y, Liu Y, Tang J, Zhang H, Feng WH. Attenuation of highly pathogenic porcine reproductive and respiratory syndrome virus by inserting an additional transcription unit. Vaccine 2014; 32:5740-8. [PMID: 25171845 PMCID: PMC7115595 DOI: 10.1016/j.vaccine.2014.08.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/06/2014] [Accepted: 08/15/2014] [Indexed: 01/29/2023]
Abstract
We constructed a recombinant HP-PRRSV expressing an additional transcription unit. The additional transcription unit insertion promoted RNA recombination. Genome instability conferred attenuation of HP-PRRSV both in vitro and in vivo. Full investigation should be performed before this approach is used to develop expression/vaccine vector.
Transcription regulatory sequences (TRSs) play a key role in the synthesis of porcine reproductive and respiratory syndrome virus (PRRSV) subgenomic mRNAs, which resembles similarity-assisted RNA recombination. In this study, genome instability was found when a highly pathogenic PRRSV (HP-PRRSV) strain was inserted by an additional transcription unit in which a foreign gene GFP was expressed from TRS2 while a copy of TRS6 drove ORF2a/b transcription. Structural protein gene-deleted genomes resulted from enhanced RNA recombinations were identified in the recombinant virus rHV-GFP. Moreover, rHV-GFP replicated slower than parental viruses, and caused less cell death in porcine alveolar macrophages. Pigs infected with rHV-GFP survived with no or mild syndromes, whereas all pigs infected with parental viruses died within 12 days. Our data showed that additional transcription unit insertion could confer genome instability and attenuation of HP-PRRSV.
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Affiliation(s)
- Lianghai Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jun Hou
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Li Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xue-kun Guo
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhibin Yu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaohua Zhu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yihao Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jun Tang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hexiao Zhang
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing 100026, China
| | - Wen-hai Feng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing 100193, China; Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Uccellini L, Ossiboff RJ, de Matos REC, Morrisey JK, Petrosov A, Navarrete-Macias I, Jain K, Hicks AL, Buckles EL, Tokarz R, McAloose D, Lipkin WI. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius). Virol J 2014; 11:144. [PMID: 25106433 PMCID: PMC4254391 DOI: 10.1186/1743-422x-11-144] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/08/2014] [Indexed: 11/23/2022] Open
Abstract
Background Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. Findings Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. Conclusions This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA.
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Balasuriya UBR, Zhang J, Go YY, MacLachlan NJ. Experiences with infectious cDNA clones of equine arteritis virus: lessons learned and insights gained. Virology 2014; 462-463:388-403. [PMID: 24913633 PMCID: PMC7172799 DOI: 10.1016/j.virol.2014.04.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/16/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
The advent of recombinant DNA technology, development of infectious cDNA clones of RNA viruses, and reverse genetic technologies have revolutionized how viruses are studied. Genetic manipulation of full-length cDNA clones has become an especially important and widely used tool to study the biology, pathogenesis, and virulence determinants of both positive and negative stranded RNA viruses. The first full-length infectious cDNA clone of equine arteritis virus (EAV) was developed in 1996 and was also the first full-length infectious cDNA clone constructed from a member of the order Nidovirales. This clone was extensively used to characterize the molecular biology of EAV and other Nidoviruses. The objective of this review is to summarize the characterization of the virulence (or attenuation) phenotype of the recombinant viruses derived from several infectious cDNA clones of EAV in horses, as well as their application for characterization of the molecular basis of viral neutralization, persistence, and cellular tropism.
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Affiliation(s)
- Udeni B R Balasuriya
- 108 Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Yun Young Go
- Virus Research and Testing Group, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, Daejeon 305-343, South Korea
| | - N James MacLachlan
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Identification of cis-acting elements on positive-strand subgenomic mRNA required for the synthesis of negative-strand counterpart in bovine coronavirus. Viruses 2014; 6:2938-59. [PMID: 25080125 PMCID: PMC4147681 DOI: 10.3390/v6082938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/12/2014] [Accepted: 07/15/2014] [Indexed: 01/06/2023] Open
Abstract
It has been demonstrated that, in addition to genomic RNA, sgmRNA is able to serve as a template for the synthesis of the negative-strand [(−)-strand] complement. However, the cis-acting elements on the positive-strand [(+)-strand] sgmRNA required for (−)-strand sgmRNA synthesis have not yet been systematically identified. In this study, we employed real-time quantitative reverse transcription polymerase chain reaction to analyze the cis-acting elements on bovine coronavirus (BCoV) sgmRNA 7 required for the synthesis of its (−)-strand counterpart by deletion mutagenesis. The major findings are as follows. (1) Deletion of the 5'-terminal leader sequence on sgmRNA 7 decreased the synthesis of the (−)-strand sgmRNA complement. (2) Deletions of the 3' untranslated region (UTR) bulged stem-loop showed no effect on (−)-strand sgmRNA synthesis; however, deletion of the 3' UTR pseudoknot decreased the yield of (−)-strand sgmRNA. (3) Nucleotides positioned from −15 to −34 of the sgmRNA 7 3'-terminal region are required for efficient (−)-strand sgmRNA synthesis. (4) Nucleotide species at the 3'-most position (−1) of sgmRNA 7 is correlated to the efficiency of (−)-strand sgmRNA synthesis. These results together suggest, in principle, that the 5'- and 3'-terminal sequences on sgmRNA 7 harbor cis-acting elements are critical for efficient (−)-strand sgmRNA synthesis in BCoV.
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Bouvet M, Lugari A, Posthuma CC, Zevenhoven JC, Bernard S, Betzi S, Imbert I, Canard B, Guillemot JC, Lécine P, Pfefferle S, Drosten C, Snijder EJ, Decroly E, Morelli X. Coronavirus Nsp10, a critical co-factor for activation of multiple replicative enzymes. J Biol Chem 2014; 289:25783-96. [PMID: 25074927 PMCID: PMC4162180 DOI: 10.1074/jbc.m114.577353] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The RNA-synthesizing machinery of the severe acute respiratory syndrome
Coronavirus (SARS-CoV) is composed of 16 non-structural
proteins (nsp1–16) encoded by ORF1a/1b. The 148-amino acid nsp10 subunit
contains two zinc fingers and is known to interact with both nsp14 and nsp16,
stimulating their respective 3′-5′ exoribonuclease and
2′-O-methyltransferase activities. Using
alanine-scanning mutagenesis, in cellulo bioluminescence
resonance energy transfer experiments, and in vitro pulldown
assays, we have now identified the key residues on the nsp10 surface that
interact with nsp14. The functional consequences of mutations introduced at
these positions were first evaluated biochemically by monitoring nsp14
exoribonuclease activity. Disruption of the nsp10-nsp14 interaction abrogated
the nsp10-driven activation of the nsp14 exoribonuclease. We further showed that
the nsp10 surface interacting with nsp14 overlaps with the surface involved in
the nsp10-mediated activation of nsp16
2′-O-methyltransferase activity, suggesting that nsp10
is a major regulator of SARS-CoV replicase function. In line with this notion,
reverse genetics experiments supported an essential role of the nsp10 surface
that interacts with nsp14 in SARS-CoV replication, as several mutations that
abolished the interaction in vitro yielded a
replication-negative viral phenotype. In contrast, mutants in which the
nsp10-nsp16 interaction was disturbed proved to be crippled but viable. These
experiments imply that the nsp10 surface that interacts with nsp14 and nsp16 and
possibly other subunits of the viral replication complex may be a target for the
development of antiviral compounds against pathogenic coronaviruses.
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Affiliation(s)
- Mickaël Bouvet
- From the Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Adrien Lugari
- Cancer Research Center of Marseille (CRCM), CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, F-13009 Marseille, France
| | - Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, P. O. Box 9600, 2300RC Leiden, The Netherlands
| | - Jessika C Zevenhoven
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, P. O. Box 9600, 2300RC Leiden, The Netherlands
| | - Stéphanie Bernard
- Cancer Research Center of Marseille (CRCM), CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, F-13009 Marseille, France
| | - Stéphane Betzi
- Cancer Research Center of Marseille (CRCM), CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, F-13009 Marseille, France
| | - Isabelle Imbert
- From the Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Bruno Canard
- From the Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Jean-Claude Guillemot
- From the Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France, CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Patrick Lécine
- CIRI, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, 69007 Lyon, France, and
| | - Susanne Pfefferle
- Institute of Virology, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, P. O. Box 9600, 2300RC Leiden, The Netherlands
| | - Etienne Decroly
- From the Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France, CNRS, AFMB UMR 7257, 13288 Marseille, France,
| | - Xavier Morelli
- Cancer Research Center of Marseille (CRCM), CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, F-13009 Marseille, France,
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Genetic manipulation of a transcription-regulating sequence of porcine reproductive and respiratory syndrome virus reveals key nucleotides determining its activity. Arch Virol 2014; 159:1927-40. [PMID: 24562427 DOI: 10.1007/s00705-014-2018-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/16/2013] [Indexed: 10/25/2022]
Abstract
The factors that determine the transcription-regulating sequence (TRS) activity of porcine reproductive and respiratory syndrome virus (PRRSV) remain largely unclear. In this study, the effect of mutagenesis of conserved C nucleotides at positions 5 and 6 in the leader TRS (TRS-L) and/or canonical body TRS7 (TRS-B7) on the synthesis of subgenomic (sg) mRNA and virus infectivity was investigated in the context of a type 2 PRRSV infectious cDNA clone. The results showed that a double C mutation in the leader TRS completely abolished sg mRNAs synthesis and virus infectivity, but a single C mutation did not. A single C or double C mutation in TRS-B7.1 or/and TRS-B7.2 impaired or abolished the corresponding sg mRNA synthesis. Introduction of identical mutations in the leader and body TRSs partially restored sg mRNA7.1 and/or sg mRNA7.2 transcription, indicating that the base-pairing interaction between sense TRS-L and cTRS-B is a crucial factor influencing sg mRNA synthesis. Analysis of the mRNA leader-body junctions of mutants provided evidence for a mechanism of discontinuous minus-strand transcription. This study also showed that mutational inactivation of TRS-B7.1 or TRS-B7.2 did not affect the production of infectious progeny virus, and the sg mRNA formed from each of them could express N protein. However, TRS-B7.1 plays more important roles than TRS-B7.2 in maintaining the growth characteristic of type 2 PRRSV. These results provide more insight into the molecular mechanism of genome expression and subgenomic mRNA transcription of PRRSV.
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129
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Angelini MM, Neuman BW, Buchmeier MJ. Untangling membrane rearrangement in the nidovirales. DNA Cell Biol 2014; 33:122-7. [PMID: 24410069 DOI: 10.1089/dna.2013.2304] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
All known positive sense single-stranded RNA viruses induce host cell membrane rearrangement for purposes of aiding viral genome replication and transcription. Members of the Nidovirales order are no exception, inducing intricate regions of double membrane vesicles and convoluted membranes crucial for the production of viral progeny. Although these structures have been well studied for some members of this order, much remains unclear regarding the biogenesis of these rearranged membranes. Here, we discuss what is known about these structures and their formation, compare some of the driving viral proteins behind this process across the nidovirus order, and examine possible routes of mechanism by which membrane rearrangement may occur.
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Affiliation(s)
- Megan Mary Angelini
- 1 Department of Molecular Biology and Biochemistry, University of California , Irvine, Irvine, California
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130
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Drexler JF, Corman VM, Drosten C. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antiviral Res 2014; 101:45-56. [PMID: 24184128 PMCID: PMC7113851 DOI: 10.1016/j.antiviral.2013.10.013] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/30/2013] [Accepted: 10/21/2013] [Indexed: 01/22/2023]
Abstract
In 2002/2003, a novel coronavirus (CoV) caused a pandemic, infecting more than 8000 people, of whom nearly 10% died. This virus, termed severe acute respiratory syndrome-CoV was linked to a zoonotic origin from rhinolophid bats in 2005. Since then, numerous studies have described novel bat CoVs, including close relatives of the newly emerging Middle East respiratory syndrome (MERS)-CoV. In this paper we discuss CoV genomic properties and compare different taxonomic approaches in light of the technical difficulties of obtaining full genomic sequences directly from bat specimens. We first present an overview of the available studies on bat CoVs, with details on their chiropteran hosts, then comparatively analyze the increase in bat CoV studies and novel genomic sequences obtained since the SARS pandemic. We then conduct a comprehensive phylogenetic analysis of the genera Alpha- and Betacoronavirus, to show that bats harbour more CoV diversity than other mammalian hosts and are widely represented in most, but not all parts of the tree of mammalian CoVs. We next discuss preliminary evidence for phylogenetic co-segregation of CoVs and bat hosts encompassing the Betacoronavirus clades b and d, with an emphasis on the sampling bias that exists among bat species and other mammals, then present examples of CoVs infecting different hosts on the one hand and viruses apparently confined to host genera on the other. We also demonstrate a geographic bias within available studies on bat CoVs, and identify a critical lack of information from biodiversity hotspots in Africa, Asia and Latin America. We then present evidence for a zoonotic origin of four of the six known human CoVs (HCoV), three of which likely involved bats, namely SARS-CoV, MERS-CoV and HCoV-229E; compare the available data on CoV pathogenesis in bats to that in other mammalian hosts; and discuss hypotheses on the putative insect origins of CoV ancestors. Finally, we suggest caution with conclusions on the zoonotic potential of bat viruses, based only on genomic sequence data, and emphasize the need to preserve these ecologically highly relevant animals. This paper forms part of a symposium in Antiviral Research on "from SARS to MERS: 10years of research on highly pathogenic human coronaviruses".
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131
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Deng Z, Lehmann KC, Li X, Feng C, Wang G, Zhang Q, Qi X, Yu L, Zhang X, Feng W, Wu W, Gong P, Tao Y, Posthuma CC, Snijder EJ, Gorbalenya AE, Chen Z. Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase. Nucleic Acids Res 2013; 42:3464-77. [PMID: 24369429 PMCID: PMC3950703 DOI: 10.1093/nar/gkt1310] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
All positive-stranded RNA viruses with genomes >∼7 kb encode helicases, which generally are poorly characterized. The core of the nidovirus superfamily 1 helicase (HEL1) is associated with a unique N-terminal zinc-binding domain (ZBD) that was previously implicated in helicase regulation, genome replication and subgenomic mRNA synthesis. The high-resolution structure of the arterivirus helicase (nsp10), alone and in complex with a polynucleotide substrate, now provides first insights into the structural basis for nidovirus helicase function. A previously uncharacterized domain 1B connects HEL1 domains 1A and 2A to a long linker of ZBD, which further consists of a novel RING-like module and treble-clef zinc finger, together coordinating three Zn atoms. On substrate binding, major conformational changes were evident outside the HEL1 domains, notably in domain 1B. Structural characterization, mutagenesis and biochemistry revealed that helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes.
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Affiliation(s)
- Zengqin Deng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China, Department of Medical Microbiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands, Clinical Medicine Research Center, Affiliated Hospital of Guangdong Medical College, Guangdong 524001, China, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China, Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
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132
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Ke TY, Liao WY, Wu HY. A leaderless genome identified during persistent bovine coronavirus infection is associated with attenuation of gene expression. PLoS One 2013; 8:e82176. [PMID: 24349214 PMCID: PMC3861326 DOI: 10.1371/journal.pone.0082176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/21/2013] [Indexed: 01/22/2023] Open
Abstract
The establishment of persistent viral infection is often associated with the selection of one or more mutant viruses. For example, it has been found that an intraleader open reading frame (ORF) in genomic and subgenomic mRNA (sgmRNA) molecules is selected during bovine coronavirus (BCoV) persistence which leads to translation attenuation of the downstream ORF. Here, we report the unexpected identification of leaderless genomes, in addition to leader-containing genomes, in a cell culture persistently infected with BCoV. The discovery was made by using a head-to-tail ligation method that examines genomic 5′-terminal sequences at different times postinfection. Functional analyses of the leaderless genomic RNA in a BCoV defective interfering (DI) RNA revealed that (1) the leaderless genome was able to serve as a template for the synthesis of negative-strand genome, although it cannot perform replicative positive-strand genomic RNA synthesis, and (2) the leaderless genome retained its function in translation and transcription, although the efficiency of these processes was impaired. Therefore, this previously unidentified leaderless genome is associated with the attenuation of genome expression. Whether the leaderless genome contributes to the establishment of persistent infection remains to be determined.
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Affiliation(s)
- Ting-Yung Ke
- Institute of Pathobiology, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan ROC
| | - Wei-Yu Liao
- Institute of Pathobiology, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan ROC
| | - Hung-Yi Wu
- Institute of Pathobiology, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan ROC
- * E-mail:
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133
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Yun SI, Lee YM. Overview: Replication of porcine reproductive and respiratory syndrome virus. J Microbiol 2013; 51:711-23. [PMID: 24385346 PMCID: PMC7091224 DOI: 10.1007/s12275-013-3431-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/07/2013] [Indexed: 02/06/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that causes significant losses in the pig industry, is one of the most important animal pathogens of global significance. Since the discovery of the virus, significant progress has been made in understanding its epidemiology and transmission, but no adequate control measures are yet available to eliminate infection with this pathogen. The genome replication of PRRSV is required to reproduce, within a few hours of infection, the millions of progeny virions that establish, disseminate, and maintain infection. Replication of the viral RNA genome is a multistep process involving a replication complex that is formed not only from components of viral and cellular origin but also from the viral genomic RNA template; this replication complex is embedded within particular virus-induced membrane vesicles. PRRSV RNA replication is directed by at least 14 replicase proteins that have both common enzymatic activities, including viral RNA polymerase, and also unusual and poorly understood RNA-processing functions. In this review, we summarize our current understanding of PRRSV replication, which is important for developing a successful strategy for the prevention and control of this pathogen.
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Affiliation(s)
- Sang-Im Yun
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322-4815 USA
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322-4815 USA
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134
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Balasuriya UBR, Go YY, MacLachlan NJ. Equine arteritis virus. Vet Microbiol 2013; 167:93-122. [PMID: 23891306 PMCID: PMC7126873 DOI: 10.1016/j.vetmic.2013.06.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 11/13/2022]
Abstract
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory and reproductive disease of equids. There has been significant recent progress in understanding the molecular biology of EAV and the pathogenesis of its infection in horses. In particular, the use of contemporary genomic techniques, along with the development and reverse genetic manipulation of infectious cDNA clones of several strains of EAV, has generated significant novel information regarding the basic molecular biology of the virus. Therefore, the objective of this review is to summarize current understanding of EAV virion architecture, replication, evolution, molecular epidemiology and genetic variation, pathogenesis including the influence of host genetics on disease susceptibility, host immune response, and potential vaccination and treatment strategies.
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Affiliation(s)
- Udeni B R Balasuriya
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
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135
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Characterization of a novel betacoronavirus related to middle East respiratory syndrome coronavirus in European hedgehogs. J Virol 2013; 88:717-24. [PMID: 24131722 DOI: 10.1128/jvi.01600-13] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bats are known to host viruses closely related to important human coronaviruses (HCoVs), such as HCoV-229E, severe-acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome CoV (MERS-CoV). As RNA viruses may coevolve with their hosts, we sought to investigate the closest sister taxon to bats, the Eulipotyphla, and screened European hedgehogs (Erinaceus europaeus) from Germany for CoV by nested reverse transcriptase PCR. A novel betacoronavirus species in a phylogenetic sister relationship to MERS-CoV and clade c bat CoVs was detected and characterized on the whole-genome level. A total of 58.9% of hedgehog fecal specimens were positive for the novel CoV (EriCoV) at 7.9 log10 mean RNA copies per ml. EriCoV RNA concentrations were higher in the intestine than in other solid organs, blood, or urine. Detailed analyses of the full hedgehog intestine showed the highest EriCoV concentrations in lower gastrointestinal tract specimens, compatible with viral replication in the lower intestine and fecal-oral transmission. Thirteen of 27 (48.2%) hedgehog sera contained non-neutralizing antibodies against MERS-CoV. The animal origins of this betacoronavirus clade that includes MERS-CoV may thus include both bat and nonbat hosts.
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136
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Hilgenfeld R, Peiris M. From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses. Antiviral Res 2013; 100:286-95. [PMID: 24012996 PMCID: PMC7113673 DOI: 10.1016/j.antiviral.2013.08.015] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 08/18/2013] [Indexed: 12/13/2022]
Abstract
We review the outbreak of severe acute respiratory syndrome (SARS) in 2002–2003 and antiviral treatment of patients. We review efforts towards the rational design of anti-SARS therapeutics. We present a comprehensive list of all available 3-dimensional structures of coronavirus proteins. We discuss the emerging MERS coronavirus and review the few antivirals available for treatment. We critically discuss which lessons have been learned from SARS and which are yet to be learned.
This article introduces a series of invited papers in Antiviral Research marking the 10th anniversary of the outbreak of severe acute respiratory syndrome (SARS), caused by a novel coronavirus that emerged in southern China in late 2002. Until that time, coronaviruses had not been recognized as agents causing severe disease in humans, hence, the emergence of the SARS-CoV came as a complete surprise. Research during the past ten years has revealed the existence of a diverse pool of coronaviruses circulating among various bat species and other animals, suggesting that further introductions of highly pathogenic coronaviruses into the human population are not merely probable, but inevitable. The recent emergence of another coronavirus causing severe disease, Middle East respiratory syndrome (MERS), in humans, has made it clear that coronaviruses pose a major threat to human health, and that more research is urgently needed to elucidate their replication mechanisms, identify potential drug targets, and develop effective countermeasures. In this series, experts in many different aspects of coronavirus replication and disease will provide authoritative, up-to-date reviews of the following topics: – clinical management and infection control of SARS; – reservoir hosts of coronaviruses; – receptor recognition and cross-species transmission of SARS-CoV; – SARS-CoV evasion of innate immune responses; – structures and functions of individual coronaviral proteins; – anti-coronavirus drug discovery and development; and – the public health legacy of the SARS outbreak. Each article will be identified in the last line of its abstract as belonging to the series “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.
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137
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Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles. mBio 2013; 4:mBio.00524-13. [PMID: 23943763 PMCID: PMC3747587 DOI: 10.1128/mbio.00524-13] [Citation(s) in RCA: 349] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Coronaviruses (CoV), like other positive-stranded RNA viruses, redirect and rearrange host cell membranes for use as part of the viral genome replication and transcription machinery. Specifically, coronaviruses induce the formation of double-membrane vesicles in infected cells. Although these double-membrane vesicles have been well characterized, the mechanism behind their formation remains unclear, including which viral proteins are responsible. Here, we use transfection of plasmid constructs encoding full-length versions of the three transmembrane-containing nonstructural proteins (nsps) of the severe acute respiratory syndrome (SARS) coronavirus to examine the ability of each to induce double-membrane vesicles in tissue culture. nsp3 has membrane disordering and proliferation ability, both in its full-length form and in a C-terminal-truncated form. nsp3 and nsp4 working together have the ability to pair membranes. nsp6 has membrane proliferation ability as well, inducing perinuclear vesicles localized around the microtubule organizing center. Together, nsp3, nsp4, and nsp6 have the ability to induce double-membrane vesicles that are similar to those observed in SARS coronavirus-infected cells. This activity appears to require the full-length form of nsp3 for action, as double-membrane vesicles were not seen in cells coexpressing the C-terminal truncation nsp3 with nsp4 and nsp6. Although the majority of infections caused by coronaviruses in humans are relatively mild, the SARS outbreak of 2002 to 2003 and the emergence of the human coronavirus Middle Eastern respiratory syndrome (MERS-CoV) in 2012 highlight the ability of these viruses to cause severe pathology and fatality. Insight into the molecular biology of how coronaviruses take over the host cell is critical for a full understanding of any known and possible future outbreaks caused by these viruses. Additionally, since membrane rearrangement is a tactic used by all known positive-sense single-stranded RNA viruses, this work adds to that body of knowledge and may prove beneficial in the development of future therapies not only for human coronavirus infections but for other pathogens as well.
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Abstract
Arteriviruses are positive-stranded RNA viruses that infect mammals. They can cause persistent or asymptomatic infections, but also acute disease associated with a respiratory syndrome, abortion or lethal haemorrhagic fever. During the past two decades, porcine reproductive and respiratory syndrome virus (PRRSV) and, to a lesser extent, equine arteritis virus (EAV) have attracted attention as veterinary pathogens with significant economic impact. Particularly noteworthy were the 'porcine high fever disease' outbreaks in South-East Asia and the emergence of new virulent PRRSV strains in the USA. Recently, the family was expanded with several previously unknown arteriviruses isolated from different African monkey species. At the molecular level, arteriviruses share an intriguing but distant evolutionary relationship with coronaviruses and other members of the order Nidovirales. Nevertheless, several of their characteristics are unique, including virion composition and structure, and the conservation of only a subset of the replicase domains encountered in nidoviruses with larger genomes. During the past 15 years, the advent of reverse genetics systems for EAV and PRRSV has changed and accelerated the structure-function analysis of arterivirus RNA and protein sequences. These systems now also facilitate studies into host immune responses and arterivirus immune evasion and pathogenesis. In this review, we have summarized recent advances in the areas of arterivirus genome expression, RNA and protein functions, virion architecture, virus-host interactions, immunity, and pathogenesis. We have also briefly reviewed the impact of these advances on disease management, the engineering of novel candidate live vaccines and the diagnosis of arterivirus infection.
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Affiliation(s)
- Eric J Snijder
- Molecular Virology Department, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Department, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
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139
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Bentley K, Armesto M, Britton P. Infectious Bronchitis Virus as a Vector for the Expression of Heterologous Genes. PLoS One 2013; 8:e67875. [PMID: 23840781 PMCID: PMC3694013 DOI: 10.1371/journal.pone.0067875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/23/2013] [Indexed: 01/31/2023] Open
Abstract
The avian coronavirus infectious bronchitis virus (IBV) is the causative agent of the respiratory disease infectious bronchitis of domestic fowl, and is controlled by routine vaccination. To explore the potential use of IBV as a vaccine vector a reverse genetics system was utilised to generate infectious recombinant IBVs (rIBVs) expressing the reporter genes enhanced green fluorescent protein (eGFP) or humanised Renilla luciferase (hRluc). Infectious rIBVs were obtained following the replacement of Gene 5 or the intergenic region (IR) with eGFP or hRluc, or the replacement of ORFs 3a and 3b with hRluc. The replacement of Gene 5 with an IBV codon-optimised version of the hRluc gene also resulted in successful rescue of infectious rIBV. Reporter gene expression was confirmed by fluorescence microscopy, or luciferase activity assays, for all successfully rescued rIBVs following infection of primary chick kidney (CK) cells. The genetic stability of rIBVs was analysed by serial passage on CK cells. Recombinant IBV stability varied depending on the genome region being replaced, with the reporter genes maintained up to at least passage 8 (P8) following replacement of Gene 5, P7 for replacement of the IR and P5 for replacement of ORFs 3a and 3b. Codon-optimisation of the hRluc gene, when replacing Gene 5, resulted in an increase in genome stability, with hRluc expression stable up to P10 compared to P8 for standard hRluc. Repeated passaging of rIBVs expressing hRluc at an MOI of 0.01 demonstrated an increase in stability, with hRluc expression stable up to at least P12 following the replacement of Gene 5. This study has demonstrated that heterologous genes can be incorporated into, and expressed from a range of IBV genome locations and that replacement of accessory Gene 5 offers a promising target for realising the potential of IBV as a vaccine vector for other avian pathogens.
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Affiliation(s)
- Kirsten Bentley
- Compton Laboratory, Avian Viral Diseases, The Pirbright Institute, Compton, Newbury, Berkshire, United Kingdom
| | - Maria Armesto
- Compton Laboratory, Avian Viral Diseases, The Pirbright Institute, Compton, Newbury, Berkshire, United Kingdom
| | - Paul Britton
- Compton Laboratory, Avian Viral Diseases, The Pirbright Institute, Compton, Newbury, Berkshire, United Kingdom
- * E-mail:
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140
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Kuwata R, Satho T, Isawa H, Yen NT, Phong TV, Nga PT, Kurashige T, Hiramatsu Y, Fukumitsu Y, Hoshino K, Sasaki T, Kobayashi M, Mizutani T, Sawabe K. Characterization of Dak Nong virus, an insect nidovirus isolated from Culex mosquitoes in Vietnam. Arch Virol 2013; 158:2273-84. [PMID: 23728735 PMCID: PMC7087109 DOI: 10.1007/s00705-013-1741-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 04/19/2013] [Indexed: 11/30/2022]
Abstract
In this study, we isolated and characterized an insect nidovirus from the mosquito Culex tritaeniorhynchus Giles (Diptera: Culicidae) in Vietnam, as an additional member of the new family Mesoniviridae in the order Nidovirales. The virus, designated “Dak Nong virus (DKNV),” shared many characteristics with Cavally virus and Nam Dinh virus, which have also been discovered recently in mosquitoes, and these viruses should be considered members of a single virus species, Alphamesonivirus 1. DKNV grew in cultured mosquito cells but could not replicate in the cultured vertebrate cells tested. N-terminal sequencing of the DKNV structural proteins revealed two posttranslational cleavage sites in the spike glycoprotein precursor. DKNV is assumed to be a new member of the species Alphamesonivirus 1, and the current study provides further understanding of viruses belonging to the new family Mesoniviridae.
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Affiliation(s)
- Ryusei Kuwata
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
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141
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Zirkel F, Roth H, Kurth A, Drosten C, Ziebuhr J, Junglen S. Identification and characterization of genetically divergent members of the newly established family Mesoniviridae. J Virol 2013; 87:6346-58. [PMID: 23536661 PMCID: PMC3648093 DOI: 10.1128/jvi.00416-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/18/2013] [Indexed: 12/16/2022] Open
Abstract
The recently established family Mesoniviridae (order Nidovirales) contains a single species represented by two closely related viruses, Cavally virus (CavV) and Nam Dinh virus (NDiV), which were isolated from mosquitoes collected in Côte d'Ivoire and Vietnam, respectively. They represent the first nidoviruses to be discovered in insects. Here, we report the molecular characterization of four novel mesoniviruses, Hana virus, Méno virus, Nsé virus, and Moumo virus, all of which were identified in a geographical region in Côte d'Ivoire with high CavV prevalence. The viruses were found with prevalences between 0.5 and 2.8%, and genome sequence analyses and phylogenetic studies suggest that they represent at least three novel species. Electron microscopy revealed prominent club-shaped surface projections protruding from spherical, enveloped virions of about 120 nm. Northern blot data show that the four mesoniviruses analyzed in this study produce two major 3'-coterminal subgenomic mRNAs containing two types of 5' leader sequences resulting from the use of different pairs of leader and body transcription-regulating sequences that are conserved among mesoniviruses. Protein sequencing, mass spectroscopy, and Western blot data show that mesonivirus particles contain eight major structural protein species, including the putative nucleocapsid protein (25 kDa), differentially glycosylated forms of the putative membrane protein (20, 19, 18, and 17 kDa), and the putative spike (S) protein (77 kDa), which is proteolytically cleaved at a conserved site to produce S protein subunits of 23 and 57 kDa. The data provide fundamental new insight into common and distinguishing biological properties of members of this newly identified virus family.
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Affiliation(s)
- Florian Zirkel
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Hanna Roth
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Kurth
- Center for Biological Safety, Robert Koch Institute, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Sandra Junglen
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
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142
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Dunowska M, Gopakumar G, Perrott MR. Development of a real-time reverse transcription PCR assay for detection of a novel nidovirus associated with a neurological disease of the Australian brushtail possum (Trichosurus vulpecula). N Z Vet J 2013; 61:286-91. [PMID: 23600460 DOI: 10.1080/00480169.2013.780279] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AIMS To develop a quantitative reverse transcription PCR (RT-qPCR) assay for detection of the putative wobbly possum disease (WPD) virus and to apply this test to investigate the viral load in archival tissues from past WPD transmission studies. METHODS The real-time assay was developed as a two-step RT-qPCR in a SYBR green format and validated using serial dilutions of a linearised plasmid containing target DNA. The copy number values were normalised to the amount of RNA in each reverse transcription reaction and presented as the number of viral copies per μg of total [corrected] RNA. The viral load was determined in archival samples from animals that had received inoculations of infectious WPD tissue suspensions. Thirty samples originating from 22 possums, comprising five samples from three healthy possums and 25 samples from 19 possums that had received inoculations of infectious WPD tissue suspensions were tested. RESULTS The assay was linear (R(2) > 0.99) within the tested range from 1 to 10(7) target copies/µL, with an efficiency of >90%. The intra-assay variability CV values ranged from 0.8 to 4.5% for different standards, with the inter-assay variability CV values ranging from 0.4 to 2.5%, indicating good precision and reproducibility of the assay. The novel nidovirus was detected in all 25 samples from WPD-affected possums. Tissues from three control possums and from one experimentally infected rabbit were negative for WPD RNA. The viral load in WPD-positive tissues differed between individual possums and between tissue types, ranging from 2.2 to 359,980 copies/pg RNA. The highest viral load was detected in liver, followed by brain, spleen, kidney and urine. There was a more than four log difference in the viral load between pools of tissues originating from two outbreaks of WPD in different geographical regions. CONCLUSIONS Detection of viral RNA in a variety of tissues from WPD affected possums, including brain, is consistent with the multi-organ distribution of histopathological lesions observed in WPD. Our data suggest that liver may constitute the sample of choice for diagnostic testing. Differences in the viral load in tissues from possums inoculated with infectious WPD tissue suspensions from Rotorua or Invermay origin suggest that WPD viruses with different biological properties may exist. CLINICAL RELEVANCE We have developed a RT-qPCR assay for detection of the putative WPD virus. The test showed good sensitivity and reproducibility over the wide dynamic range of template concentrations. It provides a tool for future diagnostic and research purposes.
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Affiliation(s)
- M Dunowska
- Institute of Veterinary Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
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143
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Dolja VV, Koonin EV. The closterovirus-derived gene expression and RNA interference vectors as tools for research and plant biotechnology. Front Microbiol 2013; 4:83. [PMID: 23596441 PMCID: PMC3622897 DOI: 10.3389/fmicb.2013.00083] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 03/22/2013] [Indexed: 12/24/2022] Open
Abstract
Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing. Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large closterovirus genomes offer genetic capacity and stability unrivaled by other plant viral vectors. These features provided immense opportunities for using closterovirus vectors for the functional genomics studies and pathogen control in economically valuable crops. This review briefly summarizes advances in closterovirus research during the last decade, explores the relationships between virus biology and vector design, and outlines the most promising directions for future application of closterovirus vectors.
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Affiliation(s)
- Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA ; Center for Genome Research and Biocomputing, Oregon State University Corvallis, OR, USA
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144
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Yin Y, Liu C, Liu P, Yao H, Wei Z, Lu J, Tong G, Gao F, Yuan S. Conserved nucleotides in the terminus of the 3' UTR region are important for the replication and infectivity of porcine reproductive and respiratory syndrome virus. Arch Virol 2013; 158:1719-32. [PMID: 23512575 DOI: 10.1007/s00705-013-1661-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/03/2013] [Indexed: 12/11/2022]
Abstract
The 3' untranslated region (3' UTR), including the poly (A) tail, reportedly plays an important role in arterivirus replication, but the roles of the cis-acting elements present in the 3' UTR of porcine reproductive and respiratory syndrome virus (PRRSV) remain largely unknown. In the present study, PCR-based mutagenic analysis was conducted on the 3' UTR of PRRSV infectious full-length cDNA clone pAPRRS to investigate the structure and function of the conserved terminal nucleotides between the poly (A) tail and the 3' UTR region. Our findings indicated that the conservation of the primary sequence of the 3' terminal nucleotides, rather than the surrounding secondary structure, was vital for viral replication and infectivity. Four nucleotides (nt) (5'-(15517)AAUU(15520)-3') at the 3' proximal end of the 3' UTR and the dinucleotide 5'-AU-3' exerted an important regulatory effect on viral viability. Of the five 3'-terminal nucleotides of the 3' UTR (5'-(15503)AACCA(15507)-3'), at least three, including the last dinucleotide (5'-CA-3'), were essential for maintaining viral infectivity. Taken together, the 3'-terminal conserved sequence plays a critical role in PRRSV replication and may function as a contact site for specific assembly of the replication complex.
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Affiliation(s)
- Yang Yin
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Minhang District, Shanghai 200241, People's Republic of China
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145
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Gao F, Yao H, Lu J, Wei Z, Zheng H, Zhuang J, Tong G, Yuan S. Replacement of the heterologous 5' untranslated region allows preservation of the fully functional activities of type 2 porcine reproductive and respiratory syndrome virus. Virology 2013; 439:1-12. [PMID: 23453581 PMCID: PMC7111940 DOI: 10.1016/j.virol.2012.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 12/20/2012] [Accepted: 12/25/2012] [Indexed: 10/27/2022]
Abstract
The 5' untranslated region (UTR) is believed to be vital for the replication of porcine reproductive and respiratory syndrome virus (PRRSV), yet its functional mechanism remains largely unknown. In this study, to define the cis-acting elements for viral replication and infectivity, The 5' UTR swapping chimeric clones pTLV8 and pSHSP5 were constructed based on two different genotypes full-length infectious cDNA clone pAPRRS and pSHE backbones. Between them, vTLV8 could be rescued from pTLV8 and had similar virological properties to vAPRRS, including phenotypic characteristic and RNA synthesis level. However, pSHSP5 exhibited no evidence of infectivity. Taken together, the results presented here demonstrate that only the 5' UTR of type 1 PRRSV did not affect the infectivity and replication of type 2 PRRSV in vitro. The 5' UTR of type 2 PRRSV could be functionally replaced by its counterpart from type 1.
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Affiliation(s)
- Fei Gao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
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146
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Nedialkova DD, Gorbalenya AE, Snijder EJ. Arterivirus Papain-like Proteinase 1β. HANDBOOK OF PROTEOLYTIC ENZYMES 2013. [PMCID: PMC7150162 DOI: 10.1016/b978-0-12-382219-2.00499-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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147
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Nedialkova DD, Gorbalenya AE, Snijder EJ. Arterivirus Papain-like Proteinase 1α. HANDBOOK OF PROTEOLYTIC ENZYMES 2013. [PMCID: PMC7149378 DOI: 10.1016/b978-0-12-382219-2.00498-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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148
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Sun L, Li Y, Liu R, Wang X, Gao F, Lin T, Huang T, Yao H, Tong G, Fan H, Wei Z, Yuan S. Porcine reproductive and respiratory syndrome virus ORF5a protein is essential for virus viability. Virus Res 2013; 171:178-85. [DOI: 10.1016/j.virusres.2012.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/08/2012] [Accepted: 11/14/2012] [Indexed: 11/16/2022]
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149
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Guo XK, Zhang Q, Gao L, Li N, Chen XX, Feng WH. Increasing expression of microRNA 181 inhibits porcine reproductive and respiratory syndrome virus replication and has implications for controlling virus infection. J Virol 2013; 87:1159-71. [PMID: 23152505 PMCID: PMC3554091 DOI: 10.1128/jvi.02386-12] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/01/2012] [Indexed: 02/03/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important viral pathogens in the swine industry. Emerging evidence indicates that the host microRNAs (miRNAs) are involved in host-pathogen interactions. However, whether host miRNAs can target PRRSV and be used to inhibit PRRSV infection has not been reported. Recently, microRNA 181 (miR-181) has been identified as a positive regulator of immune response, and here we report that miR-181 can directly impair PRRSV infection. Our results showed that delivered miR-181 mimics can strongly inhibit PRRSV replication in vitro through specifically binding to a highly (over 96%) conserved region in the downstream of open reading frame 4 (ORF4) of the viral genomic RNA. The inhibition of PRRSV replication was specific and dose dependent. In PRRSV-infected Marc-145 cells, the viral mRNAs could compete with miR-181-targeted sequence in luciferase vector to interact with miR-181 and result in less inhibition of luciferase activity, further demonstrating the specific interactions between miR-181 and PRRSV RNAs. As expected, miR-181 and other potential PRRSV-targeting miRNAs (such as miR-206) are expressed much more abundantly in minimally permissive cells or tissues than in highly permissive cells or tissues. Importantly, highly pathogenic PRRSV (HP-PRRSV) strain-infected pigs treated with miR-181 mimics showed substantially decreased viral loads in blood and relief from PRRSV-induced fever compared to negative-control (NC)-treated controls. These results indicate the important role of host miRNAs in modulating PRRSV infection and viral pathogenesis and also support the idea that host miRNAs could be useful for RNA interference (RNAi)-mediated antiviral therapeutic strategies.
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Affiliation(s)
- Xue-kun Guo
- State Key Laboratories of Agrobiotechnology
- Department of Microbiology and Immunology
| | - Qiong Zhang
- State Key Laboratories of Agrobiotechnology
- Department of Microbiology and Immunology
| | - Li Gao
- State Key Laboratories of Agrobiotechnology
- Department of Microbiology and Immunology
| | - Ning Li
- State Key Laboratories of Agrobiotechnology
- Department of Molecular Biology, College of Biological Science, China Agricultural University, Beijing, China
| | - Xin-xin Chen
- State Key Laboratories of Agrobiotechnology
- Department of Microbiology and Immunology
| | - Wen-hai Feng
- State Key Laboratories of Agrobiotechnology
- Department of Microbiology and Immunology
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Identification of a noncanonically transcribed subgenomic mRNA of infectious bronchitis virus and other gammacoronaviruses. J Virol 2012; 87:2128-36. [PMID: 23221558 DOI: 10.1128/jvi.02967-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Coronavirus subgenomic mRNA (sgmRNA) synthesis occurs via a process of discontinuous transcription involving transcription regulatory sequences (TRSs) located in the 5' leader sequence (TRS-L) and upstream of each structural and group-specific gene (TRS-B). Several gammacoronaviruses including infectious bronchitis virus (IBV) contain a putative open reading frame (ORF), localized between the M gene and gene 5, which is controversial due to the perceived absence of a TRS. We have studied the transcription of a novel sgmRNA associated with this potential ORF and found it to be transcribed via a previously unidentified noncanonical TRS-B. Using an IBV reverse genetics system, we demonstrated that the template-switching event during intergenic region (IR) sgmRNA synthesis occurs at the 5' end of the noncanonical TRS-B and recombines between nucleotides 5 and 6 of the 8-nucleotide consensus TRS-L. Introduction of a complete TRS-B showed that higher transcription levels are achieved by increasing the number of nucleotide matches between TRS-L and TRS-B. Translation of a protein from the sgmRNA was demonstrated using enhanced green fluorescent protein, suggesting the translation of a fifth, novel, group-specific protein for IBV. This study has resolved an issue concerning the number of ORFs expressed by members of the Gammacoronavirus genus and proposes the existence of a fifth IBV accessory protein. We confirmed previous reports that coronaviruses can produce sgmRNAs from noncanonical TRS-Bs, which may expand their repertoire of proteins. We also demonstrated that noncanonical TRS-Bs may provide a mechanism by which coronaviruses can control protein expression levels by reducing sgmRNA synthesis.
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