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Tóth F, Gáspár G, Pankovics P, Urbán P, Herczeg R, Albert M, Reuter G, Boros Á. Co-infecting viruses of species Bovine rhinitis B virus (Picornaviridae) and Bovine nidovirus 1 (Tobaniviridae) identified for the first time from a post-mortem respiratory sample of a sheep (Ovis aries) in Hungary. Infect Genet Evol 2024; 120:105585. [PMID: 38508364 DOI: 10.1016/j.meegid.2024.105585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time. The complete/nearly complete genomes of the identified viruses were determined using RT-PCR and Nanopore (MinION-Flonge) / Dye-terminator sequencing techniques. The results of detailed genomic and phylogenetic analyses indicate that the identified picornavirus most likely belongs to a type 4 genotype of species Bovine rhinitis B virus (BRBV-4, OR885914) of genus Aphthovirus, family Picornaviridae while the ovine nidovirus (OvNV, OR885915) - as a novel variant - could belong to the recently created Bovine nidovirus 1 (BoNV) species of genus Bostovirus, family Tobaniviridae. None of the identified viruses were detectable in the enteric samples using RT-PCR and generic screening primer pairs. Both viruses are well-known respiratory pathogens of cattle, but their presence was not demonstrated before in other animals, like sheep. Furthermore, neither BRBV-4 nor BoNVs were investigated in European cattle and/or sheep flocks, therefore it cannot be determined whether the presence of these viruses in sheep was a result of a single host species switch/spillover event or these viruses are circulating in not just cattle but sheep populations as well. Further studies required to investigate the spread of these viruses in Hungarian and European sheep and cattle populations and to identify their pathogenic potential in sheep.
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Affiliation(s)
- Fruzsina Tóth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | | | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary.
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Rudy K, Jeon D, Smith AA, Harding JCS, Pasternak JA. PRRSV-2 viral load in critical non-lymphoid tissues is associated with late gestation fetal compromise. Front Microbiol 2024; 15:1352315. [PMID: 38389522 PMCID: PMC10883647 DOI: 10.3389/fmicb.2024.1352315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
The impact of late gestation PRRSV-2 infection is highly variable within a litter, with a subset of fetuses displaying varying degrees of compromise following infection while others remain viable despite significant systemic viral load. To understand the underlying cause of this variation, we examined the susceptibility, distribution and impact of viral infection within non-lymphoid tissues. Samples of brain, heart, kidney, liver, lung, and skeletal muscle were obtained from fetuses of pregnant gilts at gestation day 86, and the presence and distribution of CD163+ cells within each tissue evaluated via immunohistofluorescence. Equivalent samples were collected from phenotypic extremes representing resistant, resilient and susceptible fetuses at 21 days following infection of pregnant gilts with PRRSV-2 at day 86 of gestation. Viral load and its impact in each tissue was evaluated by a combination of qPCR, in vitro viral recovery, and local expression of IFNG and CD163. Resting populations of CD163+ cells were observed in all six non-lymphoid tissues from healthy day 86 fetuses, though the apparent density and the morphology of positive cells varied between tissue. Viral RNA was detected in all six tissues derived from fetuses previously classified as highly infected, and infectious viral particles successfully recovered. Significantly more viral RNA was detected in heart, brain, lung and skeletal muscle of susceptible fetuses, relative to their viable counterparts. Infection was associated with an increase in the expression of CD163 in brain, kidney and lung. In addition, the presence of virus in each tissue coincided with a significant upregulation in the expression of IFNG, but the scale of this response was not associated with fetal susceptibility. Thus, PRRSV-2 is widely distributed across these susceptible non-lymphoid fetal tissues, and fetal outcome is associated with local viral load in critical fetal organs.
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Affiliation(s)
- K Rudy
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - D Jeon
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - A A Smith
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - J C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - J A Pasternak
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Kron NS, Neuman BW, Kumar S, Blackwelder PL, Vidal D, Walker-Phelan DZ, Gibbs PDI, Fieber LA, Schmale MC. Expression dynamics of the aplysia abyssovirus. Virology 2024; 589:109890. [PMID: 37951086 PMCID: PMC10842508 DOI: 10.1016/j.virol.2023.109890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 11/13/2023]
Abstract
Two recent studies documented the genome of a novel, extremely large (35.9 kb), nidovirus in RNA sequence databases from the marine neural model Aplysia californica. The goal of the present study was to document the distribution and transcriptional dynamics of this virus, Aplysia abyssovirus 1 (AAbV), in maricultured and wild animals. We confirmed previous findings that AAbV RNA is widespread and reaches extraordinary levels in apparently healthy animals. Transmission electron microscopy identified viral replication factories in ciliated gill epithelial cells but not in neurons where viral RNA is most highly expressed. Viral transcripts do not exhibit evidence of discontinuous RNA synthesis as in coronaviruses but are consistent with production of a single leaderless subgenomic RNA, as in the Gill-associated virus of Penaeus monodon. Splicing patterns in chronically infected adults suggested high levels of defective genomes, possibly explaining the lack of obvious disease signs in high viral load animals.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149.
| | - Benjamin W Neuman
- Department of Biology, Department of Molecular Pathogenesis and Immunology and Division of Research, Texas A&M University, 400 Bizzell St., College Station, TX, USA, 77843
| | - Sathish Kumar
- Department of Biology, Department of Molecular Pathogenesis and Immunology and Division of Research, Texas A&M University, 400 Bizzell St., College Station, TX, USA, 77843
| | - Patricia L Blackwelder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149; University of Miami Center for Advanced Microscopy, University of Miami, 142B Physics, Coral Gables, FL, USA, 33146
| | - Dayana Vidal
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Delphina Z Walker-Phelan
- Department of Immunology, University of Washington, South Lake Union E-411 750 Republican St. UW Box 358059, Seattle, WA, 98109, USA
| | - Patrick D I Gibbs
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
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Marschang RE, Salzmann E, Pees M. Diagnostics of Infectious Respiratory Pathogens in Reptiles. Vet Clin North Am Exot Anim Pract 2021; 24:369-395. [PMID: 33892892 DOI: 10.1016/j.cvex.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Methods for the detection of pathogens associated with respiratory disease in reptiles, including viruses, bacteria, fungi, and parasites, are constantly evolving as is the understanding of the specific roles played by various pathogens in disease processes. Some are known to be primary pathogens with high prevalence in captive reptiles, for example, serpentoviruses in pythons or mycoplasma in tortoises. Others are very commonly found in reptiles with respiratory disease but are most often considered secondary, for example, gram-negative bacteria. Detection methods as well as specific pathogens associated with upper- and lower-respiratory disease are discussed.
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Affiliation(s)
| | | | - Michael Pees
- Department for Birds and Reptiles, University Veterinary Teaching Hospital, University of Leipzig, Clinic for Birds and Reptiles, An den Tierkliniken 17, Leipzig 04103, Germany
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Keep S, Britton P, Bickerton E. Transient Dominant Selection for the Modification and Generation of Recombinant Infectious Bronchitis Coronaviruses. Methods Mol Biol 2020; 2203:147-165. [PMID: 32833211 DOI: 10.1007/978-1-0716-0900-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have developed a reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) in which a full-length cDNA corresponding to the IBV genome is inserted into the vaccinia virus genome under the control of a T7 promoter sequence. Vaccinia virus as a vector for the full-length IBV cDNA has the advantage that modifications can be introduced into the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. Here, we describe the use of transient dominant selection as a method for introducing modifications into the IBV cDNA that has been successfully used for the substitution of specific nucleotides, deletion of genomic regions, and the exchange of complete genes. Infectious recombinant IBVs are generated in situ following the transfection of vaccinia virus DNA, containing the modified IBV cDNA, into cells infected with a recombinant fowlpox virus expressing T7 DNA-dependent RNA polymerase.
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Chang T, Guo M, Zhang W, Niu J, Wang JJ. First Report of a Mesonivirus and Its Derived Small RNAs in an Aphid Species Aphis citricidus (Hemiptera: Aphididae), Implying Viral Infection Activity. J Insect Sci 2020; 20:14. [PMID: 32282036 PMCID: PMC7153580 DOI: 10.1093/jisesa/ieaa022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Indexed: 06/11/2023]
Abstract
We report a new positive-sense single-stranded RNA (ss RNA+) virus from the brown citrus aphid Aphis citricidus. The 20,300 nucleotide (nt)-long viral genome contains five open-reading frames and encodes six conserved domains (TM2, 3CLpro, TM3, RdRp, Zm, and HEL1). Phylogenetic analysis and amino acid sequence analysis revealed this virus might belong to an unassigned genus in the family Mesoniviridae. The presence of the virus was also confirmed in the field population. Importantly, analysis of the virus-derived small RNAs showed a 22-nt peak, implying that viral infection triggers the small interfering RNA pathway as antiviral immunity in aphids. This is the first report of a mesonivirus in invertebrates other than mosquitoes.
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Affiliation(s)
- Tengyu Chang
- College of Plant Protection, Key Laboratory of Entomology and Pest Control Engineering, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Southwest University, Chongqing, China
| | - Mengmeng Guo
- College of Plant Protection, Key Laboratory of Entomology and Pest Control Engineering, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Southwest University, Chongqing, China
| | - Wei Zhang
- College of Plant Protection, Key Laboratory of Entomology and Pest Control Engineering, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Southwest University, Chongqing, China
| | - Jinzhi Niu
- College of Plant Protection, Key Laboratory of Entomology and Pest Control Engineering, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- College of Plant Protection, Key Laboratory of Entomology and Pest Control Engineering, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Southwest University, Chongqing, China
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Blahak S, Jenckel M, Höper D, Beer M, Hoffmann B, Schlottau K. Investigations into the presence of nidoviruses in pythons. Virol J 2020; 17:6. [PMID: 31952524 PMCID: PMC6969405 DOI: 10.1186/s12985-020-1279-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/09/2020] [Indexed: 01/17/2023] Open
Abstract
Background Pneumonia and stomatitis represent severe and often fatal diseases in different captive snakes. Apart from bacterial infections, paramyxo-, adeno-, reo- and arenaviruses cause these diseases. In 2014, new viruses emerged as the cause of pneumonia in pythons. In a few publications, nidoviruses have been reported in association with pneumonia in ball pythons and a tiger python. The viruses were found using new sequencing methods from the organ tissue of dead animals. Methods Severe pneumonia and stomatitis resulted in a high mortality rate in a captive breeding collection of green tree pythons. Unbiased deep sequencing lead to the detection of nidoviral sequences. A developed RT-qPCR was used to confirm the metagenome results and to determine the importance of this virus. A total of 1554 different boid snakes, including animals suffering from respiratory diseases as well as healthy controls, were screened for nidoviruses. Furthermore, in addition to two full-length sequences, partial sequences were generated from different snake species. Results The assembled full-length snake nidovirus genomes share only an overall genome sequence identity of less than 66.9% to other published snake nidoviruses and new partial sequences vary between 99.89 and 79.4%. Highest viral loads were detected in lung samples. The snake nidovirus was not only present in diseased animals, but also in snakes showing no typical clinical signs. Conclusions Our findings further highlight the possible importance of snake nidoviruses in respiratory diseases and proof multiple circulating strains with varying disease potential. Nidovirus detection in clinical healthy individuals might represent testing during the incubation period or reconvalescence. Our investigations show new aspects of nidovirus infections in pythons. Nidoviruses should be included in routine diagnostic workup of diseased reptiles.
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Affiliation(s)
- Silvia Blahak
- Chemical and Veterinary Investigation Office, Westerfeldstraße 1, D-32758, Detmold, Germany
| | - Maria Jenckel
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany.,Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany.
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8
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Abstract
We have developed a reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) in which a full-length cDNA corresponding to the IBV genome is inserted into the vaccinia virus genome under the control of a T7 promoter sequence. Vaccinia virus as a vector for the full-length IBV cDNA has the advantage that modifications can be introduced into the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. Here, we describe the use of transient dominant selection as a method for introducing modifications into the IBV cDNA that has been successfully used for the substitution of specific nucleotides, deletion of genomic regions, and exchange of complete genes. Infectious recombinant IBVs are generated in situ following the transfection of vaccinia virus DNA, containing the modified IBV cDNA, into cells infected with a recombinant fowlpox virus expressing T7 DNA-dependant RNA polymerase.
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Affiliation(s)
- Erica Bickerton
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK.
| | - Sarah M Keep
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Paul Britton
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
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9
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Di H, McIntyre AA, Brinton MA. New insights about the regulation of Nidovirus subgenomic mRNA synthesis. Virology 2018; 517:38-43. [PMID: 29475599 PMCID: PMC5987246 DOI: 10.1016/j.virol.2018.01.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 01/19/2023]
Abstract
The members of the Order Nidovirales share a similar genome organization with two overlapping nonstructural polyproteins encoded in the 5' two-thirds and the structural proteins encoded in the 3' third. They also express their 3' region proteins from a nested set of 3' co-terminal subgenomic messenger RNAs (sg mRNAs). Some but not all of the Nidovirus sg mRNAs also have a common 5' leader sequence that is acquired by a discontinuous RNA synthesis mechanism regulated by multiple 3' body transcription regulating sequences (TRSs) and the 5' leader TRS. Initial studies detected a single major body TRS for each 3' sg mRNA with a few alternative functional TRSs reported. The recent application of advanced techniques, such as next generation sequencing and ribosomal profiling, in studies of arteriviruses and coronaviruses has revealed an expanded sg mRNA transcriptome and coding capacity.
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Affiliation(s)
- Han Di
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA
| | - Ayisha A McIntyre
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA.
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Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a reemerging swine disease, and has become economically the most significant disease in pork production worldwide. The causative agent is PRRS virus (PRRSV), which is a member virus of the family Arteriviridae. The PRRSV genome is a single-stranded positive-sense RNA and is infectious. Two strategies in the PRRSV reverse genetics system have been employed for reconstitution of progeny virus: RNA transfection and DNA transfection. The PRRSV reverse genetics has broadly been used for studies including protein structure-function relationship, foreign gene expression, vaccine development, virulence determinants, and viral pathogenesis. Herein, we describe the modification of the pFL12 "RNA launch" reverse genetic system to the CMV promoter-driven pXJ41-FL13 "DNA launch" system. The generation of progeny PRRSV using pXJ41-FL13 is further elucidated.
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Affiliation(s)
- Mingyuan Han
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.,Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Hanzhong Ke
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Yijun Du
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.,Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Qingzhan Zhang
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
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Abstract
Coronaviruses are animal and human pathogens that can cause lethal zoonotic infections like SARS and MERS. They have polycistronic plus-stranded RNA genomes and belong to the order Nidovirales, a diverse group of viruses for which common ancestry was inferred from the common principles underlying their genome organization and expression, and from the conservation of an array of core replicase domains, including key RNA-synthesizing enzymes. Coronavirus genomes (~ 26–32 kilobases) are the largest RNA genomes known to date and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. The primary functions that direct coronavirus RNA synthesis and processing reside in nonstructural protein (nsp) 7 to nsp16, which are cleavage products of two large replicase polyproteins translated from the coronavirus genome. Significant progress has now been made regarding their structural and functional characterization, stimulated by technical advances like improved methods for bioinformatics and structural biology, in vitro enzyme characterization, and site-directed mutagenesis of coronavirus genomes. Coronavirus replicase functions include more or less universal activities of plus-stranded RNA viruses, like an RNA polymerase (nsp12) and helicase (nsp13), but also a number of rare or even unique domains involved in mRNA capping (nsp14, nsp16) and fidelity control (nsp14). Several smaller subunits (nsp7–nsp10) act as crucial cofactors of these enzymes and contribute to the emerging “nsp interactome.” Understanding the structure, function, and interactions of the RNA-synthesizing machinery of coronaviruses will be key to rationalizing their evolutionary success and the development of improved control strategies.
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Affiliation(s)
- E J Snijder
- Leiden University Medical Center, Leiden, The Netherlands.
| | - E Decroly
- Aix-Marseille Université, AFMB UMR 7257, Marseille, France; CNRS, AFMB UMR 7257, Marseille, France
| | - J Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
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12
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Lehmann KC, Gorbalenya AE, Snijder EJ, Posthuma CC. Arterivirus RNA-dependent RNA polymerase: Vital enzymatic activity remains elusive. Virology 2016; 487:68-74. [PMID: 26499043 DOI: 10.1016/j.virol.2015.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/25/2015] [Accepted: 10/01/2015] [Indexed: 12/19/2022]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp), which in arteriviruses is expressed as the C-terminal domain of nonstructural protein 9 (nsp9). Previously, potent primer-dependent RdRp activity has been demonstrated for the homologous polymerase subunit (nsp12) of the distantly related coronaviruses. The only previous study focusing on the in vitro activity of nsp9 of an arterivirus (equine arteritis virus; EAV) reported weak de novo polymerase activity on homopolymeric RNA templates. However, this activity was not retained when Mn2+ ions were omitted from the assay or when biologically relevant templates were supplied, which prompted us to revisit the biochemical properties of this polymerase. Based on the properties of active-site mutants, we conclude that the RNA-synthesizing activities observed in de novo and primer-dependent polymerase and terminal transferase assays cannot be attributed to recombinant EAV nsp9-RdRp. Our results illustrate the potential pitfalls of characterizing polymerases using highly sensitive biochemical assays. Several recombinant RdRp preparations of Equine arteritis virus (EAV) were purified. No primer-dependent or de novo RdRp or terminal transferase activity was shown. One RdRp preparation showed products resembling those of phage T7 RNA polymerase. Mutation of the RdRp active site aspartates to alanine crippled the EAV viability. Characterizing low activity RdRp in sensitive enzymatic assays requires extra care.
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Li Y, Tas A, Sun Z, Snijder EJ, Fang Y. Proteolytic processing of the porcine reproductive and respiratory syndrome virus replicase. Virus Res 2014; 202:48-59. [PMID: 25557977 DOI: 10.1016/j.virusres.2014.12.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 01/16/2023]
Abstract
The porcine reproductive and respiratory syndrome virus (PRRSV) replicase polyproteins pp1a and pp1ab are proteolytically processed by four proteases encoded in ORF1a. In this study, a large set of PRRSV replicase cleavage products were identified and pp1a cleavage sites were verified by using a combination of bioinformatics, proteomics, immunoprecipitation, and site-directed mutagenesis. For genotype 1 PRRSV (isolate SD01-08), proteomic analysis identified H180/S181, G385/A386, and G1446/A1447 as the cleavage sites separating nsp1α/1β, nsp1β/nsp2, and nsp2/nsp3, respectively. Transient expression of nsp2-8, nsp3-8, nsp4-8, nsp5-8 (using the recombinant vaccinia virus/T7 RNA polymerase system) and immunoprecipitation identified the cleavage end products nsp2, nsp3, nsp4, nsp7α and nsp7β, and various processing intermediates. Our studies also revealed the existence of alternative proteolytic processing pathways for the processing of the nsp3-8 region, depending on the presence or absence of nsp2 as a co-factor. The identity of most cleavage products was further corroborated by site-directed mutagenesis of individual cleavage sites in constructs expressing nsp3-8 or nsp4-8. This study constitutes the first in-depth experimental analysis of PRRSV replicase processing and the data are discussed against the background of the processing scheme previously derived for the arterivirus prototype, the distantly related equine arteritis virus (EAV). Despite several differences between the two viruses, of which the functional significance remains to be studied, our study demonstrates the general conservation of the replicase pp1a processing scheme between EAV and PRRSV, and likely also the other members of the arterivirus family.
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Affiliation(s)
- Yanhua Li
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Ali Tas
- Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Zhi Sun
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Eric J Snijder
- Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
| | - Ying Fang
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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Thuy NT, Huy TQ, Nga PT, Morita K, Dunia I, Benedetti L. A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line. Virology 2013; 444:337-42. [PMID: 23891522 PMCID: PMC7111958 DOI: 10.1016/j.virol.2013.06.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/06/2013] [Accepted: 06/27/2013] [Indexed: 11/18/2022]
Abstract
We describe the ultrastructure of the NamDinh virus (NDiV), a new member of the order Nidovirales grown in the C6/36 mosquito cell line. Uninfected and NDiV-infected cells were investigated by electron microscopy 24-48 h after infection. The results show that the viral nucleocapsid-like particles form clusters concentrated in the vacuoles, the endoplasmic reticulum, and are scattered in the cytoplasm. Mature virions of NDiV were released as budding particles on the cell surface where viral components appear to lie beneath and along the plasma membrane. Free homogeneous virus particles were obtained by ultracentrifugation on sucrose gradients of culture fluids. The size of the round-shaped particles with a complete internal structure was 80 nm in diameter. This is the first study to provide information on the morphogenesis and ultrastructure of the first insect nidovirus NDiV, a missing evolutionary link in the emergence of the viruses with the largest RNA genomes.
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Affiliation(s)
- Nguyen Thanh Thuy
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hai Ba Trung District, Hanoi, Viet Nam.
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