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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Woo PCY, de Groot RJ, Haagmans B, Lau SKP, Neuman BW, Perlman S, Sola I, van der Hoek L, Wong ACP, Yeh SH. ICTV Virus Taxonomy Profile: Coronaviridae 2023. J Gen Virol 2023; 104. [PMID: 37097842 DOI: 10.1099/jgv.0.001843] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
The family Coronaviridae includes viruses with positive-sense RNA genomes of 22-36 kb that are expressed through a nested set of 3' co-terminal subgenomic mRNAs. Members of the subfamily Orthocoronavirinae are characterized by 80-160 nm diameter, enveloped virions with spike projections. The orthocoronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome-related coronavirus are extremely pathogenic for humans and in the last two decades have been responsible for the SARS and MERS epidemics. Another orthocoronavirus, severe acute respiratory syndrome coronavirus 2, was responsible for the recent global COVID-19 pandemic. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Coronaviridae which is available at www.ictv.global/report/coronaviridae.
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Affiliation(s)
- Patrick C Y Woo
- PhD Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Raoul J de Groot
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Susanna K P Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Benjamin W Neuman
- Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
| | - Stanley Perlman
- Departments of Microbiology and Immunology, and Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish, National Research Council (CNB-CSIC), Madrid, Spain
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Laboratory of Experimental Virology, Location University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Antonio C P Wong
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Shiou-Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
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3
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Prescott L. SARS-CoV-2 3CLpro whole human proteome cleavage prediction and enrichment/depletion analysis. Comput Biol Chem 2022; 98:107671. [PMID: 35429835 PMCID: PMC8958254 DOI: 10.1016/j.compbiolchem.2022.107671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
A novel coronavirus (SARS-CoV-2) has devastated the globe as a pandemic that has killed millions of people. Widespread vaccination is still uncertain, so many scientific efforts have been directed toward discovering antiviral treatments. Many drugs are being investigated to inhibit the coronavirus main protease, 3CLpro, from cleaving its viral polyprotein, but few publications have addressed this protease’s interactions with the host proteome or their probable contribution to virulence. Too few host protein cleavages have been experimentally verified to fully understand 3CLpro’s global effects on relevant cellular pathways and tissues. Here, I set out to determine this protease’s targets and corresponding potential drug targets. Using a neural network trained on cleavages from 392 coronavirus proteomes with a Matthews correlation coefficient of 0.985, I predict that a large proportion of the human proteome is vulnerable to 3CLpro, with 4898 out of approximately 20,000 human proteins containing at least one putative cleavage site. These cleavages are nonrandomly distributed and are enriched in the epithelium along the respiratory tract, brain, testis, plasma, and immune tissues and depleted in olfactory and gustatory receptors despite the prevalence of anosmia and ageusia in COVID-19 patients. Affected cellular pathways include cytoskeleton/motor/cell adhesion proteins, nuclear condensation and other epigenetics, host transcription and RNAi, ribosomal stoichiometry and nascent-chain detection and degradation, ubiquitination, pattern recognition receptors, coagulation, lipoproteins, redox, and apoptosis. This whole proteome cleavage prediction demonstrates the importance of 3CLpro in expected and nontrivial pathways affecting virulence, lead me to propose more than a dozen potential therapeutic targets against coronaviruses, and should therefore be applied to all viral proteases and subsequently experimentally verified.
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Hossain ME, Islam A, Islam S, Rahman MK, Miah M, Alam MS, Rahman MZ. Detection and Molecular Characterization of Canine Alphacoronavirus in Free-Roaming Dogs, Bangladesh. Viruses 2021; 14:67. [PMID: 35062271 PMCID: PMC8778797 DOI: 10.3390/v14010067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/13/2021] [Accepted: 12/28/2021] [Indexed: 01/01/2023] Open
Abstract
Canine coronavirus (CCoV) is widespread among the dog population and causes gastrointestinal disorders, and even fatal cases. As the zoonotic transmission of viruses from animals to humans has become a worldwide concern nowadays, it is necessary to screen free-roaming dogs for their common pathogens due to their frequent interaction with humans. We conducted a cross-sectional study to detect and characterize the known and novel Corona, Filo, Flavi, and Paramyxoviruses in free-roaming dogs in Bangladesh. Between 2009-10 and 2016-17, we collected swab samples from 69 dogs from four districts of Bangladesh, tested using RT-PCR and sequenced. None of the samples were positive for Filo, Flavi, and Paramyxoviruses. Only three samples (4.3%; 95% CI: 0.9-12.2) tested positive for Canine Coronavirus (CCoV). The CCoV strains identified were branched with strains of genotype CCoV-II with distinct distances. They are closely related to CCoVs from the UK, China, and other CoVs isolated from different species, which suggests genetic recombination and interspecies transmission of CCoVs. These findings indicate that CCoV is circulating in dogs of Bangladesh. Hence, we recommend future studies on epidemiology and genetic characterization with full-genome sequencing of emerging coronaviruses in companion animals in Bangladesh.
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Affiliation(s)
- Mohammad Enayet Hossain
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.E.H.); (M.M.); (M.S.A.); (M.Z.R.)
| | - Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (S.I.); (M.K.R.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (S.I.); (M.K.R.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh
| | - Md Kaisar Rahman
- EcoHealth Alliance, New York, NY 10001-2320, USA; (S.I.); (M.K.R.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh
| | - Mojnu Miah
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.E.H.); (M.M.); (M.S.A.); (M.Z.R.)
| | - Md Shaheen Alam
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.E.H.); (M.M.); (M.S.A.); (M.Z.R.)
| | - Mohammed Ziaur Rahman
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.E.H.); (M.M.); (M.S.A.); (M.Z.R.)
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Gorbalenya AE, Lauber C. Bioinformatics of virus taxonomy: foundations and tools for developing sequence-based hierarchical classification. Curr Opin Virol 2021; 52:48-56. [PMID: 34883443 DOI: 10.1016/j.coviro.2021.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/03/2022]
Abstract
The genome sequence is the only characteristic readily obtainable for all known viruses, underlying the growing role of comparative genomics in organizing knowledge about viruses in a systematic evolution-aware way, known as virus taxonomy. Overseen by the International Committee on Taxonomy of Viruses (ICTV), development of virus taxonomy involves taxa demarcation at 15 ranks of a hierarchical classification, often in host-specific manner. Outside the ICTV remit, researchers assess fitting numerous unclassified viruses into the established taxa. They employ different metrics of virus clustering, basing on conserved domain(s), separation of viruses in rooted phylogenetic trees and pair-wise distance space. Computational approaches differ further in respect to methodology, number of ranks considered, sensitivity to uneven virus sampling, and visualization of results. Advancing and using computational tools will be critical for improving taxa demarcation across the virosphere and resolving rank origins in research that may also inform experimental virology.
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Affiliation(s)
- Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics and Belozersky, Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899, Moscow, Russia.
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, A Joint Venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
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Sashittal P, Zhang C, Peng J, El-Kebir M. Jumper enables discontinuous transcript assembly in coronaviruses. Nat Commun 2021; 12:6728. [PMID: 34795232 PMCID: PMC8602663 DOI: 10.1038/s41467-021-26944-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
Genes in SARS-CoV-2 and other viruses in the order of Nidovirales are expressed by a process of discontinuous transcription which is distinct from alternative splicing in eukaryotes and is mediated by the viral RNA-dependent RNA polymerase. Here, we introduce the DISCONTINUOUS TRANSCRIPT ASSEMBLYproblem of finding transcripts and their abundances given an alignment of paired-end short reads under a maximum likelihood model that accounts for varying transcript lengths. We show, using simulations, that our method, JUMPER, outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1, SARS-CoV-2 and MERS-CoV samples, we find that JUMPER not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are supported by subsequent orthogonal analyses. Moreover, application of JUMPER on samples with and without treatment reveals viral drug response at the transcript level. As such, JUMPER enables detailed analyses of Nidovirales transcriptomes under varying conditions.
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Affiliation(s)
- Palash Sashittal
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chuanyi Zhang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- College of Medicine, University of ILlinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Wang IE, Cooper G, Mousa SA. Diagnostic Approaches for COVID-19 and Its Associated Complications. Diagnostics (Basel) 2021; 11:2071. [PMID: 34829418 PMCID: PMC8619505 DOI: 10.3390/diagnostics11112071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022] Open
Abstract
With almost 4 million deaths worldwide from the COVID-19 pandemic, the efficient and accurate diagnosis and identification of COVID-19-related complications are more important than ever. Scales such as the pneumonia severity index, or CURB-65, help doctors determine who should be admitted to the hospital or the intensive care unit. To properly treat and manage admitted patients, standardized sampling protocols and methods are required for COVID-19 patients. Using PubMed, relevant articles since March 2020 on COVID-19 diagnosis and its complications were analyzed. Patients with COVID-19 had elevated D-dimer, thrombomodulin, and initial factor V elevation followed by decreased factor V and factor VII and elevated IL-6, lactate dehydrogenase, and c-reactive protein, which indicated coagulopathy and possible cytokine storm. Patients with hypertension, newly diagnosed diabetes, obesity, or advanced age were at increased risk for mortality. Elevated BUN, AST, and ALT in severe COVID-19 patients was associated with acute kidney injury or other organ damage. The gold standard for screening COVID-19 is reverse transcriptase polymerase chain reaction (RT-PCR) using sputum, oropharyngeal, or nasopharyngeal routes. However, due to the low turnover rate and limited testing capacity of RT-PCR, alternative diagnostic tools such as CT-scan and serological testing (IgM and IgG) can be considered in conjunction with symptom monitoring. Advancements in CRISPR technology have also allowed the use of alternative COVID-19 testing, but unfortunately, these technologies are still under FDA review and cannot be used in patients. Nonetheless, increased turnover rates and testing capacity allow for a bright future in COVID-19 diagnosis.
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Affiliation(s)
| | | | - Shaker A. Mousa
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, 1 Discovery Drive, Rensselaer, NY 12144, USA; (I.E.W.); (G.C.)
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Wong ACP, Lau SKP, Woo PCY. Interspecies Jumping of Bat Coronaviruses. Viruses 2021; 13:2188. [PMID: 34834994 PMCID: PMC8620431 DOI: 10.3390/v13112188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.
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Affiliation(s)
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
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Parkhe P, Verma S. Evolution, Interspecies Transmission, and Zoonotic Significance of Animal Coronaviruses. Front Vet Sci 2021; 8:719834. [PMID: 34738021 PMCID: PMC8560429 DOI: 10.3389/fvets.2021.719834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.
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Affiliation(s)
| | - Subhash Verma
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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Kim CH. Anti-SARS-CoV-2 Natural Products as Potentially Therapeutic Agents. Front Pharmacol 2021; 12:590509. [PMID: 34122058 PMCID: PMC8194829 DOI: 10.3389/fphar.2021.590509] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2), a β-coronavirus, is the cause of the recently emerged pandemic and worldwide outbreak of respiratory disease. Researchers exchange information on COVID-19 to enable collaborative searches. Although there is as yet no effective antiviral agent, like tamiflu against influenza, to block SARS-CoV-2 infection to its host cells, various candidates to mitigate or treat the disease are currently being investigated. Several drugs are being screened for the ability to block virus entry on cell surfaces and/or block intracellular replication in host cells. Vaccine development is being pursued, invoking a better elucidation of the life cycle of the virus. SARS-CoV-2 recognizes O-acetylated neuraminic acids and also several membrane proteins, such as ACE2, as the result of evolutionary switches of O-Ac SA recognition specificities. To provide information related to the current development of possible anti-SARS-COV-2 viral agents, the current review deals with the known inhibitory compounds with low molecular weight. The molecules are mainly derived from natural products of plant sources by screening or chemical synthesis via molecular simulations. Artificial intelligence-based computational simulation for drug designation and large-scale inhibitor screening have recently been performed. Structure-activity relationship of the anti-SARS-CoV-2 natural compounds is discussed.
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Affiliation(s)
- Cheorl-Ho Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, Sungkyunkhwan University, Suwon, South Korea
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Sofi MS, Hamid A, Bhat SU. SARS-CoV-2: A critical review of its history, pathogenesis, transmission, diagnosis and treatment. BIOSAFETY AND HEALTH 2020; 2:217-225. [PMID: 33196035 PMCID: PMC7648888 DOI: 10.1016/j.bsheal.2020.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the deadly virus (novel coronavirus or Severe Acute Respiratory Syndrome Coronavirus-2) that emerged in December 2019, remained a controversial subject of intense speculations regarding its origin, became a worldwide health problem resulting in serious coronavirus disease 2019 (acronym COVID-19). The concern regarding this new viral strain "Severe Acute Respiratory Syndrome Coronavirus-2" (acronym SARS-CoV-2) and diseases it causes (COVID-19) is well deserved at all levels. The incidence of COVID-19 infection and infectious patients are increasing at a high rate. Coronaviruses (CoVs), enclosed positive-sense RNA viruses, are distinguished by club-like spikes extending from their surface, an exceptionally large genome of RNA, and a special mechanism for replication. Coronaviruses are associated with a broad variety of human and other animal diseases spanning from enteritis in cattle and pigs and upper chicken respiratory disease to extremely lethal human respiratory infections. With World Health Organization (WHO) declaring COVID-19 as pandemic, we deemed it necessary to provide a detailed review of coronaviruses discussing their history, current situation, coronavirus classification, pathogenesis, structure, mode of action, diagnosis and treatment, the effect of environmental factors, risk reduction and guidelines to understand the virus and develop ways to control it.
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Affiliation(s)
| | | | - Sami Ullah Bhat
- Corresponding author: Department of Environmental Science, School of Earth and Environmental Science, University of Kashmir, 190006, India
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Abstract
SARS-CoV2 infection or COVID-19 has created panic around the world since its first origin in December 2019 in Wuhan city, China. The COVID-19 pandemic has infected more than 46.4 million people, with 1,199,727 deaths. The immune system plays a crucial role in the severity of COVID-19 and the development of pneumonia-induced acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). Along with providing protection, both innate and T cell-based adaptive immune response dysregulate during severe SARS-CoV2 infection. This dysregulation is more pronounced in older population and patients with comorbidities (Diabetes, hypertension, obesity, other pulmonary and autoimmune diseases). However, COVID-19 patients develop protective antibodies (Abs) against SARS-CoV2, but they do not long for last. The induction of the immune response against the pathogen also requires metabolic energy that generates through the process of immunometabolism. The change in the metabolic stage of immune cells from homeostasis to an inflammatory or infectious environment is called immunometabolic reprogramming. The article describes the cellular immunology (macrophages, T cells, B cells, dendritic cells, NK cells and pulmonary epithelial cells (PEC) and vascular endothelial cells) and the associated immune response during COVID-19. Immunometabolism may serve as a cell-specific therapeutic approach to target COVID-19.
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Affiliation(s)
- Vijay Kumar
- Children's Health Queensland Clinical Unit, School of Clinical Medicine, Faculty of Medicine, Mater Research, University of Queensland, Brisbane, Queensland, Australia.,School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Robson F, Khan KS, Le TK, Paris C, Demirbag S, Barfuss P, Rocchi P, Ng WL. Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting. Mol Cell 2020; 79:710-727. [PMID: 32853546 PMCID: PMC7402271 DOI: 10.1016/j.molcel.2020.07.027] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) that is wreaking havoc on worldwide public health and economies has heightened awareness about the lack of effective antiviral treatments for human coronaviruses (CoVs). Many current antivirals, notably nucleoside analogs (NAs), exert their effect by incorporation into viral genomes and subsequent disruption of viral replication and fidelity. The development of anti-CoV drugs has long been hindered by the capacity of CoVs to proofread and remove mismatched nucleotides during genome replication and transcription. Here, we review the molecular basis of the CoV proofreading complex and evaluate its potential as a drug target. We also consider existing nucleoside analogs and novel genomic techniques as potential anti-CoV therapeutics that could be used individually or in combination to target the proofreading mechanism.
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Affiliation(s)
- Fran Robson
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Khadija Shahed Khan
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Thi Khanh Le
- Life Science Department, University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam; Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Clément Paris
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Sinem Demirbag
- Faculty of Engineering and Natural Sciences, Sabanci University, İstanbul, Turkey
| | - Peter Barfuss
- Université Paris-Est, Cermics (ENPC), INRIA, 77455 Marne-la-Vallée, France
| | - Palma Rocchi
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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Kumar V. Emerging Human Coronavirus Infections (SARS, MERS, and COVID-19): Where They Are Leading Us. Int Rev Immunol 2020; 40:5-53. [PMID: 32744465 DOI: 10.1080/08830185.2020.1800688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus infections are responsible for mild, moderate, and severe infections in birds and mammals. These were first isolated in humans as causal microorganisms responsible for common cold. The 2002-2003 SARS epidemic caused by SARS-CoV and 2012 MERS epidemic (64 countries affected) caused by MERS-CoV showed their acute and fatal side. These two CoV infections killed thousands of patients infected worldwide. However, WHO has still reported the MERS case in December 2019 in middle-eastern country (Saudi Arabia), indicating the MERS epidemic has not ended completely yet. Although we have not yet understood completely these two CoV epidemics, a third most dangerous and severe CoV infection has been originated in the Wuhan city, Hubei district of China in December 2019. This CoV infection called COVID-19 or SARS-CoV2 infection has now spread to 210 countries and territories around the world. COVID-19 has now been declared a pandemic by the World Health Organization (WHO). It has infected more than 16.69 million people with more than 663,540 deaths across the world. Thus the current manuscript aims to describe all three (SARS, MERS, and COVID-19) in terms of their causal organisms (SARS-CoV, MERS-CoV, and SARS-CoV2), similarities and differences in their clinical symptoms, outcomes, immunology, and immunopathogenesis, and possible future therapeutic approaches.
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Affiliation(s)
- Vijay Kumar
- Children's Health Queensland Clinical Unit, School of Clinical Medicine, Faculty of Medicine, Mater Research, University of Queensland, Brisbane, Queensland, Australia.,School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Lutz M, Steiner AR, Cattori V, Hofmann-Lehmann R, Lutz H, Kipar A, Meli ML. FCoV Viral Sequences of Systemically Infected Healthy Cats Lack Gene Mutations Previously Linked to the Development of FIP. Pathogens 2020; 9:E603. [PMID: 32722056 PMCID: PMC7459962 DOI: 10.3390/pathogens9080603] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023] Open
Abstract
Feline infectious peritonitis (FIP)-the deadliest infectious disease of young cats in shelters or catteries-is induced by highly virulent feline coronaviruses (FCoVs) emerging in infected hosts after mutations of less virulent FCoVs. Previous studies have shown that some mutations in the open reading frames (ORF) 3c and 7b and the spike (S) gene have implications for the development of FIP, but mainly indirectly, likely also due to their association with systemic spread. The aim of the present study was to determine whether FCoV detected in organs of experimentally FCoV infected healthy cats carry some of these mutations. Viral RNA isolated from different tissues of seven asymptomatic cats infected with the field strains FCoV Zu1 or FCoV Zu3 was sequenced. Deletions in the 3c gene and mutations in the 7b and S genes that have been shown to have implications for the development of FIP were not detected, suggesting that these are not essential for systemic viral dissemination. However, deletions and single nucleotide polymorphisms leading to truncations were detected in all nonstructural proteins. These were found across all analyzed ORFs, but with significantly higher frequency in ORF 7b than ORF 3a. Additionally, a previously unknown homologous recombination site was detected in FCoV Zu1.
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Affiliation(s)
- Mirjam Lutz
- Clinical Laboratory, Department of Clinical Diagnostics and Services and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland; (M.L.); (A.R.S.); (V.C.); (R.H.-L.); (H.L.)
| | - Aline R. Steiner
- Clinical Laboratory, Department of Clinical Diagnostics and Services and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland; (M.L.); (A.R.S.); (V.C.); (R.H.-L.); (H.L.)
| | - Valentino Cattori
- Clinical Laboratory, Department of Clinical Diagnostics and Services and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland; (M.L.); (A.R.S.); (V.C.); (R.H.-L.); (H.L.)
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland; (M.L.); (A.R.S.); (V.C.); (R.H.-L.); (H.L.)
| | - Hans Lutz
- Clinical Laboratory, Department of Clinical Diagnostics and Services and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland; (M.L.); (A.R.S.); (V.C.); (R.H.-L.); (H.L.)
| | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland;
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, CH 8057 Zurich, Switzerland; (M.L.); (A.R.S.); (V.C.); (R.H.-L.); (H.L.)
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SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus-Host Interaction. Int J Mol Sci 2020; 21:ijms21124549. [PMID: 32604730 PMCID: PMC7352545 DOI: 10.3390/ijms21124549] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme. Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs. Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs. The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein–carbohydrate interaction (PCI) or lectin–carbohydrate interaction (LCI). The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA–specific HEF, as in influenza virus C/D. HE acquisition, and expansion takes place by cross-species transmission over HE evolution. This reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts. The PCI or LCI stereochemistry potentiates the SA–ligand switch by a simple conformational shift of the lectin and esterase domains. Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism. A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE. A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors. The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA. Principles of the protein–glycan interaction and PCI stereochemistry potentiate the SA–ligand switch via simple conformational shifts of the lectin and esterase domains. Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism. Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents. As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development. However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients. In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future.
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Singh S, Singh R, Singh K, Singh V, Malik Y, Kamdi B, Singh R, Kashyap G. Prevalence of bovine coronavirus infection in organized dairy farms of Central and North regions, India. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1629093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Shailendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K.P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - V. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Y.P.S Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bhupesh Kamdi
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Rahul Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Gayatri Kashyap
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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Ellis S, Keep S, Britton P, de Wit S, Bickerton E, Vervelde L. Recombinant Infectious Bronchitis Viruses Expressing Chimeric Spike Glycoproteins Induce Partial Protective Immunity against Homologous Challenge despite Limited Replication In Vivo. J Virol 2018; 92:e01473-18. [PMID: 30209177 PMCID: PMC6232476 DOI: 10.1128/jvi.01473-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/03/2018] [Indexed: 12/19/2022] Open
Abstract
Vaccination regimes against Infectious bronchitis virus (IBV), which are based on a single virus serotype, often induce insufficient levels of cross-protection against serotypes and two or more antigenically diverse vaccines are used in attempt to provide broader protection. Amino acid differences in the surface protein, spike (S), in particular the S1 subunit, are associated with poor cross-protection. Here, homologous vaccination trials with recombinant IBVs (rIBVs), based on the apathogenic strain, BeauR, were conducted to elucidate the role of S1 in protection. A single vaccination of specific-pathogen-free chickens with rIBV expressing S1 of virulent strains M41 or QX, BeauR-M41(S1) and BeauR-QX(S1), gave incomplete protection against homologous challenge, based on ciliary activity and clinical signs. There could be conformational issues with the spike if heterologous S1 and S2 are linked, suggesting a homologous S2 might be essential. To address this, a homologous vaccination-challenge trial incorporating rIBVs expressing full spike from M41, BeauR-M41(S), and S2 subunit from M41, BeauR-M41(S2) was conducted. All chimeric viruses grew to similar titers in vitro, induced virus-specific partial protective immunity, evident by cellular infiltrations, reductions in viral RNA load in the trachea and conjunctiva and higher serum anti-IBV titers. Collectively, these findings show that vaccination with rIBVs primed the birds for challenge but the viruses were cleared rapidly from the mucosal tissues in the head. Chimeric S1 and S2 viruses did not protect as effectively as BeauR-M41(S) based on ciliary activity and clinical signs. Booster vaccinations and an rIBV with improved in vivo replication may improve the levels of protection.IMPORTANCE Infectious bronchitis virus causes an acute, highly contagious respiratory disease, responsible for significant economic losses to the poultry industry. Amino acid differences in the surface protein, spike (S), in particular the S1 subunit, have been associated with poor cross-protection. Available vaccines give poor cross-protection and rationally designed live attenuated vaccines, based on apathogenic BeauR, could address these. Here, to determine the role of S1 in protection, a series of homologous vaccination trials with rIBVs were conducted. Single vaccinations with chimeric rIBVs induced virus-specific partial protective immunity, characterized by reduction in viral load and serum antibody titers. However, BeauR-M41(S) was the only vaccination to improve the level of protection against clinical signs and the loss of tracheal ciliary activity. Growth characteristics show that all of the rIBVs replicated in vitro to similar levels. Booster vaccinations and an rIBV with improved in vivo replication may improve the levels of protection.
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Affiliation(s)
- Samantha Ellis
- Infection and Immunity, The Roslin Institute, University of Edinburgh, Penicuik, Midlothian, United Kingdom
| | - Sarah Keep
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Paul Britton
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | | | | | - Lonneke Vervelde
- Infection and Immunity, The Roslin Institute, University of Edinburgh, Penicuik, Midlothian, United Kingdom
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Bickerton E, Maier HJ, Stevenson-Leggett P, Armesto M, Britton P. The S2 Subunit of Infectious Bronchitis Virus Beaudette Is a Determinant of Cellular Tropism. J Virol 2018; 92:e01044-18. [PMID: 30021894 PMCID: PMC6146808 DOI: 10.1128/jvi.01044-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The spike (S) glycoprotein of the avian gammacoronavirus infectious bronchitis virus (IBV) is comprised of two subunits (S1 and S2), has a role in virulence in vivo, and is responsible for cellular tropism in vitro We have previously demonstrated that replacement of the S glycoprotein ectodomain from the avirulent Beaudette strain of IBV with the corresponding region from the virulent M41-CK strain resulted in a recombinant virus, BeauR-M41(S), with the in vitro cell tropism of M41-CK. The IBV Beaudette strain is able to replicate in both primary chick kidney cells and Vero cells, whereas the IBV M41-CK strain replicates in primary cells only. In order to investigate the region of the IBV S responsible for growth in Vero cells, we generated a series of recombinant IBVs expressing chimeric S glycoproteins, consisting of regions from the Beaudette and M41-CK S gene sequences, within the genomic background of Beaudette. The S2, but not the S1, subunit of the Beaudette S was found to confer the ability to grow in Vero cells. Various combinations of Beaudette-specific amino acids were introduced into the S2 subunit of M41 to determine the minimum requirement to confer tropism for growth in Vero cells. The ability of IBV to grow and produce infectious progeny virus in Vero cells was subsequently narrowed down to just 3 amino acids surrounding the S2' cleavage site. Conversely, swapping of the 3 Beaudette-associated amino acids with the corresponding ones from M41 was sufficient to abolish Beaudette growth in Vero cells.IMPORTANCE Infectious bronchitis remains a major problem in the global poultry industry, despite the existence of many different vaccines. IBV vaccines, both live attenuated and inactivated, are currently grown on embryonated hen's eggs, a cumbersome and expensive process due to the fact that most IBV strains do not grow in cultured cells. The reverse genetics system for IBV creates the opportunity for generating rationally designed and more effective vaccines. The observation that IBV Beaudette has the additional tropism for growth on Vero cells also invokes the possibility of generating IBV vaccines produced from cultured cells rather than by the use of embryonated eggs. The regions of the IBV Beaudette S glycoprotein involved in the determination of extended cellular tropism were identified in this study. This information will enable the rational design of a future generation of IBV vaccines that may be grown on Vero cells.
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20
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Stewart H, Brown K, Dinan AM, Irigoyen N, Snijder EJ, Firth AE. Transcriptional and Translational Landscape of Equine Torovirus. J Virol 2018; 92:e00589-18. [PMID: 29950409 PMCID: PMC6096809 DOI: 10.1128/jvi.00589-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
The genus Torovirus (subfamily Torovirinae, family Coronaviridae, order Nidovirales) encompasses a range of species that infect domestic ungulates, including cattle, sheep, goats, pigs, and horses, causing an acute self-limiting gastroenteritis. Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. RNA sequencing confirmed that EToV utilizes a unique combination of discontinuous and nondiscontinuous RNA synthesis to produce its subgenomic RNAs (sgRNAs); indeed, we identified transcripts arising from both mechanisms that would result in sgRNAs encoding the nucleocapsid. Our ribosome profiling analysis revealed that ribosomes efficiently translate two novel CUG-initiated open reading frames (ORFs), located within the so-called 5' untranslated region. We have termed the resulting proteins U1 and U2. Comparative genomic analysis confirmed that these ORFs are conserved across all available torovirus sequences, and the inferred amino acid sequences are subject to purifying selection, indicating that U1 and U2 are functionally relevant. This study provides the first high-resolution analysis of transcription and translation in this neglected group of livestock pathogens.IMPORTANCE Toroviruses infect cattle, goats, pigs, and horses worldwide and can cause gastrointestinal disease. There is no treatment or vaccine, and their ability to spill over into humans has not been assessed. These viruses are related to important human pathogens, including severe acute respiratory syndrome (SARS) coronavirus, and they share some common features; however, the mechanism that they use to produce sgRNA molecules differs. Here, we performed deep sequencing to determine how equine torovirus produces sgRNAs. In doing so, we also identified two previously unknown open reading frames "hidden" within the genome. Together these results highlight the similarities and differences between this domestic animal virus and related pathogens of humans and livestock.
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Affiliation(s)
- Hazel Stewart
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Rappe JCF, de Wilde A, Di H, Müller C, Stalder H, V'kovski P, Snijder E, Brinton MA, Ziebuhr J, Ruggli N, Thiel V. Antiviral activity of K22 against members of the order Nidovirales. Virus Res 2018; 246:28-34. [PMID: 29337162 PMCID: PMC7114538 DOI: 10.1016/j.virusres.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 01/31/2023]
Abstract
Recently, a novel antiviral compound (K22) that inhibits replication of a broad range of animal and human coronaviruses was reported to interfere with viral RNA synthesis by impairing double-membrane vesicle (DMV) formation (Lundin et al., 2014). Here we assessed potential antiviral activities of K22 against a range of viruses representing two (sub)families of the order Nidovirales, the Arteriviridae (porcine reproductive and respiratory syndrome virus [PRRSV], equine arteritis virus [EAV] and simian hemorrhagic fever virus [SHFV]), and the Torovirinae (equine torovirus [EToV] and White Bream virus [WBV]). Possible effects of K22 on nidovirus replication were studied in suitable cell lines. K22 concentrations significantly decreasing infectious titres of the viruses included in this study ranged from 25 to 50 μM. Reduction of double-stranded RNA intermediates of viral replication in nidovirus-infected cells treated with K22 confirmed the anti-viral potential of K22. Collectively, the data show that K22 has antiviral activity against diverse lineages of nidoviruses, suggesting that the inhibitor targets a critical and conserved step during nidovirus replication.
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Affiliation(s)
- Julie Christiane Françoise Rappe
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Adriaan de Wilde
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Han Di
- Department of Biology, 623 Petit Science Center, Georgia State University, 161 Jesse Hill Jr Drive, Atlanta, GA 30303, United States.
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Hanspeter Stalder
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Philip V'kovski
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Eric Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Margo A Brinton
- Department of Biology, 623 Petit Science Center, Georgia State University, 161 Jesse Hill Jr Drive, Atlanta, GA 30303, United States.
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Nicolas Ruggli
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Volker Thiel
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
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Jonsdottir HR, Dijkman R. Coronaviruses and the human airway: a universal system for virus-host interaction studies. Virol J 2016; 13:24. [PMID: 26852031 PMCID: PMC4744394 DOI: 10.1186/s12985-016-0479-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/27/2016] [Indexed: 02/08/2023] Open
Abstract
Human coronaviruses (HCoVs) are large RNA viruses that infect the human respiratory tract. The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Various animal models have been established to investigate HCoV infection, including mice and non-human primates. To establish a link between the research conducted in animal models and humans, an organotypic human airway culture system, that recapitulates the human airway epithelium, has been developed. Currently, different cell culture systems are available to recapitulate the human airways, including the Air-Liquid Interface (ALI) human airway epithelium (HAE) model. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. These organotypic human airway cultures represent a universal platform to study respiratory virus-host interaction by offering more detailed insights compared to cell lines. Additionally, the epidemic potential of this virus family highlights the need for both vaccines and antivirals. No commercial vaccine is available but various effective antivirals have been identified, some with potential for human treatment. These morphological airway cultures are also well suited for the identification of antivirals, evaluation of compound toxicity and viral inhibition.
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Affiliation(s)
- Hulda R Jonsdottir
- Federal Department of Home Affairs, Institute of Virology and Immunology, Länggassstrasse 122, 3012, Bern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Ronald Dijkman
- Federal Department of Home Affairs, Institute of Virology and Immunology, Länggassstrasse 122, 3012, Bern, Switzerland.
- Department of Infectious diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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Abstract
Members of the family Coronaviridae are evolutionarily related and play an important role in human and veterinary medicine. Taxonomic classification is based on the ultrastructure and morphogenesis of viral particles and on biochemical and molecular features. The family Coronaviridae belongs to the order Nidovirales, and is divided into two subfamilies: Coronavirinae and Torovirinae. The number of coronaviruses isolated from aquatic organisms is negligible; indeed, coronaviruses have only been identified in aquatic mammals, including harbor seal (genus Alphacoronavirus), bottlenose dolphin and beluga whale (genus Gammacoronavirus). White bream virus, isolated from the teleost Blicca bjoerkna (L.), is the type species of the genus Bafinivirus within the subfamily, Torovirinae.
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Li Z, Wang G, Wang Y, Zhang C, Wang X, Huang B, Li Q, Li L, Xue B, Ding P, Syed SF, Wang C, Cai X, Zhou EM. Rescue and evaluation of a recombinant PRRSV expressing porcine Interleukin-4. Virol J 2015; 12:185. [PMID: 26573719 PMCID: PMC4647277 DOI: 10.1186/s12985-015-0380-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current vaccines for porcine reproductive and respiratory syndrome virus (PRRSV) have failed to provide broad protection against infection by various strains of PRRSV. Porcine Interleukin-4 (pIL-4) plays an important role in the regulation of the immune response and has been used previously as an immunological adjuvant. The objective of this study was to construct a recombinant PRRSV expressing pIL-4 and to evaluate the immune response of the recombinant virus in piglets. METHODS The pIL-4 gene was inserted in the PRRSV (CH-1R strain) infectious clone by overlap PCR. Indirect immunofluorescence assay (IFA) and Western blotting were used to confirm the recombinant virus. The stability of the recombinant virus was assessed by DNA sequencing and IFA after 15 passages in vitro. Recombinant virus was injected into pigs and efficacy of immune protection was evaluated in comparison with the parental virus. RESULTS The recombinant virus (CH-1R/pIL-4) was successfully rescued and shown to have similar growth kinetics as the parental virus. The recombinant virus was stable for 15 passages in cell culture. Pigs vaccinated with CH-1R/pIL-4 produced a similar humoral response to the response elicited by parental virus, but IL-4 level in the supernatant of PBMCs from pigs vaccinated with CH-1R/pIL-4 was significantly higher than the parent virus at 28 days post-immunization (DPI). Flow cytometric (FCM) analysis showed that the percentage of CD4(+)CD8(+) double positive T (DPT) cells in the CH-1R/pIL-4 vaccinated group was significantly higher than the parental virus at 3 and 7 Days Post-Challenge (DPC), and the IL-4 level in the blood significantly increased at 7 DPC. However, the viral load and histopathology did not show significant difference between the two groups. CONCLUSIONS A recombinant PRRSV expressing porcine IL-4 was rescued and it remained genetically stable in vitro. The recombinant virus induced higher DPT ratios and IL-4 levels in the blood after HP-PRRSV challenge compared to the parental virus in piglets. However, it did not significantly improve protection efficacy of PRRSV vaccine.
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Affiliation(s)
- Zhijun Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Gang Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agriculture Science, Harbin, 150001, China.
| | - Yan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Chong Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agriculture Science, Harbin, 150001, China.
| | - Xinglong Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Baicheng Huang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Qiongyi Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Liangliang Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Biyun Xue
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Peiyang Ding
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Shahid Faraz Syed
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Chengbao Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agriculture Science, Harbin, 150001, China.
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Veterinary Biotechnology, Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
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Lojkić I, Krešić N, Šimić I, Bedeković T. Detection and molecular characterisation of bovine corona and toroviruses from Croatian cattle. BMC Vet Res 2015; 11:202. [PMID: 26268320 PMCID: PMC4535285 DOI: 10.1186/s12917-015-0511-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Bovine coronavirus (BCoV) together with bovine torovirus (BToV), both members of the Coronaviridae family, order Nidovirales are the most common viral enteric pathogens. Although studied separately, their joint occurrence and the molecular diversity in cattle in Croatia have not been investigated. METHODS A survey is carried out on 101 fecal samples from diarrheic young and adult cattle during the 3-year period from i) one large dairy herd, ii) four small herds and iii) three nasal and paired fecal samples from calves with symptoms of respiratory disease. Samples were submitted to RT-PCR and sequencing for BCoV Nucleocapsid gene, BCoV Spike gene and BToV Spike gene. RESULTS BCoV was detected in 78.8 % of fecal samples from symptomatic cattle and three nasal and paired fecal samples from calves with respiratory symptoms. BToV was detected in 43.2 % of fecal samples from symptomatic cattle and a fecal sample from calves with respiratory symptoms. Molecular characterisation of those viruses revealed some nucleotide and aminoacid differences in relation to reference strains. CONCLUSIONS BToV should be regarded as a relevant pathogen for cattle that plays a synergistic role in mixed enteric infections.
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Affiliation(s)
- Ivana Lojkić
- Department of Virology, Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
| | - Nina Krešić
- Department of Virology, Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
| | - Ivana Šimić
- Department of Virology, Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
| | - Tomislav Bedeković
- Department of Virology, Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
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26
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Anbalagan S, Peterson J, Wassman B, Elston J, Schwartz K. Genome sequence of torovirus identified from a pig with porcine epidemic diarrhea virus from the United States. GENOME ANNOUNCEMENTS 2014; 2:e01291-14. [PMID: 25523767 PMCID: PMC4271157 DOI: 10.1128/genomea.01291-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/11/2014] [Indexed: 11/27/2022]
Abstract
Porcine torovirus (PToV) strain PToV-NPL/2013 was identified from a pig that tested positive for porcine epidemic diarrhea virus (PEDV). The spike protein-encoding gene from PToV-NPL/2013 had 92% identity with PToV-SH1, suggesting that PToV circulating in the United States is slightly different from the isolates circulating in China. To our knowledge, this is the first report of PToV in the United States.
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Affiliation(s)
| | | | - Brent Wassman
- Newport Laboratories, Inc., Worthington, Minnesota, USA
| | - Josh Elston
- Newport Laboratories, Inc., Worthington, Minnesota, USA
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Hao J, Xue C, He L, Wang Y, Cao Y. Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011-2013 in Guangdong, China. Virus Genes 2014; 49:58-67. [PMID: 24771495 PMCID: PMC7088867 DOI: 10.1007/s11262-014-1055-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/06/2014] [Indexed: 10/27/2022]
Abstract
Three strains of porcine epidemic diarrhea virus (PEDV) were isolated from dead or diseased pigs at different swine farms in Guangdong during 2011-2013, and their S genes were sequenced. In the same period, seven PEDV strains were also isolated in Guangdong by other laboratories. The spike sequences of 10 Guangdong isolates were compared with vaccine strains and reference pathogenic isolates using six bioinformatics tools. The results revealed that 10 Guangdong strains, excluding strain GDS03, had distinct characteristics in terms of primary structure, secondary structure, high-specificity N-glycosylation sites, potential phosphorylation sites, and palmitoylation sites. Phylogenetic analysis also confirmed these findings and revealed that all PEDV strains were clustered into three distinct groups. Ten Guangdong strains, not including GDS03, belong to Group 1, whereas four vaccine strains and GDS03 belong to Group 3, which is evolutionarily distant from Group 1. Alignment analysis of the neutralizing region amino acid sequences indicated that the amino acid substitutions of Y/D766S, T549S, and G594S that are present in the Guangdong strains, not including GDS03, were a sign of predominant genetic changes among the isolated strains. GDS03 is closely related to the 83P-5 vaccine strain, which suggests that it might represent re-isolation of the vaccine strain or vaccine variants. Taken together, these results indicate that there have been predominant new strains circulating in Guangdong from 2011 to 2013, and the circulating PEDV strains have a genetic composition that is distant from reference strains, especially the vaccine strains; however, the vaccinations might also provide some level of cross-protection, as there have been no changes in the neutralizing epitopes of SS2 and 2C10. This explains why there have been constant but infrequent outbreaks recently in comparison to late 2010 in which PEDV outbreaks were more frequent and severe. In addition, the USA-Colorado-2013 strain had the same amino acid substitutions in the neutralizing regions as the Guangdong strains except GDS03, which suggests that the information and strategies in this study may play role in PEDV variant research in other countries.
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Affiliation(s)
- Jianwei Hao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 People’s Republic of China
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 People’s Republic of China
| | - Liangliang He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 People’s Republic of China
| | - Yang Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 People’s Republic of China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 People’s Republic of China
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Vatter HA, Di H, Donaldson EF, Radu GU, Maines TR, Brinton MA. Functional analyses of the three simian hemorrhagic fever virus nonstructural protein 1 papain-like proteases. J Virol 2014; 88:9129-40. [PMID: 24899184 PMCID: PMC4136243 DOI: 10.1128/jvi.01020-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/27/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The N-terminal region of simian hemorrhagic fever virus (SHFV) nonstructural polyprotein 1a is predicted to encode three papain-like proteases (PLP1α, PLP1β, and PLP1γ). Catalytic residues and cleavage sites for each of the SHFV PLP1s were predicted by alignment of the SHFV PLP1 region sequences with each other as well as with those of other arteriviruses, and the predicted catalytic residues were shown to be proximal by homology modeling of the SHFV nsp1s on porcine respiratory and reproductive syndrome virus (PRRSV) nsp1 crystal structures. The functionality of the predicted catalytic Cys residues and cleavage sites was tested by analysis of the autoproteolytic products generated in in vitro transcription/translation reactions done with wild-type or mutant SHFV nsp1 constructs. Cleavage sites were also analyzed by mass spectroscopy analysis of selected immunoprecipitated cleavage products. The data showed that each of the three SHFV PLP1s is an active protease. Cys63 was identified as the catalytic Cys of SHFV PLP1α and is adjacent to an Ala instead of the canonical Tyr observed in other arterivirus PLP1s. SHFV PLP1γ is able to cleave at both downstream and upstream nsp1 junction sites. Although intermediate precursor polyproteins as well as alternative products generated by each of the SHFV PLP1s cleaving at sites within the N-terminal region of nsp1β were produced in the in vitro reactions, Western blotting of SHFV-infected, MA104 cell lysates with SHFV nsp1 protein-specific antibodies detected only the three mature nsp1 proteins. IMPORTANCE SHFV is unique among arteriviruses in having three N-terminal papain-like protease 1 (PLP1) domains. Other arteriviruses encode one or two active PLP1s. This is the first functional study of the SHFV PLP1s. Analysis of the products of in vitro autoprocessing of an N-terminal SHFV nonstructural 1a polypeptide fragment showed that each of the three SHFV PLP1s is active, and the predicted catalytic Cys residues and cleavage sites for each PLP1 were confirmed by testing mutant constructs. Several unique features of the SHFV PLP1s were discovered. The SHFV PLP1α catalytic Cys63 is unique among arterivirus PLP1s in being adjacent to an Ala instead of a Trp. Other arterivirus PLP1s cleave only in cis at a single downstream site, but SHFV PLP1γ can cleave at both the downstream nsp1γ-nsp2 and upstream nsp1β-nsp1γ junctions. The three mature nsp1 proteins were produced both in the in vitro reactions and in infected cells.
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Affiliation(s)
- Heather A Vatter
- Department of Biology, Georgia State University, Atlanta Georgia, USA
| | - Han Di
- Department of Biology, Georgia State University, Atlanta Georgia, USA
| | - Eric F Donaldson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gertrud U Radu
- Department of Biology, Georgia State University, Atlanta Georgia, USA
| | - Taronna R Maines
- Department of Biology, Georgia State University, Atlanta Georgia, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta Georgia, USA
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Zhou L, Wei H, Zhou Y, Xu Z, Zhu L, Horne J. Molecular epidemiology of Porcine torovirus (PToV) in Sichuan Province, China: 2011-2013. Virol J 2014; 11:106. [PMID: 24903213 PMCID: PMC4064267 DOI: 10.1186/1743-422x-11-106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 05/30/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Porcine torovirus (PToV) is a member of the genus Torovirus which is responsible for gastrointestinal disease in both human beings and animals with particular prevalence in youth. Torovirus infections are generally asymptomatic, however, their presence may worsen disease consequences in concurrent infections with other enteric pathogens. METHODS A total of 872 diarrheic fecal samples from pigs of different ages were collected from 12 districts of Sichuan Province in the southwest of China. RT-PCR was done with PToV S gene specific primers to detect the presence of PToV positive samples. M gene specific primers were used with the PToV positive samples and the genes were sequenced. A phylogenetic tree was constructed based on the M gene nucleotide sequences from the 19 selected novel Sichuan strains and 21 PToV and BToV M gene sequences from GenBank. RESULTS A total of 331 (37.96%, 331/872) samples were found to be positive for PToV and the highest prevalence was observed in piglets aged from 1 to 3 weeks old. Through phylogenetic inference the 40 PToV M gene containing sequences were placed into two genotypes (I & II). The 19 novel Sichuan strains of genotype I showed strong correlations to two Korean gene sequences (GU-07-56-11 and GU-07-56-22). Amino-acid sequence analysis of the 40 PToV M gene strains revealed that the M gene protein was highly conserved. CONCLUSIONS This study uncovered the presence of PToV in Sichuan Province, and demonstrated the need for continuous surveillance PToV of epidemiology.
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Affiliation(s)
- Lu Zhou
- Animal Biotechnology Center, College of Veterinary Medicine, Ya’an, China
| | - Haoche Wei
- Animal Biotechnology Center, College of Veterinary Medicine, Ya’an, China
- Faculty of Bio and Biochemistry, University of Bath, Bath spa, England
| | - Yuancheng Zhou
- Animal Biotechnology Center, College of Veterinary Medicine, Ya’an, China
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Ya’an, China
- Key Laboratory of Animal Disease and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Ling Zhu
- Animal Biotechnology Center, College of Veterinary Medicine, Ya’an, China
- Key Laboratory of Animal Disease and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Jim Horne
- Faculty of Bio and Biochemistry, University of Bath, Bath spa, England
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30
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Toroviruses (Coronaviridae). REFERENCE MODULE IN BIOMEDICAL SCIENCES 2014. [PMCID: PMC7157456 DOI: 10.1016/b978-0-12-801238-3.02674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Toroviruses are single-stranded RNA peplomer-bearing enveloped viruses producing enteric disease in animals and humans. They have a unique extracellular C-shape or open torus morphology. There are four species in the genus Torovirus (family Coronaviridae, order Nidovirales): Equine torovirus (EToV), Bovine torovirus (BToV), Human torovirus (HToV), and Porcine torovirus (PToV), which have been reported worldwide. Their genome contains six ORFs, which are transcribed as a 3’-coterminal nested set of four mRNAs. ORF1a and 1b encode the replicase, and ORFs 2–5 encode the spike (S), membrane (M), hemagglutinin-esterase (HE), and nucleocapsid (N) proteins, respectively. Only EToVs and BToV Aichi/2004 propagate in cell culture.
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31
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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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32
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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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Hansa A, Rai RB, Dhama K, Wani MY, Saminathan M, Ranganath GJ. Isolation of bovine coronavirus (bcoV) in vero cell line and its confirmation by direct FAT and RT-PCR. Pak J Biol Sci 2013; 16:1342-1347. [PMID: 24511744 DOI: 10.3923/pjbs.2013.1342.1347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bovine Coronavirus (BCoV) is widespread both in dairy and beef cattle throughout the world. The virus is one of the largest RNA virus and has specific tropism for intestinal and pulmonary epithelial cells. It is responsible for huge economic losses by causing winter dysentery in adult dairy cattle and respiratory and intestinal tract infections leading to pneumo-enteritis in young calves. Isolation of BCoV has been reported to be difficult. Studies regarding epidemiology, virus isolation and molecular detection from India are very few. In the present study Vero cell line was used for isolation of the BCoV from Enzyme Linked Immunosorbent Assay (ELISA) positive samples. Direct florescent antibody technique (dFAT) and reverse transcriptase-polymerase chain reaction (RT-PCR) were used to confirm the isolated virus strains at antigenic and genomic levels, respectively. Out of the 15 positive fecal samples, virus from only seven was able to infect vero cell line. Subsequently BCoV got adapted to the vero cell line upto three passages, which was confirmed both at genomic and antigenic levels by dFAT and RT-PCR testing. It can be concluded that vero cell line can be used for isolation of BCoV, however due to the enormous stain diversity of the virus it is possible that many stains can't grow and get adapt in this cell line. Further studies are required for isolation of different viral strains, finding the susceptible cell lines and also to confirm the variations among the BCoV isolates at antigenic/genomic levels.
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Affiliation(s)
- A Hansa
- Division of Pathology, Immunology Section, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly (U.P.)-43122, India
| | - R B Rai
- Division of Pathology, Immunology Section, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly (U.P.)-43122, India
| | - K Dhama
- Division of Pathology, Immunology Section, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly (U.P.)-43122, India
| | - M Y Wani
- Division of Pathology, Immunology Section, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly (U.P.)-43122, India
| | - M Saminathan
- Division of Pathology, Immunology Section, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly (U.P.)-43122, India
| | - G J Ranganath
- Division of Pathology, Immunology Section, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly (U.P.)-43122, India
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Cong Y, Zarlenga DS, Richt JA, Wang X, Wang Y, Suo S, Wang J, Ren Y, Ren X. Evolution and homologous recombination of the hemagglutinin-esterase gene sequences from porcine torovirus. Virus Genes 2013; 47:66-74. [PMID: 23749172 PMCID: PMC7088831 DOI: 10.1007/s11262-013-0926-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/25/2013] [Indexed: 11/20/2022]
Abstract
The objective of the present study was to gain new insights into the evolution, homologous recombination, and selection pressures imposed on the porcine torovirus (PToV), by examining the changes in the hemagglutinin-esterase (HE) gene. The most recent common ancestor of PToV was estimated to have emerged 62 years ago based upon HE gene sequence data obtained from PToV isolates originating from Spain, South Korea, Netherlands, Hungary, and Italy and using the HE gene of Bovine torovirus isolates Niigata1 (AB661456) and Niigata3 (AB661458) as outgroups. The HE gene sequence data segregated all the PToV isolates into two well-supported monophyletic groups; however, various isolates from Spain, Italy, and South Korea did not segregate geographically suggesting very recent translocation of the viruses to these localities. Evidence of recombination was observed between two South Korean isolates that partitioned into two distinct subclades. Data further suggest that most of the nucleotides in the HE gene are under negative selection; however, changes within codon 237 showed an evidence of positive selection.
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Affiliation(s)
- Yingying Cong
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin, 150030 China
| | - Dante S. Zarlenga
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, Beltsville, MD USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Xin Wang
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin, 150030 China
| | - Yang Wang
- College of Life Science, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin, 150030 China
| | - Siqingaowa Suo
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin, 150030 China
| | - Jingfei Wang
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150030 China
| | - Yudong Ren
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin, 150030 China
| | - Xiaofeng Ren
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin, 150030 China
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Park SJ, Song DS, Park BK. Molecular epidemiology and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea. Arch Virol 2013; 158:1533-41. [PMID: 23462888 PMCID: PMC7087279 DOI: 10.1007/s00705-013-1651-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/25/2013] [Indexed: 01/08/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) has caused devastating enteric disease in Korean pig farms since its first identification in 1992 in Korea. In the present study, the molecular epidemiology, genetic diversity, and phylogenetic relationship of Korean PEDV field isolates to other reference strains were analyzed using the complete E gene. Genetic analysis showed that each PEDV group had several unique characteristics, which indicated that a specific group PEDVs may be differentiated from another group PEDVs. Phylogenetic analysis showed that recent prevalent Korean PEDV field isolates are closely related to the Chinese field strains and differ genetically from the European strains and the vaccine strains used in Korea, which raises questions of whether a new-type PEDV vaccine may be necessary for preventing PEDV infection more effectively in Korea. Notably, a large deletion identified only in the attenuated DR13 can be utilized as a genetic marker, and the methods developed in this study will help to rapidly detect and differentiate PEDVs.
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Affiliation(s)
- Seong-Jun Park
- Viral Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806 South Korea
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Gwanak-gu Seoul, 151-742 South Korea
| | - Dae-Sub Song
- Viral Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806 South Korea
- University of Science and Technology, Daejeon, 305-350 South Korea
| | - Bong-Kyun Park
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Gwanak-gu Seoul, 151-742 South Korea
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36
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Monastyrska I, Ulasli M, Rottier PJ, Guan JL, Reggiori F, de Haan CA. An autophagy-independent role for LC3 in equine arteritis virus replication. Autophagy 2013; 9:164-74. [PMID: 23182945 PMCID: PMC3552881 DOI: 10.4161/auto.22743] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Equine arteritis virus (EAV) is an enveloped, positive-strand RNA virus. Genome replication of EAV has been associated with modified intracellular membranes that are shaped into double-membrane vesicles (DMVs). We showed by immuno-electron microscopy that the DMVs induced in EAV-infected cells contain double-strand (ds)RNA molecules, presumed RNA replication intermediates, and are decorated with the autophagy marker protein microtubule-associated protein 1 light chain 3 (LC3). Replication of EAV, however, was not affected in autophagy-deficient cells lacking autophagy-related protein 7 (ATG7). Nevertheless, colocalization of DMVs and LC3 was still observed in these knockout cells, which only contain the nonlipidated form of LC3. Although autophagy is not required, depletion of LC3 markedly reduced the replication of EAV. EAV replication could be fully restored in these cells by expression of a nonlipidated form of LC3. These findings demonstrate an autophagy-independent role for LC3 in EAV replication. Together with the observation that EAV-induced DMVs are also positive for ER degradation-enhancing α-mannosidase-like 1 (EDEM1), our data suggested that this virus, similarly to the distantly-related mouse hepatitis coronavirus, hijacks the ER-derived membranes of EDEMosomes to ensure its efficient replication.
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Affiliation(s)
- Iryna Monastyrska
- Virology Division; Department of Infectious Diseases & Immunology; Utrecht University; Utrecht, The Netherlands
| | - Mustafa Ulasli
- Department of Cell Biology and Institute of Biomembranes; University Medical Center Utrecht; Utrecht, The Netherlands
| | - Peter J.M. Rottier
- Virology Division; Department of Infectious Diseases & Immunology; Utrecht University; Utrecht, The Netherlands
| | - Jun-Lin Guan
- Department of Internal Medicine-Division of Molecular Medicine and Genetics; Department of Cell and Developmental Biology; University of Michigan; Ann Arbor, MI USA
| | - Fulvio Reggiori
- Department of Cell Biology and Institute of Biomembranes; University Medical Center Utrecht; Utrecht, The Netherlands
| | - Cornelis A.M. de Haan
- Virology Division; Department of Infectious Diseases & Immunology; Utrecht University; Utrecht, The Netherlands
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Alonso-Padilla J, Pignatelli J, Simon-Grifé M, Plazuelo S, Casal J, Rodríguez D. Seroprevalence of porcine torovirus (PToV) in Spanish farms. BMC Res Notes 2012; 5:675. [PMID: 23217216 PMCID: PMC3556161 DOI: 10.1186/1756-0500-5-675] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 11/26/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Torovirus infections have been associated with gastroenteritis and diarrhea in horses, cows, pigs and humans, especially in young animals and in children. Although asymptomatic in a large percentage of cases, however toroviruses may pose a potential threat to worsen disease outcome in concurrent infections with other enteric pathogens. Previous studies based on the analysis of limited numbers of samples indicated high seroprevalences against porcine torovirus (PToV) in various European countries. The aim of this work was to perform a seroepidemiological survey of PToV in Spanish farms in order to define the seroprevalence against this virus. RESULTS Serum samples (n = 2664) from pigs of different ages were collected from 100 Spanish farms coming from 10 regions that concentrate 96.1% of the 3392 farms with 80 or more sows censused in Spain. Samples were screened by means of an indirect enzyme-linked immune-sorbent assay (ELISA) based on a recombinant PToV nucleocapsid protein as antigen. The analysis of the whole serum collection yielded a total of 95.7% (2550/2664) seropositive samples. The highest prevalence (99.6%, 1382/1388) and ELISA values (average O.D. ± standard deviation) were observed in the sows (1.03±0.36) and the lowest prevalence (59.4%, 98/165) and anti-PToV IgG levels (0.45±0.16) were found amongst 3-week-old piglets. Both ELISA reactivity values and seroprevalence percentages rose quickly with piglet's age from 3 to 11 weeks of age; the seroprevalence was 99.3% (2254/2270) when only the samples from sows and pigs over 11-weeks of age were considered. Antibodies against PToV were detected in all analyzed farms. CONCLUSIONS This report describes the results of the largest torovirus seroepidemiological survey in farmed swine performed so far. Overall, the seroprevalence against PToV in animals older than 11 weeks of age was >99%, indicating that this virus is endemic in pig herds from Spain.
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Affiliation(s)
- Julio Alonso-Padilla
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, Madrid, 28049, Spain
- Current address: Department of Microbiology, New York University School of Medicine, 341 East 25th ST, New York, 10010, USA
| | - Jaime Pignatelli
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal, CSIC, Av. Doctor Arce 37, Madrid, 28002, Spain
| | - Meritxell Simon-Grifé
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA and Department of Animal Health, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Susana Plazuelo
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, Madrid, 28049, Spain
| | - Jordi Casal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA and Department of Animal Health, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Dolores Rodríguez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, Madrid, 28049, Spain
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Chen X, Yang J, Yu F, Ge J, Lin T, Song T. Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China. Virus Genes 2012; 45:499-507. [PMID: 22843324 PMCID: PMC7089442 DOI: 10.1007/s11262-012-0794-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/20/2012] [Indexed: 11/28/2022]
Abstract
The outbreak of porcine epidemic diarrhea virus (PEDV) has been a big problem of swine industry in China in recent years. In this study, we investigated molecular diversity, phylogenetic relationships, and protein characterization of Fujian field samples with other PEDV reference strains. Sequence analysis of the S1 and sM genes showed that each sample had unique characteristics, and the sample P55 may be differentiated from the others by the unique deletions and insertions of sM gene. Phylogenetic analysis based on S1 or sM gene, which have high levels of variations, indicated that each sample was related to the specific reference strain, and this finding was consistent with the protein characterization prediction analysis. The study is useful to better understand the prevalence of PEDV and its prevention and control in Fujian.
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Affiliation(s)
- Xi Chen
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 China
| | - Jinxian Yang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 China
| | - Fusong Yu
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 China
| | - Junqing Ge
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 China
| | - Tianlong Lin
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 China
| | - Tieying Song
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 China
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Song D, Park B. Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines. Virus Genes 2012; 44:167-75. [PMID: 22270324 PMCID: PMC7089188 DOI: 10.1007/s11262-012-0713-1] [Citation(s) in RCA: 495] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 01/04/2012] [Indexed: 01/20/2023]
Abstract
The porcine epidemic diarrhoea virus (PEDV), a member of the Coronaviridae family, causes acute diarrhoea and dehydration in pigs. Although it was first identified in Europe, it has become increasingly problematic in many Asian countries, including Korea, China, Japan, the Philippines, and Thailand. The economic impacts of the PEDV are substantial, given that it results in significant morbidity and mortality in neonatal piglets and is associated with increased costs related to vaccination and disinfection. Recently, progress has been made in understanding the molecular epidemiology of PEDV, thereby leading to the development of new vaccines. In the current review, we first describe the molecular and genetic characteristics of the PEDV. Then we discuss its molecular epidemiology and diagnosis, what vaccines are available, and how PEDV can be treated.
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Affiliation(s)
- Daesub Song
- Viral Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806 South Korea
- University of Science and Technology, Daejeon, 305-350 South Korea
| | - Bongkyun Park
- Department of Veterinary Virology, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Seoul, 151-742 Korea
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40
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Asano A, Torigoe D, Sasaki N, Agui T. Identification of antigenic peptides derived from B-cell epitopes of nucleocapsid protein of mouse hepatitis virus for serological diagnosis. J Virol Methods 2011; 177:107-11. [DOI: 10.1016/j.jviromet.2011.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/20/2011] [Accepted: 07/18/2011] [Indexed: 11/15/2022]
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41
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Armesto M, Evans S, Cavanagh D, Abu-Median AB, Keep S, Britton P. A recombinant avian infectious bronchitis virus expressing a heterologous spike gene belonging to the 4/91 serotype. PLoS One 2011; 6:e24352. [PMID: 21912629 PMCID: PMC3166170 DOI: 10.1371/journal.pone.0024352] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/05/2011] [Indexed: 12/11/2022] Open
Abstract
We have shown previously that replacement of the spike (S) gene of the apathogenic IBV strain Beau-R with that from the pathogenic strain of the same serotype, M41, resulted in an apathogenic virus, BeauR-M41(S), that conferred protection against challenge with M41. We have constructed a recombinant IBV, BeauR-4/91(S), with the genetic backbone of Beau-R but expressing the spike protein of the pathogenic IBV strain 4/91(UK), which belongs to a different serogroup as Beaudette or M41. Similar to our previous findings with BeauR-M41(S), clinical signs observations showed that the S gene of the pathogenic 4/91 virus did not confer pathogenicity to the rIBV BeauR-4/91(S). Furthermore, protection studies showed there was homologous protection; BeauR-4/91(S) conferred protection against challenge with wild type 4/91 virus as shown by the absence of clinical signs, IBV RNA assessed by qRT-PCR and the fact that no virus was isolated from tracheas removed from birds primarily infected with BeauR-4/91(S) and challenged with IBV 4/91(UK). A degree of heterologous protection against M41 challenge was observed, albeit at a lower level.Our results confirm and extend our previous findings and conclusions that swapping of the ectodomain of the S protein is a precise and effective way of generating genetically defined candidate IBV vaccines.
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Affiliation(s)
- Maria Armesto
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Sharon Evans
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - David Cavanagh
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Abu-Bakr Abu-Median
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Sarah Keep
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Paul Britton
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
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Myrrha LW, Silva FMF, Peternelli EFDO, Junior AS, Resende M, de Almeida MR. The paradox of feline coronavirus pathogenesis: a review. Adv Virol 2011; 2011:109849. [PMID: 22312333 PMCID: PMC3265210 DOI: 10.1155/2011/109849] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 06/01/2011] [Accepted: 06/01/2011] [Indexed: 12/04/2022] Open
Abstract
Feline coronavirus (FCoV) is an enveloped single-stranded RNA virus, of the family Coronaviridae and the order Nidovirales. FCoV is an important pathogen of wild and domestic cats and can cause a mild or apparently symptomless enteric infection, especially in kittens. FCoV is also associated with a lethal, systemic disease known as feline infectious peritonitis (FIP). Although the precise cause of FIP pathogenesis remains unclear, some hypotheses have been suggested. In this review we present results from different FCoV studies and attempt to elucidate existing theories on the pathogenesis of FCoV infection.
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Affiliation(s)
- Luciana Wanderley Myrrha
- Laboratório de Infectologia Molecular Animal (LIMA), Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n Campus Universitário, 36570-000 Vicosa, MG, Brazil
| | - Fernanda Miquelitto Figueira Silva
- Laboratório de Infectologia Molecular Animal (LIMA), Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n Campus Universitário, 36570-000 Vicosa, MG, Brazil
| | - Ethel Fernandes de Oliveira Peternelli
- Laboratório de Infectologia Molecular Animal (LIMA), Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n Campus Universitário, 36570-000 Vicosa, MG, Brazil
| | - Abelardo Silva Junior
- Laboratório de Infectologia Molecular Animal (LIMA), Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n Campus Universitário, 36570-000 Vicosa, MG, Brazil
| | - Maurício Resende
- Laboratório de Doença das Aves, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627—Pampulha, 31270-901, Belo Horizonte, MG, Brazil
| | - Márcia Rogéria de Almeida
- Laboratório de Infectologia Molecular Animal (LIMA), Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n Campus Universitário, 36570-000 Vicosa, MG, Brazil
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Park SJ, Kim HK, Song DS, Moon HJ, Park BK. Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea. Arch Virol 2011; 156:577-85. [PMID: 21210162 PMCID: PMC7086862 DOI: 10.1007/s00705-010-0892-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 12/10/2010] [Indexed: 11/25/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) has caused enteric disease with devastating impact since the first identification of PEDV in 1992 in Korea. In this study, we investigated molecular epidemiology, showed genetic diversity, and analyzed phylogenetic relationships of Korean PEDV field isolates with other PEDV reference strains. Genetic analysis of the complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and this indicated that specific groups of PEDVs may be differentiated from the other PEDVs by specific nucleotide differences. Especially, ORF3 gene analysis can be used for discrimination between vaccine and wild-type PEDVs. Sequence and phylogenetic analysis showed that recent, prevalent Korean PEDV field isolates have close relationships to Chinese field strains and differ genetically from European strains and vaccine strains used in Korea. These results raise questions as to whether a new type of PEDV vaccine may be necessary for preventing PEDV infection more effectively in Korea.
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Affiliation(s)
- Seong-Jun Park
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Gwanak-gu, Seoul, 151-742 Korea
| | - Hye-Kwon Kim
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Gwanak-gu, Seoul, 151-742 Korea
| | - Dae-Sub Song
- Viral Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806 Korea
| | - Hyoung-Joon Moon
- Research Unit, Green Cross Veterinary Products, Yongin, 449-903 Korea
| | - Bong-Kyun Park
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Gwanak-gu, Seoul, 151-742 Korea
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44
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Arterivirus‡. THE SPRINGER INDEX OF VIRUSES 2011. [PMCID: PMC7176216 DOI: 10.1007/978-0-387-95919-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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45
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Snijder EJ, de Groot RJ. Torovirus‡. THE SPRINGER INDEX OF VIRUSES 2011. [PMCID: PMC7176181 DOI: 10.1007/978-0-387-95919-1_60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped, positive-sense single-stranded RNA virus belonging to the Arteriviridae family. Arteriviruses and coronaviruses are grouped together in the order Nidovirales, based on similarities in genome organization and expression strategy. Over the past decade, crystal structures of several viral proteins, electron microscopic studies of the virion, as well as biochemical and in vivo studies on protein-protein interactions have led to a greatly increased understanding of PRRSV structural biology. At this point, crystal structures are available for the viral proteases NSP1α, NSP1β and NSP4 and the nucleocapsid protein, N. The NSP1α and NSP1β structures have revealed additional non-protease domains that may be involved in modulation of host functions. The N protein forms a dimer with a novel fold so far only seen in PRRSV and other nidoviruses. Cryo-electron tomographic studies have shown the three-dimensional organization of the PRRSV virion and suggest that the viral nucleocapsid has an asymmetric, linear arrangement, rather than the isometric core previously described. Together, these studies have revealed a closer structural relationship between arteri- and coronaviruses than previously anticipated.
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Affiliation(s)
- Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
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47
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Cedano-Thomas Y, De La Rosa-Vélez J, Bonami JR, Vargas-Albores F. Gene expression kinetics of the yellow head virus in experimentally infected Litopenaeus vannamei. AQUACULTURE RESEARCH 2010; 41:1432-1443. [PMID: 32313428 PMCID: PMC7159739 DOI: 10.1111/j.1365-2109.2009.02434.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The yellow head virus (YHV) has been reported to be one of most pathogenic viruses for cultivated shrimp; however, serious problems have only been reported in farms in south and southeastern Asian. Recently, a YHV strain was detected in Litopenaeus vannamei cultivated in Mexican farms that lacked virus-associated mortalities or epizooties, and the animals were apparently healthy. The identity of the virus was confirmed by sequencing replicative and structural protein-encoding regions and comparing with homologous virus sequences. Phylogenic relationships and genetic distances were also determined and, although some differences were observed, an influence on virulence was uncertain. In addition, the expression levels of several transcripts (3CLPRO, POL, GP64 and GP116) were evaluated by quantitative real-time polymerase chain reaction during an experimental infection. Although the transcript showed varying kinetics, viral genes were expressed in infected L. vannamei, demonstrating the replicative capability of this YHV strain.
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Affiliation(s)
| | | | - Jean Robert Bonami
- Pathogens and Environment, UMR 5119, ECOLAG, CNRS/UM2, cc 093, Université Montpellier 2, Montpellier Cedex, France
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48
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Addie D, Belák S, Boucraut-Baralon C, Egberink H, Frymus T, Gruffydd-Jones T, Hartmann K, Hosie MJ, Lloret A, Lutz H, Marsilio F, Pennisi MG, Radford AD, Thiry E, Truyen U, Horzinek MC. Feline infectious peritonitis. ABCD guidelines on prevention and management. J Feline Med Surg 2009; 11:594-604. [PMID: 19481039 PMCID: PMC7129471 DOI: 10.1016/j.jfms.2009.05.008] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
OVERVIEW Feline coronavirus infection is ubiquitous in domestic cats, and is particularly common where conditions are crowded. While most FCoV-infected cats are healthy or display only a mild enteritis, some go on to develop feline infectious peritonitis, a disease that is especially common in young cats and multi-cat environments. Up to 12% of FCoV-infected cats may succumb to FIP, with stress predisposing to the development of disease. DISEASE SIGNS The 'wet' or effusive form, characterised by polyserositis (abdominal and/or thoracic effusion) and vasculitis, and the 'dry' or non-effusive form (pyogranulomatous lesions in organs) reflect clinical extremes of a continuum. The clinical picture of FIP is highly variable, depending on the distribution of the vasculitis and pyogranulomatous lesions. Fever refractory to antibiotics, lethargy, anorexia and weight loss are common non-specific signs. Ascites is the most obvious manifestation of the effusive form. DIAGNOSIS The aetiological diagnosis of FIP ante-mortem may be difficult, if not impossible. The background of the cat, its history, the clinical signs, laboratory changes, antibody titres and effusion analysis should all be used to help in decision-making about further diagnostic procedures. At the time of writing, there is no non-invasive confirmatory test available for cats without effusion. DISEASE MANAGEMENT In most cases FIP is fatal. Supportive treatment is aimed at suppressing the inflammatory and detrimental immune response. However, there are no controlled studies to prove any beneficial effect of corticosteroids. VACCINATION RECOMMENDATIONS At present, only one (intranasal) FIP vaccine is available, which is considered as being non-core. Kittens may profit from vaccination when they have not been exposed to FCoV (eg, in an early-weaning programme), particularly if they enter a FCoV-endemic environment.
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Affiliation(s)
- Diane Addie
- European Advisory Board on Cat Diseases (ABCD).
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Lorusso A, Desario C, Mari V, Campolo M, Lorusso E, Elia G, Martella V, Buonavoglia C, Decaro N. Molecular characterization of a canine respiratory coronavirus strain detected in Italy. Virus Res 2009; 141:96-100. [PMID: 19162098 PMCID: PMC7114405 DOI: 10.1016/j.virusres.2008.12.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 12/11/2008] [Accepted: 12/22/2008] [Indexed: 10/25/2022]
Abstract
Coronaviruses (CoVs) are positive-stranded, non-segmented RNA viruses generally responsible for the emergence of respiratory and enteric disease in humans, companion animals and livestock. Their aptitude to evolve by genetic recombination and/or point mutation is recognized, thus giving rise to new viral genotypes and mutants with different tissues or host tropism. In particular, a probable origin from the strictly related bovine coronavirus (BCoV) or, alternatively, from a common ancestor has been suggested for some group 2a CoVs, including canine respiratory coronavirus (CRCoV). In this study, we report the sequence analysis of the viral RNA 3'-end of an Italian CRCoV, strain 240/05, together with the sequence comparison with extant bovine-like viruses including the sole CRCoV strain 4182 previously described. Interestingly, although the structural proteins show the same features of CRCoV 4182, the genomic region between the spike and the envelope protein genes of CRCoV 240/05 encodes for three distinct products, including the equivalent bovine 4.9 kDa non-structural protein and a truncated form of the 4.8 kDa protein, whereas CRCoV 4182 has a unique 8.8 kDa protein.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nicola Decaro
- Department of Public Health and Animal Sciences, Faculty of Veterinary Medicine of Bari, Strada per Casamassima km 3, 70010 Valenzano (Bari), Italy
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50
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Ren X, Yin J, Ma D, Li G. Characterization and membrane gene-based phylogenetic analysis of avian infectious bronchitis virus Chinese strain HH06. Virus Genes 2009; 38:39-45. [PMID: 18792774 PMCID: PMC7089277 DOI: 10.1007/s11262-008-0280-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 08/19/2008] [Indexed: 11/10/2022]
Abstract
A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.
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Affiliation(s)
- Xiaofeng Ren
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
| | - Jiechao Yin
- College of Life Sciences, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
| | - Dexing Ma
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
| | - Guangxing Li
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
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