51
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Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Mol Cell 2020. [PMID: 33188728 DOI: 10.1101/2020.08.09.243451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The causative virus of the COVID-19 pandemic, SARS-CoV-2, uses its nonstructural protein 1 (Nsp1) to suppress cellular, but not viral, protein synthesis through yet unknown mechanisms. We show here that among all viral proteins, Nsp1 has the largest impact on host viability in the cells of human lung origin. Differential expression analysis of mRNA-seq data revealed that Nsp1 broadly alters the cellular transcriptome. Our cryo-EM structure of the Nsp1-40S ribosome complex shows that Nsp1 inhibits translation by plugging the mRNA entry channel of the 40S. We also determined the structure of the 48S preinitiation complex formed by Nsp1, 40S, and the cricket paralysis virus internal ribosome entry site (IRES) RNA, which shows that it is nonfunctional because of the incorrect position of the mRNA 3' region. Our results elucidate the mechanism of host translation inhibition by SARS-CoV-2 and advance understanding of the impacts from a major pathogenicity factor of SARS-CoV-2.
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MESH Headings
- Animals
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/pathology
- Chlorocebus aethiops
- Cryoelectron Microscopy
- Humans
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/virology
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- SARS-CoV-2/pathogenicity
- SARS-CoV-2/ultrastructure
- Vero Cells
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Shenping Wu
- Department of Pharmacology, Yale University, West Haven, CT 06516, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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52
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Semper C, Watanabe N, Savchenko A. Structural characterization of nonstructural protein 1 from SARS-CoV-2. iScience 2020; 24:101903. [PMID: 33319167 PMCID: PMC7721355 DOI: 10.1016/j.isci.2020.101903] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/21/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a single-stranded, enveloped RNA virus and the etiological agent of the current coronavirus disease 2019 pandemic. Efficient replication of the virus relies on the activity of nonstructural protein 1 (Nsp1), a major virulence factor shown to facilitate suppression of host gene expression through promotion of host mRNA degradation and interaction with the 40S ribosomal subunit. Here, we report the crystal structure of the globular domain of SARS-CoV-2 Nsp1, encompassing residues 13 to 127, at a resolution of 1.65 Å. Our structure features a six-stranded, capped β-barrel motif similar to Nsp1 from SARS-CoV and reveals how variations in amino acid sequence manifest as distinct structural features. Combining our high-resolution crystal structure with existing data on the C-terminus of Nsp1 from SARS-CoV-2, we propose a model of the full-length protein. Our results provide insight into the molecular structure of a major pathogenic determinant of SARS-CoV-2. SARS-CoV-2 Nsp1 features a capped β-barrel structure, similar to that of SARS-CoV Distinct structural features distinguish SARS-CoV-2 Nsp1 from its SARS-CoV ortholog The plasticity of the Nsp1 protein fold is evident through comparison with homologs
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, HSC B724 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, HSC B724 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, HSC B724 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
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53
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Tidu A, Janvier A, Schaeffer L, Sosnowski P, Kuhn L, Hammann P, Westhof E, Eriani G, Martin F. The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation. RNA (NEW YORK, N.Y.) 2020; 27:rna.078121.120. [PMID: 33268501 PMCID: PMC7901841 DOI: 10.1261/rna.078121.120] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/29/2020] [Indexed: 05/10/2023]
Abstract
SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus.
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Affiliation(s)
- Antonin Tidu
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Aurelie Janvier
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Laure Schaeffer
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen F-67084 Strasbourg (France)
| | - Piotr Sosnowski
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Lauriane Kuhn
- Institut de Biologie Moleculaire et Cellulaire, Plateforme Proteomique Strasbourg Esplanade, CNRS FRC1589, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Philippe Hammann
- Institut de Biologie Moleculaire et Cellulaire, Plateforme Proteomique Strasbourg Esplanade, CNRS FRC1589, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Eric Westhof
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Gilbert Eriani
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Franck Martin
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France);
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54
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Jain N, Shankar U, Majee P, Kumar A. Scrutinizing the SARS-CoV-2 protein information for designing an effective vaccine encompassing both the T-cell and B-cell epitopes. INFECTION GENETICS AND EVOLUTION 2020; 87:104648. [PMID: 33264668 PMCID: PMC7700730 DOI: 10.1016/j.meegid.2020.104648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022]
Abstract
Novel SARS coronavirus (SARS-CoV-2) has caused a pandemic condition worldwide. It has been declared as a public health emergency of international concern by WHO in a very short span of time. The community transmission of this highly infectious virus has severely affected various parts of China, Italy, Spain, India, and USA, among others. The prophylactic solution against SARS-CoV-2 infection is challenging due to the high mutation rate of its RNA genome. Herein, we exploited a next-generation vaccinology approach to construct a multi-epitope vaccine candidate against SARS-CoV-2 that is predicted to have high antigenicity, safety, and efficacy to combat this deadly infectious agent. The whole proteome was scrutinized for the screening of highly conserved, antigenic, non-allergen, and non-toxic epitopes having high population coverage that can elicit both humoral and cellular mediated immune response against COVID-19 infection. These epitopes along with four different adjuvants, were utilized to construct a multi-epitope-vaccine candidate that can generate strong immunological memory response having high efficacy in humans. Various physiochemical analyses revealed the formation of a stable vaccine product having a high propensity to form a protective solution against the detrimental SARS-CoV-2 strain with high efficacy. The vaccine candidate interacted with immunological receptor TLR3 with a high affinity depicting the generation of innate immunity. Further, the codon optimization and in silico expression show the plausibility of the high expression and easy purification of the vaccine product. Thus, this present study provides an initial platform for the rapid generation of an efficacious protective vaccine for combating COVID-19.
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Affiliation(s)
- Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Prativa Majee
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
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55
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Structural and functional insights into non-structural proteins of coronaviruses. Microb Pathog 2020; 150:104641. [PMID: 33242646 PMCID: PMC7682334 DOI: 10.1016/j.micpath.2020.104641] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Coronaviruses (CoVs) are causing a number of human and animal diseases because of their zoonotic nature such as Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19). These viruses can infect respiratory, gastrointestinal, hepatic and central nervous systems of human, livestock, birds, bat, mouse, and many wild animals. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerging respiratory virus and is causing CoVID-19 with high morbidity and considerable mortality. All CoVs belong to the order Nidovirales, family Coronaviridae, are enveloped positive-sense RNA viruses, characterised by club-like spikes on their surfaces and large RNA genome with a distinctive replication strategy. Coronavirus have the largest RNA genomes (~26–32 kilobases) and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. Non-structural proteins (nsp) 7–16 are cleaved from two large replicase polyproteins and guide the replication and processing of coronavirus RNA. Coronavirus replicase has more or less universal activities, such as RNA polymerase (nsp 12) and helicase (nsp 13), as well as a variety of unusual or even special mRNA capping (nsp 14, nsp 16) and fidelity regulation (nsp 14) domains. Besides that, several smaller subunits (nsp 7– nsp 10) serve as essential cofactors for these enzymes and contribute to the emerging “nsp interactome.” In spite of the significant progress in studying coronaviruses structural and functional properties, there is an urgent need to understand the coronaviruses evolutionary success that will be helpful to develop enhanced control strategies. Therefore, it is crucial to understand the structure, function, and interactions of coronaviruses RNA synthesizing machinery and their replication strategies.
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56
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Vankadari N, Jeyasankar NN, Lopes WJ. Structure of the SARS-CoV-2 Nsp1/5'-Untranslated Region Complex and Implications for Potential Therapeutic Targets, a Vaccine, and Virulence. J Phys Chem Lett 2020; 11:9659-9668. [PMID: 33135884 PMCID: PMC7641045 DOI: 10.1021/acs.jpclett.0c02818] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 is the cause of the ongoing Coronavirus disease 19 (COVID-19) pandemic around the world causing pneumonia and lower respiratory tract infections. In understanding the SARS-CoV-2 pathogenicity and mechanism of action, it is essential to depict the full repertoire of expressed viral proteins. The recent biological studies have highlighted the leader protein Nsp1 of SARS-CoV-2 importance in shutting down the host protein production. Besides, it still enigmatic how Nsp1 regulates for translation. Here we report the novel structure of Nsp1 from SARS-CoV-2 in complex with the SL1 region of 5'UTR of SARS-CoV-2, and its factual interaction is corroborated with enzyme kinetics and experimental binding affinity studies. The studies also address how leader protein Nsp1 of SARS-CoV-2 recognizes its self RNA toward translational regulation by further recruitment of the 40S ribosome. With the aid of molecular dynamics and simulations, we also demonstrated the real-time stability and functional dynamics of the Nsp1/SL1 complex. The studies also report the potential inhibitors and their mode of action to block viral protein/RNA complex formation. This enhance our understanding of the mechanism of the first viral protein Nsp1 synthesized in the human cell to regulate the translation of self and host. Understanding the structure and mechanism of SARS-CoV-2 Nsp1 and its interplay with the viral RNA and ribosome will open the arena for exploring the development of live attenuated vaccines and effective therapeutic targets for this disease.
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Affiliation(s)
- Naveen Vankadari
- Monash Biomedicine Discovery Institute and
Department of Biochemistry and Molecular Biology and
Faculty of Medicine, Nursing and Health
Science, Monash University, Clayton
Victoria 3800, Australia
| | - Nandhini Nisha Jeyasankar
- Monash Biomedicine Discovery Institute and
Department of Biochemistry and Molecular Biology and
Faculty of Medicine, Nursing and Health
Science, Monash University, Clayton
Victoria 3800, Australia
| | - Wilma Jerom Lopes
- Monash Biomedicine Discovery Institute and
Department of Biochemistry and Molecular Biology and
Faculty of Medicine, Nursing and Health
Science, Monash University, Clayton
Victoria 3800, Australia
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57
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Anjum FR, Anam S, Abbas G, Mahmood MS, Rahman SU, Goraya MU, Abdullah RM, Luqman M, Ali A, Akram MK, Chaudhry TH. Type I IFNs: A Blessing in Disguise or Partner in Crime in MERS-CoV-, SARS-CoV-, and SARS-CoV-2-Induced Pathology and Potential Use of Type I IFNs in Synergism with IFN- γ as a Novel Antiviral Approach Against COVID-19. Viral Immunol 2020; 34:321-329. [PMID: 33181057 DOI: 10.1089/vim.2020.0085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Since the end of 2019, the emergence of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has accelerated the research on host immune responses toward the coronaviruses. When there is no approved drug or vaccine to use against these culprits, host immunity is the major strategy to fight such infections. Type I interferons are an integral part of the host innate immune system and define one of the first lines of innate immune defense against viral infections. The in vitro antiviral role of type I IFNs against Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV (severe acute respiratory syndrome coronavirus) is well established. Moreover, the involvement of type I IFNs in disease pathology has also been reported. In this study, we have reviewed the protective and the immunopathogenic role of type I IFNs in the pathogenesis of MERS-CoV, SARS-CoV, and SARS-CoV-2. This review will also enlighten the potential implications of type I IFNs for the treatment of COVID-19 when used in combination with IFN-γ.
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Affiliation(s)
| | - Sidra Anam
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Ghazanfar Abbas
- Melbourne Veterinary School, The University of Melbourne, Werribee, Australia
| | | | - Sajjad Ur Rahman
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | | | | | - Muhammad Luqman
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Ashiq Ali
- Department of Pathology, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Kamran Akram
- Queensland Alliance for Agriculture and food Innovation, The University of Queensland, Brisbane, Australia
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58
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Shen Z, Zhang G, Yang Y, Li M, Yang S, Peng G. Lysine 164 is critical for SARS-CoV-2 Nsp1 inhibition of host gene expression. J Gen Virol 2020; 102. [PMID: 33151142 PMCID: PMC8116783 DOI: 10.1099/jgv.0.001513] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The emerging pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused social and economic disruption worldwide, infecting over 9.0 million people and killing over 469 000 by 24 June 2020. Unfortunately, no vaccine or antiviral drug that completely eliminates the transmissible disease coronavirus disease 2019 (COVID-19) has been developed to date. Given that coronavirus nonstructural protein 1 (nsp1) is a good target for attenuated vaccines, it is of great significance to explore the detailed characteristics of SARS-CoV-2 nsp1. Here, we first confirmed that SARS-CoV-2 nsp1 had a conserved function similar to that of SARS-CoV nsp1 in inhibiting host-protein synthesis and showed greater inhibition efficiency, as revealed by ribopuromycylation and Renilla luciferase (Rluc) reporter assays. Specifically, bioinformatics and biochemical experiments showed that by interacting with 40S ribosomal subunit, the lysine located at amino acid 164 (K164) was the key residue that enabled SARS-CoV-2 nsp1 to suppress host gene expression. Furthermore, as an inhibitor of host-protein expression, SARS-CoV-2 nsp1 contributed to cell-cycle arrest in G0/G1 phase, which might provide a favourable environment for virus production. Taken together, this research uncovered the detailed mechanism by which SARS-CoV-2 nsp1 K164 inhibited host gene expression, laying the foundation for the development of attenuated vaccines based on nsp1 modification.
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Affiliation(s)
- Zhou Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, PR China
| | - Guangxu Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Yilin Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, PR China
| | - Mengxia Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, PR China
| | - Siqi Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, PR China
- *Correspondence: Guiqing Peng,
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59
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Abstract
The periodic emergence of novel coronaviruses (CoVs) represents an ongoing public health concern with significant health and financial burden worldwide. The most recent occurrence originated in the city of Wuhan, China where a novel coronavirus (SARS-CoV-2) emerged causing severe respiratory illness and pneumonia. The continual emergence of novel coronaviruses underscores the importance of developing effective vaccines as well as novel therapeutic options that target either viral functions or host factors recruited to support coronavirus replication. The CoV nonstructural protein 1 (nsp1) has been shown to promote cellular mRNA degradation, block host cell translation, and inhibit the innate immune response to virus infection. Interestingly, deletion of the nsp1-coding region in infectious clones prevented the virus from productively infecting cultured cells. Because of nsp1's importance in the CoV lifecycle, it has been highlighted as a viable target for both antiviral therapy and vaccine development. However, the fundamental molecular and structural mechanisms that underlie nsp1 function remain poorly understood, despite its critical role in the viral lifecycle. Here we report the high-resolution crystal structure of the amino, globular portion of SARS-CoV-2 nsp1 (residues 10 - 127) at 1.77Å resolution. A comparison of our structure with the SARS-CoV-1 nsp1 structure reveals how mutations alter the conformation of flexible loops, inducing the formation of novel secondary structural elements and new surface features. Paired with the recently published structure of the carboxyl end of nsp1 (residues 148 - 180), our results provide the groundwork for future studies focusing on SARS-CoV-2 nsp1 structure and function during the viral lifecycle. IMPORTANCE The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic. One protein known to play a critical role in the coronavirus lifecycle is nonstructural protein1 (nsp1). As such, it has been highlighted in numerous studies as a target for both the development of antivirals and for the design of live-attenuated vaccines. Here we report the high-resolution crystal structure of nsp1 derived from SARS-CoV-2 at 1.77Å resolution. This structure will facilitate future studies focusing on understanding the relationship between structure and function for nsp1. In turn, understanding these structure-function relationships will allow nsp1 to be fully exploited as a target for both antiviral development and vaccine design.
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60
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Mirzaei R, Mohammadzadeh R, Mahdavi F, Badrzadeh F, Kazemi S, Ebrahimi M, Soltani F, Kazemi S, Jeda AS, Darvishmotevalli M, Yousefimashouf R, Keyvani H, Karampoor S. Overview of the current promising approaches for the development of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine. Int Immunopharmacol 2020; 88:106928. [PMID: 32862110 PMCID: PMC7444935 DOI: 10.1016/j.intimp.2020.106928] [Citation(s) in RCA: 16] [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: 06/19/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by the novel coronavirus called SARS-CoV-2. There is a gap in our understanding regarding the immunopathogenesis of COVID-19. However, many clinical trials are underway across the world for screening effective drugs against COVID-19. Nevertheless, currently, no proven effective therapies for this virus exists. The vaccines are deemed as a significant part of disease prevention for emerging viral diseases, since, in several cases, other therapeutic choices are limited or non-existent, or that diseases result in such an accelerated clinical worsening that the efficacy of treatments is restricted. Therefore, effective vaccines against COVID-19 are urgently required to overcome the tremendous burden of mortality and morbidity correlated with SARS-CoV-2. In this review, we will describe the latest evidence regarding outstanding vaccine approaches and the challenges for vaccine production.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Rokhsareh Mohammadzadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzad Mahdavi
- Department of Medical Parasitology and Mycology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariba Badrzadeh
- Faculty of Medicine, Golestan University of Medical Sciences, Golestan, Iran
| | - Sheida Kazemi
- Students' Seientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Ebrahimi
- Department of Environmental Health, School of Health, Guilan University of Medical Sciences, Rasht, Iran
| | - Fatemeh Soltani
- Health Safety and Environment Management Department, Azad University, Ahvaz Branch, Ahvaz, Iran
| | - Sima Kazemi
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Salimi Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Darvishmotevalli
- Research Center For Health, Safety And Environment (RCHSE), Alborz University of Medical Sciences, Karaj, Iran
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Sajad Karampoor
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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61
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Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Mol Cell 2020; 80:1055-1066.e6. [PMID: 33188728 PMCID: PMC7833686 DOI: 10.1016/j.molcel.2020.10.034] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022]
Abstract
The causative virus of the COVID-19 pandemic, SARS-CoV-2, uses its nonstructural protein 1 (Nsp1) to suppress cellular, but not viral, protein synthesis through yet unknown mechanisms. We show here that among all viral proteins, Nsp1 has the largest impact on host viability in the cells of human lung origin. Differential expression analysis of mRNA-seq data revealed that Nsp1 broadly alters the cellular transcriptome. Our cryo-EM structure of the Nsp1-40S ribosome complex shows that Nsp1 inhibits translation by plugging the mRNA entry channel of the 40S. We also determined the structure of the 48S preinitiation complex formed by Nsp1, 40S, and the cricket paralysis virus internal ribosome entry site (IRES) RNA, which shows that it is nonfunctional because of the incorrect position of the mRNA 3′ region. Our results elucidate the mechanism of host translation inhibition by SARS-CoV-2 and advance understanding of the impacts from a major pathogenicity factor of SARS-CoV-2.
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MESH Headings
- Animals
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/pathology
- Chlorocebus aethiops
- Cryoelectron Microscopy
- Humans
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/virology
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- SARS-CoV-2/pathogenicity
- SARS-CoV-2/ultrastructure
- Vero Cells
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Shenping Wu
- Department of Pharmacology, Yale University, West Haven, CT 06516, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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Pawar HA, Pawar AH, Pawar SA, Pawar PA. CORONAVIRUS and COVID-19: A Systematic Review and Perspective. CURRENT DRUG THERAPY 2020. [DOI: 10.2174/1574885515999200719142835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus (CoV) is an enveloped positive-sense RNA virus. Coronavirus disease 2019
(COVID-19) is an acute respiratory disease, induced by a new type of coronavirus, SARS-CoV-2.
COVID-19 has originated in China and spread quickly all over the world. WHO acknowledged the
outbreak of a global pandemic on March 11, 2020. The spread of COVID-19 signified a big threat
to social life, the economy, and public health. As of April 14, 2020, WHO reported a total of
1,812,734 confirmed cases of COVID-19 and 113,675 (6.27 %) deaths throughout the world. Numerous
nations around the globe took assorted measures because of the danger of SARS-CoV-2 and
created wide-ranging preventive approaches. No particular drug or vaccines/antibodies are yet accessible
for the treatment of this unforeseen and lethal illness. The pandemic has brought about
travel limitations and across the country lockdowns in most of the nations. The objective behind
this article was to provide recent updates and well-authenticated information to the scientific community,
health care personnel’s and common public about Coronavirus, their types, characteristic
features, structure and origin, mode of transmission, pathogenesis, clinical symptoms, diagnostic
methods, drug development approach, prevention and treatment of COVID-19.
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Affiliation(s)
- Harshal Ashok Pawar
- Department of Pharmacognosy, Dr. L. H. Hiranandani College of Pharmacy, Ulhasnagar-421003, Maharashtra, India
| | - Anjali Harshal Pawar
- Naturopathiest, Aai Nature Cure, Ram Baug Lane-1, Kalyan (W)-421301, Maharashtra, India
| | - Sandip Ashok Pawar
- Manufacturing Science and Technology, Sandoz - A Division of Novartis, Kalwe, Navi Mumbai-400708, Maharashtra, India
| | - Prashant Ashok Pawar
- Executive-External Manufacturing, Glenmark Pharmaceuticals Pvt. Ltd., Andheri (E), Mumbai-400099, Maharashtra, India
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63
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Li Z, Ma Z, Li Y, Gao S, Xiao S. Porcine epidemic diarrhea virus: Molecular mechanisms of attenuation and vaccines. Microb Pathog 2020; 149:104553. [PMID: 33011361 PMCID: PMC7527827 DOI: 10.1016/j.micpath.2020.104553] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/29/2020] [Accepted: 09/29/2020] [Indexed: 12/29/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) causes an emerging and re-emerging coronavirus disease characterized by vomiting, acute diarrhea, dehydration, and up to 100% mortality in neonatal suckling piglets, leading to huge economic losses in the global swine industry. Vaccination remains the most promising and effective way to prevent and control PEDV. However, effective vaccines for PEDV are still under development. Understanding the genomic structure and function of PEDV and the influence of the viral components on innate immunity is essential for developing effective vaccines. In the current review, we systematically describe the recent developments in vaccine against PEDV and the roles of structural proteins, non-structural proteins and accessory proteins of PEDV in affecting viral virulence and regulating innate immunity, which will provide insight into the rational design of effective and safe vaccines for PEDV or other coronaviruses. Advances in vaccines of PEDV, such as inactivated and attenuated live vaccines, subunit vaccines, and nucleic acid vaccines. The application of reverse genetics in the development of live attenuated PEDV vaccines. The roles of PEDV proteins in affecting viral virulence and regulating innate immunity.
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Affiliation(s)
- Zhiwei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiqian Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yang Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Sheng Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuqi Xiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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64
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Min YQ, Mo Q, Wang J, Deng F, Wang H, Ning YJ. SARS-CoV-2 nsp1: Bioinformatics, Potential Structural and Functional Features, and Implications for Drug/Vaccine Designs. Front Microbiol 2020; 11:587317. [PMID: 33133055 PMCID: PMC7550470 DOI: 10.3389/fmicb.2020.587317] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
The emerging coronavirus disease (COVID-19) caused by SARS-CoV-2 has led to social and economic disruption globally. It is urgently needed to understand the structure and function of the viral proteins for understanding of the viral infection and pathogenesis and development of prophylaxis and treatment strategies. Coronavirus non-structural protein 1 (nsp1) is a notable virulence factor with versatile roles in virus-host interactions and exhibits unique characteristics on sequence, structure, and function mode. However, the roles and characteristics of SARS-CoV-2 nsp1 are currently unclear. Here, we analyze the nsp1 of SARS-CoV-2 from the following perspectives: (1) bioinformatics analysis reveals that the novel nsp1 is conserved among SARS-CoV-2 strains and shares significant sequence identity with SARS-CoV nsp1; (2) structure modeling shows a 3D α/β-fold of SARS-CoV-2 nsp1 highly similar to that of the SARS-CoV homolog; (3) by detailed, functional review of nsp1 proteins from other coronaviruses (especially SARS-CoV) and comparison of the protein sequence and structure, we further analyzed the potential roles of SARS-CoV-2 nsp1 in manipulating host mRNA translation, antiviral innate immunity and inflammation response and thus likely promoting viral infection and pathogenesis, which are merited to be tested in the future. Finally, we discussed how understanding of the novel nsp1 may provide valuable insights into the designs of drugs and vaccines against the unprecedented coronavirus pandemic.
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Affiliation(s)
- Yuan-Qin Min
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Qiong Mo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yun-Jia Ning
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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65
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Torres Acosta MA, Singer BD. Pathogenesis of COVID-19-induced ARDS: implications for an ageing population. Eur Respir J 2020; 56:13993003.02049-2020. [PMID: 32747391 PMCID: PMC7397945 DOI: 10.1183/13993003.02049-2020] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has elicited a swift response by the scientific community to elucidate the pathogenesis of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2)-induced lung injury and develop effective therapeutics. Clinical data indicate that severe COVID-19 most commonly manifests as viral pneumonia-induced acute respiratory distress syndrome (ARDS), a clinical entity mechanistically understood best in the context of influenza A virus-induced pneumonia. Similar to influenza, advanced age has emerged as the leading host risk factor for developing severe COVID-19. In this review we connect the current understanding of the SARS-CoV-2 replication cycle and host response to the clinical presentation of COVID-19, borrowing concepts from influenza A virus-induced ARDS pathogenesis and discussing how these ideas inform our evolving understanding of COVID-19-induced ARDS. We also consider important differences between COVID-19 and influenza, mainly the protean clinical presentation and associated lymphopenia of COVID-19, the contrasting role of interferon-γ in mediating the host immune response to these viruses, and the tropism for vascular endothelial cells of SARS-CoV-2, commenting on the potential limitations of influenza as a model for COVID-19. Finally, we explore hallmarks of ageing that could explain the association between advanced age and susceptibility to severe COVID-19. Review of viral ARDS pathogenesis, how it informs evolving models of COVID-19, and how hallmarks of ageing explain the age-related morbidity and mortality of severe COVID-19https://bit.ly/39Ca0c0
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Affiliation(s)
- Manuel A Torres Acosta
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA .,Dept of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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66
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Wang Y, Grunewald M, Perlman S. Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol Biol 2020; 2203:1-29. [PMID: 32833200 DOI: 10.1007/978-1-0716-0900-2_1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. CoVs cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs, and upper respiratory tract and kidney disease in chickens to lethal human respiratory infections. Most recently, the novel coronavirus, SARS-CoV-2, which was first identified in Wuhan, China in December 2019, is the cause of a catastrophic pandemic, COVID-19, with more than 8 million infections diagnosed worldwide by mid-June 2020. Here we provide a brief introduction to CoVs discussing their replication, pathogenicity, and current prevention and treatment strategies. We will also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), which are relevant for understanding COVID-19.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Matthew Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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67
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Hartenian E, Nandakumar D, Lari A, Ly M, Tucker JM, Glaunsinger BA. The molecular virology of coronaviruses. J Biol Chem 2020; 295:12910-12934. [PMID: 32661197 PMCID: PMC7489918 DOI: 10.1074/jbc.rev120.013930] [Citation(s) in RCA: 302] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Few human pathogens have been the focus of as much concentrated worldwide attention as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID-19. Its emergence into the human population and ensuing pandemic came on the heels of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), two other highly pathogenic coronavirus spillovers, which collectively have reshaped our view of a virus family previously associated primarily with the common cold. It has placed intense pressure on the collective scientific community to develop therapeutics and vaccines, whose engineering relies on a detailed understanding of coronavirus biology. Here, we present the molecular virology of coronavirus infection, including its entry into cells, its remarkably sophisticated gene expression and replication mechanisms, its extensive remodeling of the intracellular environment, and its multifaceted immune evasion strategies. We highlight aspects of the viral life cycle that may be amenable to antiviral targeting as well as key features of its biology that await discovery.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Divya Nandakumar
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Azra Lari
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Michael Ly
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessica M Tucker
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Britt A Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA.
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68
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SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol 2020; 27:959-966. [DOI: 10.1038/s41594-020-0511-8] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022]
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69
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Haque SKM, Ashwaq O, Sarief A, Azad John Mohamed AK. A comprehensive review about SARS-CoV-2. Future Virol 2020; 15:625-648. [PMID: 33224265 PMCID: PMC7664148 DOI: 10.2217/fvl-2020-0124] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
The coronavirus disease (COVID-19) was first identified in China, December 2019. Since then, it has spread the length and breadth of the world at an unprecedented, alarming rate. Severe acute respiratory syndrome coronavirus (SARS-CoV)-2, which causes COVID-19, has much in common with its closest homologs, SARS-CoV and Middle East respiratory syndrome-CoV. The virus-host interaction of SARS-CoV-2 uses the same receptor, ACE2, which is similar to that of SARS-CoV, which spreads through the respiratory tract. Patients with COVID-19 report symptoms including mild-to-severe fever, cough and fatigue; very few patients report gastrointestinal infections. There are no specific antiviral strategies. A few strong medications are under investigation, so we have to focus on proposals which ought to be taken to forestall this infection in a living host.
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Affiliation(s)
- SK Manirul Haque
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
| | - Omar Ashwaq
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
| | - Abdulla Sarief
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
| | - Abdul Kalam Azad John Mohamed
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
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70
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Pandey SC, Pande V, Sati D, Upreti S, Samant M. Vaccination strategies to combat novel corona virus SARS-CoV-2. Life Sci 2020; 256:117956. [PMID: 32535078 PMCID: PMC7289747 DOI: 10.1016/j.lfs.2020.117956] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/30/2020] [Accepted: 06/08/2020] [Indexed: 01/08/2023]
Abstract
The 2019-novel coronavirus disease (COVID-19) is caused by SARS-CoV-2 is transmitted from human to human has recently reported in China. Now COVID-19 has been spread all over the world and declared epidemics by WHO. It has caused a Public Health Emergency of International Concern. The elderly and people with underlying diseases are susceptible to infection and prone to serious outcomes, which may be associated with acute respiratory distress syndrome (ARDS) and cytokine storm. Due to the rapid increase of SARS-CoV-2 infections and unavailability of antiviral therapeutic agents, developing an effective SAR-CoV-2 vaccine is urgently required. SARS-CoV-2 which is genetically similar to SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) is an enveloped, single and positive-stranded RNA virus with a genome comprising 29,891 nucleotides, which encode the 12 putative open reading frames responsible for the synthesis of viral structural and nonstructural proteins which are very similar to SARS-CoV and MERS-CoV proteins. In this review we have summarized various vaccine candidates i.e., nucleotide, subunit and vector based as well as attenuated and inactivated forms, which have already been demonstrated their prophylactic efficacy against MERS-CoV and SARS-CoV, so these candidates could be used as a potential tool for the development of a safe and effective vaccine against SARS-CoV-2.
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Affiliation(s)
- Satish Chandra Pandey
- Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India; Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand, India
| | - Veni Pande
- Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India; Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand, India
| | - Diksha Sati
- Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
| | - Shobha Upreti
- Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
| | - Mukesh Samant
- Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India.
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71
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Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. J Biosci 2020. [PMID: 32713863 PMCID: PMC7366452 DOI: 10.1007/s12038-020-00069-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.
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72
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Shen Z, Yang Y, Yang S, Zhang G, Xiao S, Fu ZF, Peng G. Structural and Biological Basis of Alphacoronavirus nsp1 Associated with Host Proliferation and Immune Evasion. Viruses 2020; 12:v12080812. [PMID: 32731335 PMCID: PMC7472224 DOI: 10.3390/v12080812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
Non-structural protein 1 (nsp1) is only characterized in alphacoronaviruses (α-CoVs) and betacoronaviruses (β-CoVs). There have been extensive researches on how the β-CoVs nsp1 regulates viral virulence by inhibiting host protein synthesis, but the regulatory mechanism of the α-CoVs nsp1 is still unclear. Here, we report the 2.1-Å full-length crystal structure of nsp1 in emerging porcine SADS-CoV and the 1.8-Å full-length crystal structure of nsp1 in the highly lethal cat FIPV. Although they belong to different subtypes of α-CoVs, these viruses all have a bucket-shaped fold composed of six β-sheets, similar to the crystal structure of PEDV and TGEV nsp1. Comparing the above four structures, we found that the structure of α-CoVs nsp1 in the same subtype was more conserved. We then selected mammalian cells that were treated with SADS-CoV and FIPV nsp1 for RNA sequencing analysis and found that nsp1 had a specific inhibitory effect on interferon (IFN) and cell cycle genes. Using the Renilla luciferase (Rluc) assay and Western blotting, we confirmed that seven representative α-CoVs nsp1s could significantly inhibit the phosphorylation of STAT1-S727 and interfere with the effect of IFN-I. Moreover, the cell cycle experiment confirmed that α-CoVs nsp1 could encourage host cells to stay in the G0/G1 phase. Based on these findings, we not only greatly improved the crystal structure data on α-CoVs nsp1, but we also speculated that α-CoVs nsp1 regulated host proliferation and immune evasion-related biological functions by inhibiting the synthesis of host proteins, thus creating an environment conducive to the virus.
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Affiliation(s)
- Zhou Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yiling Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Siqi Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
| | - Guangxu Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Zhen F. Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.S.); (Y.Y.); (S.Y.); (G.Z.); (S.X.); (Z.F.F.)
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-8728-0170
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73
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Abstract
Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine.
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Legnardi M, Tucciarone CM, Franzo G, Cecchinato M. Infectious Bronchitis Virus Evolution, Diagnosis and Control. Vet Sci 2020; 7:E79. [PMID: 32580381 PMCID: PMC7356646 DOI: 10.3390/vetsci7020079] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/09/2023] Open
Abstract
RNA viruses are characterized by high mutation and recombination rates, which allow a rapid adaptation to new environments. Most of the emerging diseases and host jumps are therefore sustained by these viruses. Rapid evolution may also hinder the understanding of molecular epidemiology, affect the sensitivity of diagnostic assays, limit the vaccine efficacy and favor episodes of immune escape, thus significantly complicating the control of even well-known pathogens. The history of infectious bronchitis virus (IBV) fits well with the above-mentioned scenario. Despite being known since the 1930s, it still represents one of the main causes of disease and economic losses for the poultry industry. A plethora of strategies have been developed and applied over time, with variable success, to limit its impact. However, they have rarely been evaluated objectively and on an adequate scale. Therefore, the actual advantages and disadvantages of IBV detection and control strategies, as well as their implementation, still largely depend on individual sensibility. The present manuscript aims to review the main features of IBV biology and evolution, focusing on their relevance and potential applications in terms of diagnosis and control.
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Affiliation(s)
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell’Università, 16, 35020 Legnaro, Italy; (M.L.); (G.F.); (M.C.)
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Cagliani R, Forni D, Clerici M, Sironi M. Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2. J Virol 2020; 94:e00411-20. [PMID: 32238584 PMCID: PMC7307108 DOI: 10.1128/jvi.00411-20] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/26/2020] [Indexed: 11/20/2022] Open
Abstract
The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously in horseshoe bats. We analyzed the selective events that accompanied the divergence of SARS-CoV-2 from BatCoV RaTG13. To this end, we applied a population genetics-phylogenetics approach, which leverages within-population variation and divergence from an outgroup. Results indicated that most sites in the viral open reading frames (ORFs) evolved under conditions of strong to moderate purifying selection. The most highly constrained sequences corresponded to some nonstructural proteins (nsps) and to the M protein. Conversely, nsp1 and accessory ORFs, particularly ORF8, had a nonnegligible proportion of codons evolving under conditions of very weak purifying selection or close to selective neutrality. Overall, limited evidence of positive selection was detected. The 6 bona fide positively selected sites were located in the N protein, in ORF8, and in nsp1. A signal of positive selection was also detected in the receptor-binding motif (RBM) of the spike protein but most likely resulted from a recombination event that involved the BatCoV RaTG13 sequence. In line with previous data, we suggest that the common ancestor of SARS-CoV-2 and BatCoV RaTG13 encoded/encodes an RBM similar to that observed in SARS-CoV-2 itself and in some pangolin viruses. It is presently unknown whether the common ancestor still exists and, if so, which animals it infects. Our data, however, indicate that divergence of SARS-CoV-2 from BatCoV RaTG13 was accompanied by limited episodes of positive selection, suggesting that the common ancestor of the two viruses was poised for human infection.IMPORTANCE Coronaviruses are dangerous zoonotic pathogens; in the last 2 decades, three coronaviruses have crossed the species barrier and caused human epidemics. One of these is the recently emerged SARS-CoV-2. We investigated how, since its divergence from a closely related bat virus, natural selection shaped the genome of SARS-CoV-2. We found that distinct coding regions in the SARS-CoV-2 genome evolved under conditions of different degrees of constraint and are consequently more or less prone to tolerate amino acid substitutions. In practical terms, the level of constraint provides indications about which proteins/protein regions are better suited as possible targets for the development of antivirals or vaccines. We also detected limited signals of positive selection in three viral ORFs. However, we warn that, in the absence of knowledge about the chain of events that determined the human spillover, these signals should not be necessarily interpreted as evidence of an adaptation to our species.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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Abstract
This review provides an overview regarding the main aspects of candidate COVID-19 vaccines and pathophysiology of disease. The types of biotechnological candidate vaccines to be developed against COVID-19, their degree of protection and the pathophysiological mechanism of the disease were analyzed in this review article. The literature data on which cruxes for the development of biotechnological candidate vaccines to be wended are based was researched. Data that could give reference to various biotechnological candidate vaccines were reviewed. For this purpose, up-to-date literature data was utilized. The ways to succeed in the development of a vaccine requiring a technological infrastructure are to synthesize the data obtained from long term trials and to put them into practice subsequently. The vaccines to be developed by means of recombinant DNA technology will be a source of inspiration to people for further studies. After a rapid process of vaccine development, the use of COVID-19 vaccine can be mainstreamed among people to prevent the disease. As a result of these practices, the evaluation of which vaccine will be more safe, reliable and effective will be performed after phase studies.
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77
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Thi Nhu Thao T, Labroussaa F, Ebert N, V'kovski P, Stalder H, Portmann J, Kelly J, Steiner S, Holwerda M, Kratzel A, Gultom M, Schmied K, Laloli L, Hüsser L, Wider M, Pfaender S, Hirt D, Cippà V, Crespo-Pomar S, Schröder S, Muth D, Niemeyer D, Corman VM, Müller MA, Drosten C, Dijkman R, Jores J, Thiel V. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature 2020; 582:561-565. [PMID: 32365353 DOI: 10.1038/s41586-020-2294-9] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate in Escherichia coli owing to the size and occasional instability of the genome1-3. Therefore, an alternative rapid and robust reverse-genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Pneumoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples or synthetic DNA, and these fragments were then reassembled in one step in Saccharomyces cerevisiae using transformation-associated recombination cloning to maintain the genome as a yeast artificial chromosome. T7 RNA polymerase was then used to generate infectious RNA to rescue viable virus. Using this platform, we were able to engineer and generate chemically synthesized clones of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)4, which has caused the recent pandemic of coronavirus disease (COVID-19), in only a week after receipt of the synthetic DNA fragments. The technical advance that we describe here facilitates rapid responses to emerging viruses as it enables the real-time generation and functional characterization of evolving RNA virus variants during an outbreak.
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Affiliation(s)
- Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Mitra Gultom
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Linda Hüsser
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manon Wider
- Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Department for Molecular and Medical Virology, Ruhr-Universität Bochum, Bochum, Germany
| | - Dagny Hirt
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Valentina Cippà
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvia Crespo-Pomar
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Simon Schröder
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Doreen Muth
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. .,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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The molecular biology of intracellular events during Coronavirus infection cycle. Virusdisease 2020; 31:75-79. [PMID: 32368569 PMCID: PMC7197239 DOI: 10.1007/s13337-020-00591-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/24/2020] [Indexed: 11/06/2022] Open
Abstract
CoV-2 which is the causative agent of COVID-19 belongs to genus betacoronaviruses. The sequence analysis of S protein of CoV-2 has shown that it has acquired a ‘polybasic cleavage site’ consisting of 12 aminoacids that has been predicted to enable its cleavage by other cellular proteases possibly increasing its transmissibility. The aminoacids present in receptor binding domain of S protein of SARS CoV which are critical for its binding to cellular receptor are different in CoV-2. The presence of heptanucleotide slippery sequence in ORF1 resulting in ribosomal frameshifting, and presence of transcription regulatory sequences between ORFs resulting in discontinuous transcription, are peculiar features of Coronavirus infection cycle. The exonuclease activity of nsp14 provides possible proofreading ability to RNA polymerase makes coronaviruses different from other RNA viruses allowing coronaviruses to maintain their relatively large genome size. This mini-review summarizes the peculiar features of Coronaviruses genome and the critical events during the infection cycle with focus on CoV-2.
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79
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Ong E, Wong MU, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.20.000141. [PMID: 32511333 PMCID: PMC7239068 DOI: 10.1101/2020.03.20.000141] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
To ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that the whole virus, as well as the spike (S) protein, nucleocapsid (N) protein, and membrane (M) protein, have been tested for vaccine development against SARS and MERS. However, these vaccine candidates might lack the induction of complete protection and have safety concerns. We then applied the Vaxign reverse vaccinology tool and the newly developed Vaxign-ML machine learning tool to predict COVID-19 vaccine candidates. By investigating the entire proteome of SARS-CoV-2, six proteins, including the S protein and five non-structural proteins (nsp3, 3CL-pro, and nsp8-10), were predicted to be adhesins, which are crucial to the viral adhering and host invasion. The S, nsp3, and nsp8 proteins were also predicted by Vaxign-ML to induce high protective antigenicity. Besides the commonly used S protein, the nsp3 protein has not been tested in any coronavirus vaccine studies and was selected for further investigation. The nsp3 was found to be more conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV than among 15 coronaviruses infecting human and other animals. The protein was also predicted to contain promiscuous MHC-I and MHC-II T-cell epitopes, and linear B-cell epitopes localized in specific locations and functional domains of the protein. By applying reverse vaccinology and machine learning, we predicted potential vaccine targets for effective and safe COVID-19 vaccine development. We then propose that an "Sp/Nsp cocktail vaccine" containing a structural protein(s) (Sp) and a non-structural protein(s) (Nsp) would stimulate effective complementary immune responses.
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80
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Cárdenas-Conejo Y, Liñan-Rico A, García-Rodríguez DA, Centeno-Leija S, Serrano-Posada H. An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2). J Med Virol 2020; 92:688-692. [PMID: 32167166 PMCID: PMC7228214 DOI: 10.1002/jmv.25758] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 01/11/2023]
Abstract
The city of Wuhan, Hubei province, China, was the origin of a severe pneumonia outbreak in December 2019, attributed to a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), causing a total of 2761 deaths and 81109 cases (25 February 2020). SARS-CoV-2 belongs to genus Betacoronavirus, subgenus Sarbecovirus. The polyprotein 1ab (pp1ab) remains unstudied thoroughly since it is similar to other sarbecoviruses. In this short communication, we performed phylogenetic-structural sequence analysis of pp1ab protein of SARS-CoV-2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was found in a virus isolated from a Japanese patient that did not display critical symptoms. While comparing pp1ab protein with other betacoronaviruses, we found a 42 amino acid signature that is only present in SARS-CoV-2 (AS-SCoV2). Members from clade 2 of sarbecoviruses have traces of this signature. The AS-SCoV2 located in the acidic-domain of papain-like protein of SARS-CoV-2 and bat-SL-CoV-RatG13 guided us to suggest that the novel 2019 coronavirus probably emerged by genetic drift from bat-SL-CoV-RaTG13. The implication of this amino acid signature in papain-like protein structure arrangement and function is something worth to be explored.
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Affiliation(s)
- Yair Cárdenas-Conejo
- Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico
| | - Andrómeda Liñan-Rico
- University Center for Biomedical Research, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico
| | | | - Sara Centeno-Leija
- Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico
| | - Hugo Serrano-Posada
- Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico
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81
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Bourogâa H, Larbi I, Miled K, Hellal YK, Hassen J, Behi I, Nsiri J, Ghram A. Evaluation of protection conferred by a vaccination program based on the H120 and CR88 commercial vaccines against a field variant of avian infectious bronchitis virus. J APPL POULTRY RES 2019; 23:156-164. [PMID: 32288459 PMCID: PMC7109893 DOI: 10.3382/japr.2013-00828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/23/2014] [Indexed: 12/13/2022] Open
Abstract
Due to serotype variations among different avian infectious bronchitis viruses isolated in Tunisia since 2000, protection of chicks, especially broiler flocks, with Mass H120 vaccine often fails. Therefore, association of CR88 (793B type) with H120 vaccines was used for better response. Challenge experiments were then conducted to evaluate tracheal and renal cross-protection in chickens immunized via nasal and eye drops. Conferred protection was measured by clinical signs and macroscopic lesions observed, based on scores attributed according to their severities. The results showed a low protection conferred by H120 alone, as vaccination did not reduce tracheal and kidney lesions (70% scored as 3) after TN20/00 virus challenge, which also led to 10% mortality. Conversely, the challenge results indicated that the combination of the 2 strains (H120/CR88) allow high protection. Based on the results of the challenge experiments, a vaccination protocol coupling CR88 to H120 was applied for industrial broiler flocks. Clinical observations and serological results confirmed that association of heterologous serotypes (H120 and CR88 vaccines) increased the levels of protection against infectious bronchitis viruses compared with the H120 vaccine given alone.
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Affiliation(s)
- Hager Bourogâa
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Imen Larbi
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Khaled Miled
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Ymene Kort Hellal
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Jihene Hassen
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Imen Behi
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Jihene Nsiri
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
| | - Abdeljelil Ghram
- Université Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03 Epidemiology and Veterinary Microbiology, 13, Place Pasteur, BP 74 1002 Tunis-Belvédère, Tunisia
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82
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Hou Y, Wang Q. Emerging Highly Virulent Porcine Epidemic Diarrhea Virus: Molecular Mechanisms of Attenuation and Rational Design of Live Attenuated Vaccines. Int J Mol Sci 2019; 20:E5478. [PMID: 31689903 PMCID: PMC6862049 DOI: 10.3390/ijms20215478] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022] Open
Abstract
The highly virulent porcine epidemic diarrhea virus (PEDV) emerged in China in 2010. It infects pigs of all ages, and causes severe diarrhea and high mortality rates in newborn pigs, leading to devastating economic losses in the pork industry worldwide. Effective and safe vaccines against highly virulent PEDV strains are still unavailable, hampering the further prevention, control and eradication of the disease in herds. Vaccination of pregnant sows with live attenuated vaccines (LAVs) is the most effective strategy to induce lactogenic immunity in the sows, which provides A passive protection of suckling piglets against PEDV via the colostrum (beestings, or first milk) and milk. Several LAV candidates have been developed via serially passaging the highly virulent PEDV isolates in non-porcine Vero cells. However, their efficacies in the induction of sufficient protection against virulent PEDV challenge vary in vivo. In this review, we summarize the current knowledge of the virulence-related mutations of PEDV and their potential roles in PEDV attenuation in vivo. With the successful development of reverse genetics systems for PEDV, we also discuss how to use them to generate promising LAV candidates that are safe, effective and genetically stable. This article provides timely insight into the rational design of effective and safe PEDV LAV candidates.
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Affiliation(s)
- Yixuan Hou
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA.
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agriculture and Environmental Sciences, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA.
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83
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DeDiego ML, Martinez-Sobrido L, Topham DJ. Novel Functions of IFI44L as a Feedback Regulator of Host Antiviral Responses. J Virol 2019; 93:e01159-19. [PMID: 31434731 PMCID: PMC6803278 DOI: 10.1128/jvi.01159-19] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 11/20/2022] Open
Abstract
We describe a novel function for the interferon (IFN)-induced protein 44-like (IFI44L) gene in negatively modulating innate immune responses induced after virus infections. Furthermore, we show that decreasing IFI44L expression impairs virus production and that IFI44L expression negatively modulates the antiviral state induced by an analog of double-stranded RNA (dsRNA) or by IFN treatment. The mechanism likely involves the interaction of IFI44L with cellular FK506-binding protein 5 (FKBP5), which in turn interacts with kinases essential for type I and III IFN responses, such as inhibitor of nuclear factor kappa B (IκB) kinase alpha (IKKα), IKKβ, and IKKε. Consequently, binding of IFI44L to FKBP5 decreased interferon regulatory factor 3 (IRF-3)-mediated and nuclear factor kappa-B (NF-κB) inhibitor (IκBα)-mediated phosphorylation by IKKε and IKKβ, respectively. According to these results, IFI44L is a good target for treatment of diseases associated with excessive IFN levels and/or proinflammatory responses and for reduction of viral replication.IMPORTANCE Excessive innate immune responses can be deleterious for the host, and therefore, negative feedback is needed. Here, we describe a completely novel function for IFI44L in negatively modulating innate immune responses induced after virus infections. In addition, we show that decreasing IFI44L expression impairs virus production and that IFI44L expression negatively modulates the antiviral state induced by an analog of dsRNA or by IFN treatment. IFI44L binds to the cellular protein FKBP5, which in turn interacts with kinases essential for type I and III IFN induction and signaling, such as the kinases IKKα, IKKβ, and IKKε. IFI44L binding to FKBP5 decreased the phosphorylation of IRF-3 and IκBα mediated by IKKε and IKKβ, respectively, providing an explanation for the function of IFI44L in negatively modulating IFN responses. Therefore, IFI44L is a candidate target for reducing virus replication.
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Affiliation(s)
- Marta L DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
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84
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Shen Z, Wang G, Yang Y, Shi J, Fang L, Li F, Xiao S, Fu ZF, Peng G. A conserved region of nonstructural protein 1 from alphacoronaviruses inhibits host gene expression and is critical for viral virulence. J Biol Chem 2019; 294:13606-13618. [PMID: 31350335 PMCID: PMC6746460 DOI: 10.1074/jbc.ra119.009713] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/24/2019] [Indexed: 12/22/2022] Open
Abstract
Coronaviruses are enveloped, single-stranded RNA viruses that are distributed worldwide. They include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and the human coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), many of which seriously endanger human health and well-being. Only alphacoronaviruses and betacoronaviruses harbor nonstructural protein 1 (nsp1), which performs multiple functions in inhibiting antiviral host responses. The role of the C terminus of betacoronavirus nsp1 in virulence has been characterized, but the location of the alphacoronavirus nsp1 region that is important for virulence remains unclear. Here, using TGEV nsp1 as a model to explore the function of this protein in alphacoronaviruses, we demonstrate that alphacoronavirus nsp1 inhibits host gene expression. Solving the crystal structure of full-length TGEV at 1.85-Å resolution and conducting several biochemical analyses, we observed that a specific motif (amino acids 91-95) of alphacoronavirus nsp1 is a conserved region that inhibits host protein synthesis. Using a reverse-genetics system based on CRISPR/Cas9 technology to construct a recombinant TGEV in which this specific nsp1 motif was altered, we found that this mutation does not affect virus replication in cell culture but significantly reduces TGEV pathogenicity in pigs. Taken together, our findings suggest that alphacoronavirus nsp1 is an essential virulence determinant, providing a potential paradigm for the development of a new attenuated vaccine based on modified nsp1.
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Affiliation(s)
- Zhou Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Gang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yiling Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota 55108
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China .,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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85
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Chen F, Knutson TP, Rossow S, Saif LJ, Marthaler DG. Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States. Sci Rep 2019; 9:3953. [PMID: 30850666 PMCID: PMC6408454 DOI: 10.1038/s41598-019-40564-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 02/11/2019] [Indexed: 01/16/2023] Open
Abstract
The epidemiology and genetic diversity of transmissible gastroenteritis virus (TGEV) in the United States (US) was investigated by testing clinical cases for TGEV by real time RT-PCR between January 2008 and November 2016. Prevalence of TGEV ranged between 3.8–6.8% and peaked during cold months until March 2013, in which prevalence decreased to < 0.1%. Nineteen complete TGEV genomes and a single strain of porcine respiratory coronavirus (PRCV) from the US were generated and compared to historical strains to investigate the evolution of these endemic coronaviruses. Sixteen of our TGEV strains share 8 unique deletions and 119 distinct amino acid changes, which might greatly affect the biological characteristics of the variant TGEV, and resulted in a “variant” genotype of TGEV. The “variant” genotype shared similar unique deletions and amino acid changes with the recent PRCV strain identified in this study, suggesting a recombination event occurred between the ‘‘variant’’ TGEV and PRCV. Moreover, the results indicate the “variant” genotype is the dominant genotype circulating in the US. Therefore, this study provides insight into the occurrence, origin, genetic characteristics, and evolution of TGEV and PRCV circulating in the US.
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Affiliation(s)
- Fangzhou Chen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Todd P Knutson
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Stephanie Rossow
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Linda J Saif
- Department of Veterinary Preventive Medicine, The Ohio State University, Food Animal Health Research Program, OARDC, CFAES, Wooster, Ohio, United States of America
| | - Douglas G Marthaler
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America. .,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America.
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86
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V'kovski P, Gerber M, Kelly J, Pfaender S, Ebert N, Braga Lagache S, Simillion C, Portmann J, Stalder H, Gaschen V, Bruggmann R, Stoffel MH, Heller M, Dijkman R, Thiel V. Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife 2019; 8:42037. [PMID: 30632963 PMCID: PMC6372286 DOI: 10.7554/elife.42037] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022] Open
Abstract
Positive-sense RNA viruses hijack intracellular membranes that provide niches for viral RNA synthesis and a platform for interactions with host proteins. However, little is known about host factors at the interface between replicase complexes and the host cytoplasm. We engineered a biotin ligase into a coronaviral replication/transcription complex (RTC) and identified >500 host proteins constituting the RTC microenvironment. siRNA-silencing of each RTC-proximal host factor demonstrated importance of vesicular trafficking pathways, ubiquitin-dependent and autophagy-related processes, and translation initiation factors. Notably, detection of translation initiation factors at the RTC was instrumental to visualize and demonstrate active translation proximal to replication complexes of several coronaviruses. Collectively, we establish a spatial link between viral RNA synthesis and diverse host factors of unprecedented breadth. Our data may serve as a paradigm for other positive-strand RNA viruses and provide a starting point for a comprehensive analysis of critical virus-host interactions that represent targets for therapeutic intervention. Coronaviruses can infect the nose and throat and are a main cause of the common cold. Infections are usually mild and short-lived, but sometimes they can turn nasty. In 2002 and 2012, two dangerous new coronaviruses emerged and caused diseases known as SARS and MERS. These viruses caused much more serious symptoms and in some cases proved deadly. The question is, why are some coronaviruses more dangerous than others? Scientists know that the body's response to virus infection can make a difference to whether someone had mild or severe disease. So, to understand why some coronaviruses cause a cold and others kill, they also need to learn how people react to virus infection. Coronaviruses hijack membranes inside cells and turn them into virus factories. Within these factories, the viruses build molecular machinery called replicase complexes to copy their genetic code, which is needed for the next generation of virus particles. The viruses steal and repurpose proteins from their host cell that will assist in the copying process. However, scientists do not yet know which host proteins are essential for the virus to multiply. So, to find out, V’kovski et al. developed a way to tag any host protein that came near the virus factories. The new technique involved attaching an enzyme called a biotin ligase to the replicase complex. This enzyme acts as a molecular label gun, attaching a chemical tag to any protein that comes within ten nanometres. The label gun revealed that more than 500 different proteins come into contact with the replicase complex. To find out what these proteins were doing, the next step was to switch off their genes one by one. This revealed the key cell machinery that coronaviruses hijack when they are replicating. It included the cell's cargo transport system, the waste disposal system, and the protein production system. Using these systems allows the viruses to copy their genetic code next to machines that can turn it straight into viral proteins. These new results provide clues about which proteins viruses actually need from their host cells. They also do not just apply to coronaviruses. Other viruses use similar strategies to complete their infection cycle. These findings could help researchers to understand more generally about how viruses multiply. In the future, this knowledge could lead to new ways to combat virus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Markus Gerber
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sophie Braga Lagache
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Cedric Simillion
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Véronique Gaschen
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Michael H Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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87
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Graham RL, Deming DJ, Deming ME, Yount BL, Baric RS. Evaluation of a recombination-resistant coronavirus as a broadly applicable, rapidly implementable vaccine platform. Commun Biol 2018; 1:179. [PMID: 30393776 PMCID: PMC6206136 DOI: 10.1038/s42003-018-0175-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/19/2018] [Indexed: 12/15/2022] Open
Abstract
Emerging and re-emerging zoonotic viral diseases are major threats to global health, economic stability, and national security. Vaccines are key for reducing coronaviral disease burden; however, the utility of live-attenuated vaccines is limited by risks of reversion or repair. Because of their history of emergence events due to their prevalence in zoonotic pools, designing live-attenuated coronavirus vaccines that can be rapidly and broadly implemented is essential for outbreak preparedness. Here, we show that coronaviruses with completely rewired transcription regulatory networks (TRNs) are effective vaccines against SARS-CoV. The TRN-rewired viruses are attenuated and protect against lethal SARS-CoV challenge. While a 3-nt rewired TRN reverts via second-site mutation upon serial passage, a 7-nt rewired TRN is more stable, suggesting that a more extensively rewired TRN might be essential for avoiding growth selection. In summary, rewiring the TRN is a feasible strategy for limiting reversion in an effective live-attenuated coronavirus vaccine candidate that is potentially portable across the Nidovirales order.
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Affiliation(s)
- Rachel L Graham
- Department of Epidemiology, The University of North Carolina at Chapel Hill, 2107 McGavran-Greenberg, CB 7435, Chapel Hill, NC, 27599, USA
| | - Damon J Deming
- Department of Epidemiology, The University of North Carolina at Chapel Hill, 2107 McGavran-Greenberg, CB 7435, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Food and Drug Administration, 10933 New Hampshire Avenue, Bldg 22, Rm 6170, Silver Spring, MD, 20993, USA
| | - Meagan E Deming
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- University of Maryland Medical Center, Department of Medicine, Division of Infectious Disease, Institute of Human Virology, 725 West Lombard Street, Room 211A, Baltimore, MD, 21201, USA
| | - Boyd L Yount
- Department of Epidemiology, The University of North Carolina at Chapel Hill, 2107 McGavran-Greenberg, CB 7435, Chapel Hill, NC, 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, 2107 McGavran-Greenberg, CB 7435, Chapel Hill, NC, 27599, USA.
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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88
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The Endonucleolytic RNA Cleavage Function of nsp1 of Middle East Respiratory Syndrome Coronavirus Promotes the Production of Infectious Virus Particles in Specific Human Cell Lines. J Virol 2018; 92:JVI.01157-18. [PMID: 30111568 DOI: 10.1128/jvi.01157-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/11/2018] [Indexed: 01/10/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) nsp1 suppresses host gene expression in expressed cells by inhibiting translation and inducing endonucleolytic cleavage of host mRNAs, the latter of which leads to mRNA decay. We examined the biological functions of nsp1 in infected cells and its role in virus replication by using wild-type MERS-CoV and two mutant viruses with specific mutations in the nsp1; one mutant lacked both biological functions, while the other lacked the RNA cleavage function but retained the translation inhibition function. In Vero cells, all three viruses replicated efficiently with similar replication kinetics, while wild-type virus induced stronger host translational suppression and host mRNA degradation than the mutants, demonstrating that nsp1 suppressed host gene expression in infected cells. The mutant viruses replicated less efficiently than wild-type virus in Huh-7 cells, HeLa-derived cells, and 293-derived cells, the latter two of which stably expressed a viral receptor protein. In 293-derived cells, the three viruses accumulated similar levels of nsp1 and major viral structural proteins and did not induce IFN-β and IFN-λ mRNAs; however, both mutants were unable to generate intracellular virus particles as efficiently as wild-type virus, leading to inefficient production of infectious viruses. These data strongly suggest that the endonucleolytic RNA cleavage function of the nsp1 promoted MERS-CoV assembly and/or budding in a 293-derived cell line. MERS-CoV nsp1 represents the first CoV gene 1 protein that plays an important role in virus assembly/budding and is the first identified viral protein whose RNA cleavage-inducing function promotes virus assembly/budding.IMPORTANCE MERS-CoV represents a high public health threat. Because CoV nsp1 is a major viral virulence factor, uncovering the biological functions of MERS-CoV nsp1 could contribute to our understanding of MERS-CoV pathogenicity and spur development of medical countermeasures. Expressed MERS-CoV nsp1 suppresses host gene expression, but its biological functions for virus replication and effects on host gene expression in infected cells are largely unexplored. We found that nsp1 suppressed host gene expression in infected cells. Our data further demonstrated that nsp1, which was not detected in virus particles, promoted virus assembly or budding in a 293-derived cell line, leading to efficient virus replication. These data suggest that nsp1 plays an important role in MERS-CoV replication and possibly affects virus-induced diseases by promoting virus particle production in infected hosts. Our data, which uncovered an unexpected novel biological function of nsp1 in virus replication, contribute to further understanding of the MERS-CoV replication strategies.
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89
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Structural Basis for the Inhibition of Host Gene Expression by Porcine Epidemic Diarrhea Virus nsp1. J Virol 2018; 92:JVI.01896-17. [PMID: 29237834 DOI: 10.1128/jvi.01896-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/29/2017] [Indexed: 01/21/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), an enteropathogenic Alphacoronavirus, has caused enormous economic losses in the pork industry. Nonstructural protein 1 (nsp1) is a characteristic feature of alpha- and betacoronaviruses, which exhibits both functional conservation and mechanistic diversity in inhibiting host gene expression and antiviral responses. However, the detailed structure and molecular mechanisms underlying the Alphacoronavirus nsp1 inhibition of host gene expression remain unclear. Here, we report the first full-length crystal structure of Alphacoronavirus nsp1 from PEDV. The structure displays a six-stranded β-barrel fold in the middle of two α-helices. The core structure of PEDV nsp1 shows high similarity to those of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp1 and transmissible gastroenteritis virus (TGEV) nsp1, despite its low degree of sequence homology. Using ribopuromycylation and Renilla luciferase reporter assays, we showed that PEDV nsp1 can dramatically inhibit general host gene expression. Furthermore, three motifs (amino acids [aa] 67 to 71, 78 to 85, and 103 to 110) of PEDV nsp1 create a stable functional region for inhibiting protein synthesis, differing considerably from Betacoronavirus nsp1. These results elucidate the detailed structural basis through which PEDV nsp1 inhibits host gene expression, providing insight into the development of a new attenuated vaccine with nsp1 modifications.IMPORTANCE Porcine epidemic diarrhea virus (PEDV) has led to tremendous economic losses in the global swine industry. PEDV nsp1 plays a crucial role in inhibiting host gene expression, but its functional mechanism remains unclear. Here, we report the full-length structure of PEDV nsp1, the first among coronaviruses to be reported. The 1.25-Å resolution crystal structure of PEDV nsp1 shows high similarity to severe acute respiratory syndrome coronavirus (SARS-CoV) nsp113-128 and transmissible gastroenteritis virus (TGEV) nsp11-104, despite a lack of sequence homology. Structural and biochemical characterization demonstrated that PEDV nsp1 possesses a stable functional region for inhibition of host protein synthesis, which is formed by loops at residues 67 to 71, 78 to 85, and 103 to 110. The different functional regions in PEDV nsp1 and SARS-CoV nsp1 may explain their distinct mechanisms. Importantly, our structural data are conducive to understanding the mechanism of PEDV nsp1 inhibition of the expression of host genes and may aid in the development of a new attenuated vaccine.
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90
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Type III Interferon Restriction by Porcine Epidemic Diarrhea Virus and the Role of Viral Protein nsp1 in IRF1 Signaling. J Virol 2018; 92:JVI.01677-17. [PMID: 29187542 DOI: 10.1128/jvi.01677-17] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/21/2017] [Indexed: 01/16/2023] Open
Abstract
Type III interferons (IFNs) play a vital role in maintaining the antiviral state of the mucosal epithelial surface in the gut, and in turn, enteric viruses may have evolved to evade the type III IFN responses during infection. To study the possible immune evasion of the type III IFN response by porcine epidemic diarrhea virus (PEDV), a line of porcine intestinal epithelial cells was developed as a cell model for PEDV replication. IFN-λ1 and IFN-λ3 inhibited PEDV replication, indicating the anti-PEDV activity of type III IFNs. Of the 21 PEDV proteins, nsp1, nsp3, nsp5, nsp8, nsp14, nsp15, nsp16, open reading frame 3 (ORF3), E, M, and N were found to suppress type III IFN activities, and IRF1 (interferon regulatory factor 1) signaling mediated the suppression. PEDV specifically inhibited IRF1 nuclear translocation. The peroxisome is the innate antiviral signaling platform for the activation of IRF1-mediated IFN-λ production, and the numbers of peroxisomes were found to be decreased in PEDV-infected cells. PEDV nsp1 blocked the nuclear translocation of IRF1 and reduced the number of peroxisomes to suppress IRF1-mediated type III IFNs. Mutational studies showed that the conserved residues of nsp1 were crucial for IRF1-mediated IFN-λ suppression. Our study for the first time provides evidence that the porcine enteric virus PEDV downregulates and evades IRF1-mediated type III IFN responses by reducing the number of peroxisomes.IMPORTANCE Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric coronavirus that emerged in swine in the United States and has caused severe economic losses. PEDV targets intestinal epithelial cells in the gut, and intestinal epithelial cells selectively induce and respond to the production of type III interferons (IFNs). However, little is known about the modulation of the type III IFN response by PEDV in intestinal epithelial cells. In this study, we established a porcine intestinal epithelial cell model for PEDV replication. We found that PEDV inhibited IRF1-mediated type III IFN production by decreasing the number of peroxisomes in porcine intestinal epithelial cells. We also demonstrated that the conserved residues in the PEDV nsp1 protein were crucial for IFN suppression. This study for the first time shows PEDV evasion of the type III IFN response in intestinal epithelial cells, and it provides valuable information on host cell-virus interactions not only for PEDV but also for other enteric viral infections in swine.
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91
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Terada Y, Kawachi K, Matsuura Y, Kamitani W. MERS coronavirus nsp1 participates in an efficient propagation through a specific interaction with viral RNA. Virology 2017; 511:95-105. [PMID: 28843094 PMCID: PMC7118922 DOI: 10.1016/j.virol.2017.08.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022]
Abstract
MERS-CoV is the only lethal human CoV still endemic in the Arabian Peninsula and neither vaccine nor therapeutics against MERS-CoV infection is available. The nsp1 of CoV is thought to be a major virulence factor because it suppresses protein synthesis through the degradation of host mRNA. In contrast, viral RNA circumvents the nsp1-mediated translational shutoff for an efficient propagation. In this study, we identified amino acid residue in MERS-CoV nsp1 that differ from those of SARS-CoV nsp1, and that appear to be crucial for circumventing the translational shutoff. In addition, reverse genetics analysis suggested the presence of a cis-acting element at the 5'-terminus of the nsp1-coding region, which contributes to the specific recognition of viral RNA that is required for an efficient viral replication. Our results suggest the CoVs share a common mechanism for circumventing the nsp1-mediated translational shutoff.
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Affiliation(s)
- Yutaka Terada
- Laboratory of Clinical Research on Infectious Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kengo Kawachi
- Laboratory of Clinical Research on Infectious Diseases, Osaka University, Osaka 565-0871, Japan; Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Wataru Kamitani
- Laboratory of Clinical Research on Infectious Diseases, Osaka University, Osaka 565-0871, Japan; Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki 305-0843, Japan.
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92
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Hammond RG, Tan X, Johnson MA. SARS-unique fold in the Rousettus bat coronavirus HKU9. Protein Sci 2017; 26:1726-1737. [PMID: 28580734 PMCID: PMC5563143 DOI: 10.1002/pro.3208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/28/2022]
Abstract
The coronavirus nonstructural protein 3 (nsp3) is a multifunctional protein that comprises multiple structural domains. This protein assists viral polyprotein cleavage, host immune interference, and may play other roles in genome replication or transcription. Here, we report the solution NMR structure of a protein from the “SARS‐unique region” of the bat coronavirus HKU9. The protein contains a frataxin fold or double‐wing motif, which is an α + β fold that is associated with protein/protein interactions, DNA binding, and metal ion binding. High structural similarity to the human severe acute respiratory syndrome (SARS) coronavirus nsp3 is present. A possible functional site that is conserved among some betacoronaviruses has been identified using bioinformatics and biochemical analyses. This structure provides strong experimental support for the recent proposal advanced by us and others that the “SARS‐unique” region is not unique to the human SARS virus, but is conserved among several different phylogenetic groups of coronaviruses and provides essential functions. PDB Code(s): 5UTV
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Affiliation(s)
- Robert G Hammond
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Xuan Tan
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Margaret A Johnson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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93
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Han M, Ke H, Zhang Q, Yoo D. Nuclear imprisonment of host cellular mRNA by nsp1β protein of porcine reproductive and respiratory syndrome virus. Virology 2017; 505:42-55. [PMID: 28235682 PMCID: PMC7111332 DOI: 10.1016/j.virol.2017.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/03/2017] [Accepted: 02/08/2017] [Indexed: 02/07/2023]
Abstract
Positive-strand RNA genomes function as mRNA for viral protein synthesis which is fully reliant on host cell translation machinery. Competing with cellular protein translation apparatus needs to ensure the production of viral proteins, but this also stifles host innate defense. In the present study, we showed that porcine reproductive and respiratory syndrome virus (PRRSV), whose replication takes place in the cytoplasm, imprisoned host cell mRNA in the nucleus, which suggests a novel mechanism to enhance translation of PRRSV genome. PRRSV nonstructural protein (nsp) 1β was identified as the nuclear protein playing the role for host mRNA nuclear retention and subversion of host protein synthesis. A SAP (SAF-A/B, Acinus, and PIAS) motif was identified in nsp1β with the consensus sequence of 126-LQxxLxxxGL-135. In situ hybridization unveiled that SAP mutants were unable to cause nuclear retention of host cell mRNAs and did not suppress host protein synthesis. In addition, these SAP mutants reverted PRRSV-nsp1β-mediated suppression of interferon (IFN) production, IFN signaling, and TNF-α production pathway. Using reverse genetics, a series of SAP mutant PRRS viruses, vK124A, vL126A, vG134A, and vL135A were generated. No mRNA nuclear retention was observed during vL126A and vL135A infections. Importantly, vL126A and vL135A did not suppress IFN production. For other arteriviruses, mRNA nuclear accumulation was also observed for LDV-nsp1β and SHFV-nsp1β. EAV-nsp1 was exceptional and did not block the host mRNA nuclear export. PRRS virus blocks host mRNA nuclear export to the cytoplasm. PRRSV nsp1β is the viral protein responsible for host mRNA nuclear retention. SAP domain in nsp1β is essential for host mRNA nuclear retention and type I interferon suppression. Mutation in the SAP domain of nsp1β causes the loss of function. Host mRNA nuclear retention by nsp1β is common in the family Arteriviridae, except equine arteritis virus.
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Affiliation(s)
- Mingyuan Han
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, Urbana, IL 61802, USA.
| | - Hanzhong Ke
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, Urbana, IL 61802, USA
| | - Qingzhan Zhang
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, Urbana, IL 61802, USA
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, Urbana, IL 61802, USA.
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94
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Teeravechyan S, Frantz PN, Wongthida P, Chailangkarn T, Jaru-Ampornpan P, Koonpaew S, Jongkaewwattana A. Deciphering the biology of porcine epidemic diarrhea virus in the era of reverse genetics. Virus Res 2016; 226:152-171. [PMID: 27212685 PMCID: PMC7114553 DOI: 10.1016/j.virusres.2016.05.003] [Citation(s) in RCA: 21] [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: 03/31/2016] [Revised: 05/04/2016] [Accepted: 05/04/2016] [Indexed: 01/01/2023]
Abstract
Emergence of the porcine epidemic diarrhea virus (PEDV) as a global threat to the swine industry underlies the urgent need for deeper understanding of this virus. To date, we have yet to identify functions for all the major gene products, much less grasp their implications for the viral life cycle and pathogenic mechanisms. A major reason is the lack of genetic tools for studying PEDV. In this review, we discuss the reverse genetics approaches that have been successfully used to engineer infectious clones of PEDV as well as other potential and complementary methods that have yet to be applied to PEDV. The importance of proper cell culture for successful PEDV propagation and maintenance of disease phenotype are addressed in our survey of permissive cell lines. We also highlight areas of particular relevance to PEDV pathogenesis and disease that have benefited from reverse genetics studies and pressing questions that await resolution by such studies. In particular, we examine the spike protein as a determinant of viral tropism, entry and virulence, ORF3 and its association with cell culture adaptation, and the nucleocapsid protein and its potential role in modulating PEDV pathogenicity. Finally, we conclude with an exploration of how reverse genetics can help mitigate the global impact of PEDV by addressing the challenges of vaccine development.
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Affiliation(s)
- Samaporn Teeravechyan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand
| | - Phanramphoei Namprachan Frantz
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand
| | - Phonphimon Wongthida
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand
| | - Thanathom Chailangkarn
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand
| | - Surapong Koonpaew
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120 Thailand.
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95
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Liu WJ, Zhao M, Liu K, Xu K, Wong G, Tan W, Gao GF. T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV. Antiviral Res 2016; 137:82-92. [PMID: 27840203 PMCID: PMC7113894 DOI: 10.1016/j.antiviral.2016.11.006] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 12/14/2022]
Abstract
Over 12 years have elapsed since severe acute respiratory syndrome (SARS) triggered the first global alert for coronavirus infections. Virus transmission in humans was quickly halted by public health measures and human infections of SARS coronavirus (SARS-CoV) have not been observed since. However, other coronaviruses still pose a continuous threat to human health, as exemplified by the recent emergence of Middle East respiratory syndrome (MERS) in humans. The work on SARS-CoV widens our knowledge on the epidemiology, pathophysiology and immunology of coronaviruses and may shed light on MERS coronavirus (MERS-CoV). It has been confirmed that T-cell immunity plays an important role in recovery from SARS-CoV infection. Herein, we summarize T-cell immunological studies of SARS-CoV and discuss the potential cross-reactivity of the SARS-CoV-specific immunity against MERS-CoV, which may provide useful recommendations for the development of broad-spectrum vaccines against coronavirus infections. T-cell epitopes identified throughout the SARS-CoV proteome may act as candidates for vaccine development. Both SARS-CoV and MERS-CoV-recovered donors have had long-lasting memory T-cell immunity. The structures of HLA/SARS-CoV-epitopes illuminate the molecular bases of cellular immunogenicity. Potential cross-T-cell immune reactivities of SARS-CoV and MERS-CoV benefit vaccine development.
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Affiliation(s)
- William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kefang Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gary Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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96
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Fibroblastic reticular cells regulate intestinal inflammation via IL-15-mediated control of group 1 ILCs. Nat Immunol 2016; 17:1388-1396. [PMID: 27798617 PMCID: PMC7097164 DOI: 10.1038/ni.3566] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/25/2016] [Indexed: 12/11/2022]
Abstract
Fibroblastic reticular cells influence the function of lymphocytes in secondary lymphoid organs. Ludewig and colleagues demonstrate that they also specifically restrain the activation of group 1 innate lymphoid cells in the presence of microbial stimulation to prevent immunopathology. Fibroblastic reticular cells (FRCs) of secondary lymphoid organs form distinct niches for interaction with hematopoietic cells. We found here that production of the cytokine IL-15 by FRCs was essential for the maintenance of group 1 innate lymphoid cells (ILCs) in Peyer's patches and mesenteric lymph nodes. Moreover, FRC-specific ablation of the innate immunological sensing adaptor MyD88 unleashed IL-15 production by FRCs during infection with an enteropathogenic virus, which led to hyperactivation of group 1 ILCs and substantially altered the differentiation of helper T cells. Accelerated clearance of virus by group 1 ILCs precipitated severe intestinal inflammatory disease with commensal dysbiosis, loss of intestinal barrier function and diminished resistance to colonization. In sum, FRCs act as an 'on-demand' immunological 'rheostat' by restraining activation of group 1 ILCs and thereby preventing immunopathological damage in the intestine.
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97
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Abstract
Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells.
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Affiliation(s)
- E Kindler
- University of Bern, Bern, Switzerland; Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - V Thiel
- University of Bern, Bern, Switzerland; Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - F Weber
- Institute of Virology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany.
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98
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Abstract
Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA-RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.
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Affiliation(s)
- R Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - M Fricke
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - M Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany; FLI Leibniz Institute for Age Research, Jena, Germany
| | - J Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
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99
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Enjuanes L, Zuñiga S, Castaño-Rodriguez C, Gutierrez-Alvarez J, Canton J, Sola I. Molecular Basis of Coronavirus Virulence and Vaccine Development. Adv Virus Res 2016; 96:245-286. [PMID: 27712626 PMCID: PMC7112271 DOI: 10.1016/bs.aivir.2016.08.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Virus vaccines have to be immunogenic, sufficiently stable, safe, and suitable to induce long-lasting immunity. To meet these requirements, vaccine studies need to provide a comprehensive understanding of (i) the protective roles of antiviral B and T-cell-mediated immune responses, (ii) the complexity and plasticity of major viral antigens, and (iii) virus molecular biology and pathogenesis. There are many types of vaccines including subunit vaccines, whole-inactivated virus, vectored, and live-attenuated virus vaccines, each of which featuring specific advantages and limitations. While nonliving virus vaccines have clear advantages in being safe and stable, they may cause side effects and be less efficacious compared to live-attenuated virus vaccines. In most cases, the latter induce long-lasting immunity but they may require special safety measures to prevent reversion to highly virulent viruses following vaccination. The chapter summarizes the recent progress in the development of coronavirus (CoV) vaccines, focusing on two zoonotic CoVs, the severe acute respiratory syndrome CoV (SARS-CoV), and the Middle East respiratory syndrome CoV, both of which cause deadly disease and epidemics in humans. The development of attenuated virus vaccines to combat infections caused by highly pathogenic CoVs was largely based on the identification and characterization of viral virulence proteins that, for example, interfere with the innate and adaptive immune response or are involved in interactions with specific cell types, such as macrophages, dendritic and epithelial cells, and T lymphocytes, thereby modulating antiviral host responses and viral pathogenesis and potentially resulting in deleterious side effects following vaccination.
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Affiliation(s)
- L Enjuanes
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain.
| | - S Zuñiga
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - C Castaño-Rodriguez
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J Gutierrez-Alvarez
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - J Canton
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - I Sola
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain.
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100
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Infectious Bronchitis Coronavirus Limits Interferon Production by Inducing a Host Shutoff That Requires Accessory Protein 5b. J Virol 2016; 90:7519-7528. [PMID: 27279618 DOI: 10.1128/jvi.00627-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/01/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED During infection of their host cells, viruses often inhibit the production of host proteins, a process that is referred to as host shutoff. By doing this, viruses limit the production of antiviral proteins and increase production capacity for viral proteins. Coronaviruses from the genera Alphacoronavirus and Betacoronavirus, such as severe acute respiratory syndrome coronavirus (SARS-CoV), establish host shutoff via their nonstructural protein 1 (nsp1). The Gammacoronavirus and Deltacoronavirus genomes, however, do not encode nsp1, and it has been suggested that these viruses do not induce host shutoff. Here, we show that the Gammacoronavirus infectious bronchitis virus (IBV) does induce host shutoff, and we find that its accessory protein 5b is indispensable for this function. Importantly, we found that 5b-null viruses, unlike wild-type viruses, induce production of high concentrations of type I interferon protein in vitro, indicating that host shutoff by IBV plays an important role in antagonizing the host's innate immune response. Altogether, we demonstrate that 5b is a functional equivalent of nsp1, thereby answering the longstanding question of whether lack of nsp1 in gammacoronaviruses is compensated for by another viral protein. As such, our study is a significant step forward in the understanding of coronavirus biology and closes a gap in the understanding of some IBV virulence strategies. IMPORTANCE Many viruses inhibit protein synthesis by their host cell to enhance virus replication and to antagonize antiviral defense mechanisms. This process is referred to as host shutoff. We studied gene expression and protein synthesis in chicken cells infected with the important poultry pathogen infectious bronchitis virus (IBV). We show that IBV inhibits synthesis of host proteins, including that of type I interferon, a key component of the antiviral response. The IBV-induced host shutoff, however, does not require degradation of host RNA. Furthermore, we demonstrate that accessory protein 5b of IBV plays a crucial role in the onset of host shutoff. Our findings suggest that inhibition of host protein synthesis is a common feature of coronaviruses and primarily serves to inhibit the antiviral response of the host.
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