1
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Maurina SF, O'Sullivan JP, Sharma G, Pineda Rodriguez DC, MacFadden A, Cendali F, Henen MA, Vögeli B, Kieft JS, Glasgow A, Steckelberg AL. An Evolutionarily Conserved Strategy for Ribosome Binding and Host Translation Inhibition by β-coronavirus Non-structural Protein 1. J Mol Biol 2023; 435:168259. [PMID: 37660941 PMCID: PMC10543557 DOI: 10.1016/j.jmb.2023.168259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Non-structural protein 1 (Nsp1), which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from β-Coronaviruses (β-CoV) inhibits translation through ribosome binding. The C-terminal domain (CTD) of all β-CoV Nsp1s confers high-affinity ribosome binding despite low sequence conservation. Modeling of interactions of four Nsp1s with the ribosome identified the few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the β-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal "effector" domain. Finally, we show that a cis-acting viral RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aid future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2 and related human-pathogenic β-CoVs. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.
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Affiliation(s)
- Stephanie F Maurina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John P O'Sullivan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Geetika Sharma
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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2
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Xiang Y, Mou C, Shi K, Chen X, Meng X, Bao W, Chen Z. SADS-CoV nsp1 inhibits the IFN-β production by preventing TBK1 phosphorylation and inducing CBP degradation. J Med Virol 2023; 95:e29104. [PMID: 37721411 DOI: 10.1002/jmv.29104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/07/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Swine acute diarrhea syndrome (SADS) is first reported in January 2017 in Southern China. It subsequently causes widespread outbreaks in multiple pig farms, leading to economic losses. Therefore, it is an urgent to understand the molecular mechanisms underlying the pathogenesis and immune evasion of Swine acute diarrhea syndrome coronavirus (SADS-CoV). Our research discovered that SADS-CoV inhibited the production of interferon-β (IFN-β) during viral infection. The nonstructural protein 1 (nsp1) prevented the phosphorylation of TBK1 by obstructing the interaction between TBK1 and Ub protein. Moreover, nsp1 induced the degradation of CREB-binding protein (CBP) through the proteasome-dependent pathway, thereby disrupting the IFN-β enhancer and inhibiting IFN transcription. Finally, we identified nsp1-Phe39 as the critical amino acid that downregulated IFN production. In conclusion, our findings described two mechanisms in nsp1 that inhibited IFN production and provided new insights into the evasion strategy adopted by SADS-CoV to evade host antiviral immunity.
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Affiliation(s)
- Yingjie Xiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety,The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kaichuang Shi
- Guangxi Center for Animal Disease Control and Prevention, Nanning, Guangxi, China
| | - Xiang Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xia Meng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety,The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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3
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Pustake M, Giri P, Ganiyani MA, Mumtaz K, Deshmukh K, Saju M, Nunez JV, Orlova N, Das A. Drawing Parallels between SARS, MERS, and COVID-19: A Comparative Overview of Epidemiology, Pathogenesis, and Pathological Features. Indian J Community Med 2023; 48:518-524. [PMID: 37662119 PMCID: PMC10470569 DOI: 10.4103/ijcm.ijcm_460_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 05/22/2023] [Indexed: 09/05/2023] Open
Abstract
Background Since November 2019, when the novel coronavirus arose in Wuhan City, over 188 million people worldwide have been infected with COVID-19. It is the third coronavirus outbreak in the twenty-first century. Until now, practically all coronavirus epidemics have occurred due to zoonotic spread from an animal or transitional host or through the consumption of their products. Coronaviruses can infect humans and cause severe illness and even death. Material and Methods This review was designed to help us recognize and harmonize the similarities and differences between these three coronaviridae family members. Result Measures aimed at containing the epidemic should be emphasized in this circumstance. Prioritizing and planning these activities require an understanding of the particulars of these three viruses. Given the pandemic's enormous death toll and rapid spread, we should be cognizant of the parallels and differences between these three viruses. Additionally, this pandemic warns us to be cautious against the possibility of a future pandemic. Conclusion We highlight the fundamental characteristics of coronaviruses that are critical for recognizing coronavirus epidemiology, pathogenesis, and pathological features that reveal numerous significant pathological attributes and evolutionary patterns in the viral genome that aid in better understanding and anticipating future epidemics.
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Affiliation(s)
- Manas Pustake
- Department of Internal Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
- Harvard Medical School, Harvard University, Boston, MA, USA
| | - Purushottam Giri
- Department of Community Medicine, IIMSR Medical College, Jalna, Maharashtra, India
| | - Mohammad Arfat Ganiyani
- Department of Internal Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | - Kahkashan Mumtaz
- Department of Pediatrics, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | - Krishna Deshmukh
- Department of Internal Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | - Michael Saju
- Department of Community Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | | | | | - Arghadip Das
- Department of Pathology, Nil Ratan Sircar Medical College and Hospital, Kolkata, West Bengal, India
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4
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Chen SC, Xu CT, Chang CF, Chao TY, Lin CC, Fu PW, Yu CH. Optimization of 5'UTR to evade SARS-CoV-2 Nonstructural protein 1-directed inhibition of protein synthesis in cells. Appl Microbiol Biotechnol 2023; 107:2451-2468. [PMID: 36843199 PMCID: PMC9968647 DOI: 10.1007/s00253-023-12442-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Maximizing the expression level of therapeutic proteins in cells is the general goal for DNA/mRNA therapies. It is particularly challenging to achieve efficient protein expression in the cellular contexts with inhibited translation machineries, such as in the presence of cellular Nonstructural protein 1 (Nsp1) of coronaviruses (CoVs) that has been reported to inhibit overall protein synthesis of host genes and exogenously delivered mRNAs/DNAs. In this study, we thoroughly examined the sequence and structure contexts of viral and non-viral 5'UTRs that determine the protein expression levels of exogenously delivered DNAs and mRNAs in cells expressing SARS-CoV-2 Nsp1. It was found that high 5'-proximal A/U content promotes an escape from Nsp1-directed inhibition of protein synthesis and results in selective protein expression. Furthermore, 5'-proximal Cs were found to significantly enhance the protein expression in an Nsp1-dependent manner, while Gs located at a specific window close to the 5'-end counteract such enhancement. The distinct protein expression levels resulted from different 5'UTRs were found correlated to Nsp1-induced mRNA degradations. These findings ultimately enabled rational designs for optimized 5'UTRs that lead to strong expression of exogenous proteins regardless of the translationally repressive Nsp1. On the other hand, we have also identified several 5'-proximal sequences derived from host genes that are capable of mediating the escapes. These results provided novel perspectives to the optimizations of 5'UTRs for DNA/mRNA therapies and/or vaccinations, as well as shedding light on the potential host escapees from Nsp1-directed translational shutoffs. KEY POINTS: • The 5'-proximal SL1 and 5a/b derived from SARS-CoV-2 genomic RNA promote exogenous protein synthesis in cells expressing Nsp1 comparing with non-specific 5'UTRs. • Specific 5'-proximal sequence contexts are the key determinants of the escapes from Nsp1-directed translational repression and thereby enhance protein expressions. • Systematic mutagenesis identified optimized 5'UTRs that strongly enhance protein expression and promote resistance to Nsp1-induced translational repression and RNA degradation.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, New Taipei, Taiwan
| | - Cui-Ting Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan-Fu Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yu Chao
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Chi Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Wen Fu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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5
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Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Microorganisms 2023; 11:microorganisms11020445. [PMID: 36838410 PMCID: PMC9961755 DOI: 10.3390/microorganisms11020445] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.
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Affiliation(s)
- Cameron M. Harrison
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Jayden M. Doster
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Emily H. Landwehr
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Nidhi P. Kumar
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Ethan J. White
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Dia C. Beachboard
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Christopher C. Stobart
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
- Correspondence:
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6
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Bermudez Y, Miles J, Muller M. Nonstructural protein 1 widespread RNA decay phenotype varies among coronaviruses. iScience 2023; 26:105887. [PMID: 36590901 PMCID: PMC9794394 DOI: 10.1016/j.isci.2022.105887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/15/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Extensive remodeling of host gene expression by nonstructural protein 1 (nsp1) of coronaviruses is a well-documented and conserved aspect of coronavirus-host takeover. Using comparative transcriptomics we investigated the diversity of transcriptional targets between various nsp1 proteins. Additionally, affinity purification followed by mass spectrometry was implemented to identify common interactors between the different nsp1 proteins. Although we detected widespread RNA destabilization, closely related nsp1 showed little similarities in clustering of targeted genes. We observed a partial overlap in transcriptional targeting between α-CoV 229E and MERS nsp1, which may suggest a common targeting mechanism, as MERS nsp1 preferentially targets nuclear transcripts. Our interactome data show great variability between nsp1 interactions, with 229E nsp1, the smallest nsp1 tested here, interacting with the most number of host proteins. Although nsp1 is a rather well-conserved protein with conserved functions across different coronaviruses, our data indicate that its precise effects on the host cell are virus specific.
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Affiliation(s)
- Yahaira Bermudez
- Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant street, Morrill IV North, MA 01003 USA
| | - Jacob Miles
- Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant street, Morrill IV North, MA 01003 USA
| | - Mandy Muller
- Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant street, Morrill IV North, MA 01003 USA,Corresponding author
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Single-cell RNA-sequencing data analysis reveals a highly correlated triphasic transcriptional response to SARS-CoV-2 infection. Commun Biol 2022; 5:1302. [PMID: 36435849 PMCID: PMC9701238 DOI: 10.1038/s42003-022-04253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is currently one of the most powerful techniques available to study the transcriptional response of thousands of cells to an external perturbation. Here, we perform a pseudotime analysis of SARS-CoV-2 infection using publicly available scRNA-seq data from human bronchial epithelial cells and colon and ileum organoids. Our results reveal that, for most genes, the transcriptional response to SARS-CoV-2 infection follows a non-linear pattern characterized by an initial and a final down-regulatory phase separated by an intermediate up-regulatory stage. A correlation analysis of transcriptional profiles suggests a common mechanism regulating the mRNA levels of most genes. Interestingly, genes encoded in the mitochondria or involved in translation exhibited distinct pseudotime profiles. To explain our results, we propose a simple model where nuclear export inhibition of nsp1-sensitive transcripts will be sufficient to explain the transcriptional shutdown of SARS-CoV-2 infected cells.
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8
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Abstract
Many viruses induce shutoff of host gene expression (host shutoff) as a strategy to take over cellular machinery and evade host immunity. Without host shutoff activity, these viruses generally replicate poorly in vivo, attesting to the importance of this antiviral strategy. In this review, we discuss one particularly advantageous way for viruses to induce host shutoff: triggering widespread host messenger RNA (mRNA) decay. Viruses can trigger increased mRNA destruction either directly, by encoding RNA cleaving or decapping enzymes, or indirectly, by activating cellular RNA degradation pathways. We review what is known about the mechanism of action of several viral RNA degradation factors. We then discuss the consequences of widespread RNA degradation on host gene expression and on the mechanisms of immune evasion, highlighting open questions. Answering these questions is critical to understanding how viral RNA degradation factors regulate host gene expression and how this process helps viruses evade host responses and replicate.
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Affiliation(s)
- Léa Gaucherand
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Graduate Program in Molecular Microbiology, Tufts Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA;
| | - Marta Maria Gaglia
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Graduate Program in Molecular Microbiology, Tufts Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA;
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9
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Mutations in Porcine Epidemic Diarrhea Virus nsp1 Cause Increased Viral Sensitivity to Host Interferon Responses and Attenuation In Vivo. J Virol 2022; 96:e0046922. [PMID: 35583324 DOI: 10.1128/jvi.00469-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Coronavirus (CoV) nonstructural protein 1 (nsp1) inhibits cellular gene expression and antagonizes interferon (IFN) response. Porcine epidemic diarrhea virus (PEDV) infects pigs and causes high mortality in neonatal piglets. We hypothesized that a recombinant PEDV carrying mutations at the conserved residues N93 and N95 of nsp1 induces higher IFN responses and is more sensitive to IFN responses, leading to virus attenuation. We mutated PEDV nsp1 N93 and N95 to A93 and A95 to generate the recombinant N93/95A virus using the infectious clone of a highly virulent PEDV strain, PC22A (icPC22A), and evaluated N93/95A virus in vitro and in vivo. Compared with icPC22A, the N93/95A mutant replicated to significantly lower infectious titers, triggered stronger type I and III IFN responses, and was more sensitive to IFN treatment in vitro. To evaluate the pathogenicity and immunogenicity, 5-day-old gnotobiotic piglets were orally inoculated with the N93/95A or icPC22A strain or mock inoculated and then challenged at 22 days postinoculation (dpi) with icPC22A. icPC22A in all pigs (100% [5/5]) caused severe diarrhea and death within 6 dpi. Only one pig (25% [1/4]) died in the N93/95A group. Compared with the icPC22A group, significantly delayed and diminished fecal PEDV shedding was detected in the N93/95A group. Postchallenge, all piglets in N93/95A group were protected from severe diarrhea and death, whereas all pigs in the mock-challenged group developed severe diarrhea, and 25% (1/4) of them died. In summary, nsp1 N93A and N95A mutations attenuated PEDV but retained viral immunogenicity and can be targets for the development of live attenuated vaccines for PEDV. IMPORTANCE PEDV causes porcine epidemic diarrhea (PED) and remains a great threat to the swine industry worldwide because no effective vaccines are available yet. Safe and effective live attenuated vaccines can be designed using reverse genetics to induce lactogenic immunity in pregnant sows to protect piglets from the deadly PED. We found that an engineered PEDV mutant carrying N93A and N95A mutations of nsp1 was partially attenuated and remained immunogenic in neonatal pigs. Our study suggested that nsp1 N93 and N95 can be good targets for the rational design of live attenuated vaccines for PEDV using reverse genetics. Because CoV nsp1 is conserved among alphacoronaviruses (α-CoVs) and betacoronaviruses (β-CoVs), it may be a good target for vaccine development for other α-CoVs or β-CoVs.
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10
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Agback P, Agback T, Dominguez F, Frolova EI, Seisenbaeva GA, Kessler VG. Site-specific recognition of SARS-CoV-2 nsp1 protein with a tailored titanium dioxide nanoparticle - elucidation of the complex structure using NMR data and theoretical calculation. NANOSCALE ADVANCES 2022; 4:1527-1532. [PMID: 36134379 PMCID: PMC9419012 DOI: 10.1039/d1na00855b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/16/2023]
Abstract
The ongoing world-wide Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) pandemic shows the need for new potential sensing and therapeutic means against the CoV viruses. The SARS-CoV-2 nsp1 protein is important, both for replication and pathogenesis, making it an attractive target for intervention. In this study we investigated the interaction of this protein with two types of titania nanoparticles by NMR and discovered that while lactate capped particles essentially did not interact with the protein chain, the aminoalcohol-capped ones showed strong complexation with a distinct part of an ordered α-helix fragment. The structure of the forming complex was elucidated based on NMR data and theoretical calculation. To the best of our knowledge, this is the first time that a tailored titanium oxide nanoparticle was shown to interact specifically with a unique site of the full-length SARS-CoV-2 nsp1 protein, possibly interfering with its functionality.
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
| | - Francisco Dominguez
- Department of Microbiology, University of Alabama at Birmingham 1720 2nd Ave South Birmingham AL 35294 USA
| | - Elena I Frolova
- Department of Microbiology, University of Alabama at Birmingham 1720 2nd Ave South Birmingham AL 35294 USA
| | - Gulaim A Seisenbaeva
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
| | - Vadim G Kessler
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
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11
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Agback T, Dominguez F, Frolov I, Frolova EI, Agback P. 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. PLoS One 2021; 16:e0251834. [PMID: 34874953 PMCID: PMC8651119 DOI: 10.1371/journal.pone.0251834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022] Open
Abstract
Structural characterization of the SARS-CoV-2 full length nsp1 protein will be an essential tool for developing new target-directed antiviral drugs against SARS-CoV-2 and for further understanding of intra- and intermolecular interactions of this protein. As a first step in the NMR studies of the protein, we report the 1H, 13C and 15N resonance backbone assignment as well as the Cβ of the apo form of the full-lengthSARS-CoV-2 nsp1 including the folded domain together with the flaking N- and C- terminal intrinsically disordered fragments. The 19.8 kD protein was characterized by high-resolution NMR. Validation of assignment have been done by using two different mutants, H81P and K129E/D48E as well as by amino acid specific experiments. According to the obtained assignment, the secondary structure of the folded domain in solution was almost identical to its previously published X-ray structure as well as another published secondary structure obtained by NMR, but some discrepancies have been detected. In the solution SARS-CoV-2 nsp1 exhibited disordered, flexible N- and C-termini with different dynamic characteristics. The short peptide in the beginning of the disordered C-terminal domain adopted two different conformations distinguishable on the NMR time scale. We propose that the disordered and folded nsp1 domains are not fully independent units but are rather involved in intramolecular interactions. Studies of the structure and dynamics of the SARS-CoV-2 mutant in solution are on-going and will provide important insights into the molecular mechanisms underlying these interactions.
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Affiliation(s)
- Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Francisco Dominguez
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Elena I. Frolova
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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12
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Yuan S, Balaji S, Lomakin IB, Xiong Y. Coronavirus Nsp1: Immune Response Suppression and Protein Expression Inhibition. Front Microbiol 2021; 12:752214. [PMID: 34659188 PMCID: PMC8512706 DOI: 10.3389/fmicb.2021.752214] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 12/30/2022] Open
Abstract
Coronaviruses have brought severe challenges to public health all over the world in the past 20years. SARS-CoV-2, the causative agent of the COVID-19 pandemic that has led to millions of deaths, belongs to the genus beta-coronavirus. Alpha- and beta-coronaviruses encode a unique protein, nonstructural protein 1 (Nsp1) that both suppresses host immune responses and reduces global gene expression levels in the host cells. As a key pathogenicity factor of coronaviruses, Nsp1 redirects the host translation machinery to increase synthesis of viral proteins. Through multiple mechanisms, coronaviruses impede host protein expression through Nsp1, while escaping inhibition to allow the translation of viral RNA. In this review, we discuss current data about suppression of the immune responses and inhibition of protein synthesis induced by coronavirus Nsp1, as well as the prospect of live-attenuated vaccine development with virulence-attenuated viruses with mutations in Nsp1.
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Shravani Balaji
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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Rao S, Hoskins I, Tonn T, Garcia PD, Ozadam H, Sarinay Cenik E, Cenik C. Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. RNA (NEW YORK, N.Y.) 2021; 27:1025-1045. [PMID: 34127534 PMCID: PMC8370740 DOI: 10.1261/rna.078661.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/08/2021] [Indexed: 05/05/2023]
Abstract
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a nonstructural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation levels. We discover that a functionally coherent subset of human genes is preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5' terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5' UTRs from TOP transcripts can drive preferential expression in the presence of Nsp1. Finally, we found that LARP1, a key effector protein in the mTOR pathway, may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine-tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
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Affiliation(s)
- Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - P Daniela Garcia
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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14
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Agback P, Agback T, Dominguez F, Frolova EI, Seisenbaeva G, Kessler V. Site-specific recognition of SARS-CoV-2 nsp1 protein with a tailored titanium dioxide nanoparticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.27.453834. [PMID: 34341791 PMCID: PMC8328058 DOI: 10.1101/2021.07.27.453834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ongoing world-wide Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) pandemic shows the need for new sensing and therapeutic means against the CoV viruses. The SARS-CoV-2 nsp1 protein is important, both for replication and pathogenesis, making it an attractive target for intervention. In recent years nanoparticles have been shown to interact with peptides, ranging in size from single amino acids up to proteins. These nanoparticles can be tailor-made with specific functions and properties including bioavailability. To the best of our knowledge, in this study we show for the first time that a tailored titanium oxide nanoparticle interacts specifically with a unique site of the full-length SARS-CoV-2 nsp1 protein. This can be developed potentially into a tool for selective control of viral protein functions.
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Affiliation(s)
- P Agback
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - T Agback
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - F Dominguez
- Department of Microbiology, University of Alabama at Birmingham, 1720 2nd Ave South Birmingham, AL 35294, USA
| | - E I Frolova
- Department of Microbiology, University of Alabama at Birmingham, 1720 2nd Ave South Birmingham, AL 35294, USA
| | - G Seisenbaeva
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - V Kessler
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
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15
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Karasik A, Jones GD, DePass AV, Guydosh NR. Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences. Nucleic Acids Res 2021; 49:6007-6026. [PMID: 33556964 DOI: 10.1093/nar/gkab036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 02/03/2021] [Indexed: 11/15/2022] Open
Abstract
Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5' and 3' UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L's cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.
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Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grant D Jones
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Rao S, Hoskins I, Tonn T, Garcia PD, Ozadam H, Cenik ES, Cenik C. Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.09.13.295493. [PMID: 32995776 PMCID: PMC7523102 DOI: 10.1101/2020.09.13.295493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5' terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5' UTRs from TOP transcripts can drive preferential expression in the presence of NSP1. Finally, we found that LARP1, a key effector protein in the mTOR pathway may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
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Affiliation(s)
- Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - P. Daniela Garcia
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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17
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Merino GA, Raad J, Bugnon LA, Yones C, Kamenetzky L, Claus J, Ariel F, Milone DH, Stegmayer G. Novel SARS-CoV-2 encoded small RNAs in the passage to humans. Bioinformatics 2021; 36:5571-5581. [PMID: 33244583 PMCID: PMC7717134 DOI: 10.1093/bioinformatics/btaa1002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Motivation The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease (COVID-19). This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. Results We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprogramming of the new host upon infection.
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Affiliation(s)
- Gabriela A Merino
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina.,Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET, Entre Ríos 3100, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire CB101SD, UK
| | - Jonathan Raad
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Leandro A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, UBA-CONICET, Ciudad Autónoma de Buenos Aires 1121, Argentina.,Laboratorio de Genómica y Bioinformática de Patógenos, iB3, Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Juan Claus
- Laboratorio de Virología, FBCB, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
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18
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Agranovsky AA. Structure and Expression of Large (+)RNA Genomes of Viruses of Higher Eukaryotes. BIOCHEMISTRY (MOSCOW) 2021; 86:248-261. [PMID: 33838627 PMCID: PMC7772802 DOI: 10.1134/s0006297921030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Viral positive-sense RNA genomes evolve rapidly due to the high mutation rates during replication and RNA recombination, which allowing the viruses to acquire and modify genes for their adaptation. The size of RNA genome is limited by several factors, including low fidelity of RNA polymerases and packaging constraints. However, the 12-kb size limit is exceeded in the two groups of eukaryotic (+)RNA viruses – animal nidoviruses and plant closteroviruses. These virus groups have several traits in common. Their genomes contain 5′-proximal genes that are expressed via ribosomal frameshifting and encode one or two papain-like protease domains, membrane-binding domain(s), methyltransferase, RNA helicase, and RNA polymerase. In addition, some nidoviruses (i.e., coronaviruses) contain replication-associated domains, such as proofreading exonuclease, putative primase, nucleotidyltransferase, and endonuclease. In both nidoviruses and closteroviruses, the 3′-terminal part of the genome contains genes for structural and accessory proteins expressed via a nested set of coterminal subgenomic RNAs. Coronaviruses and closteroviruses have evolved to form flexuous helically symmetrical nucleocapsids as a mean to resolve packaging constraints. Since phylogenetic reconstructions of the RNA polymerase domains indicate only a marginal relationship between the nidoviruses and closteroviruses, their similar properties likely have evolved convergently, along with the increase in the genome size.
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Affiliation(s)
- Alexey A Agranovsky
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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19
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Nakagawa K, Makino S. Mechanisms of Coronavirus Nsp1-Mediated Control of Host and Viral Gene Expression. Cells 2021; 10:cells10020300. [PMID: 33540583 PMCID: PMC7912902 DOI: 10.3390/cells10020300] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022] Open
Abstract
Many viruses disrupt host gene expression by degrading host mRNAs and/or manipulating translation activities to create a cellular environment favorable for viral replication. Often, virus-induced suppression of host gene expression, including those involved in antiviral responses, contributes to viral pathogenicity. Accordingly, clarifying the mechanisms of virus-induced disruption of host gene expression is important for understanding virus–host cell interactions and virus pathogenesis. Three highly pathogenic human coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, and SARS-CoV-2, have emerged in the past two decades. All of them encode nonstructural protein 1 (nsp1) in their genomes. Nsp1 of SARS-CoV and MERS-CoV exhibit common biological functions for inducing endonucleolytic cleavage of host mRNAs and inhibition of host translation, while viral mRNAs evade the nsp1-induced mRNA cleavage. SARS-CoV nsp1 is a major pathogenic determinant for this virus, supporting the notion that a viral protein that suppresses host gene expression can be a virulence factor, and further suggesting the possibility that SARS-CoV-2 nsp1, which has high amino acid identity with SARS-CoV nsp1, may serve as a major virulence factor. This review summarizes the gene expression suppression functions of nsp1 of CoVs, with a primary focus on SARS-CoV nsp1 and MERS-CoV nsp1.
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Affiliation(s)
- Keisuke Nakagawa
- Laboratory of Veterinary Microbiology, Joint Department of Veterinary Medicine, Gifu University, Gifu 501-1193, Japan;
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- UTMB Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Sealy Center for Vaccine Development, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Correspondence: ; Tel.: +1-409-772-2323
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20
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Wong NA, Saier MH. The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. Int J Mol Sci 2021; 22:1308. [PMID: 33525632 PMCID: PMC7865831 DOI: 10.3390/ijms22031308] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID-19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps and parallels in function, focusing primarily on the transmembrane proteins and their influences on host membrane arrangements, secretory pathways, cellular growth inhibition, cell death and immune responses during the viral replication cycle. We also offer bioinformatic analyses of potential viroporin activities of the membrane proteins and their sequence similarities to the Envelope (E) protein. In the last major part of the review, we discuss complement, stimulation of inflammation, and immune evasion/suppression that leads to CoV-derived severe disease and mortality. The overall pathogenesis and disease progression of CoVs is put into perspective by indicating several stages in the resulting infection process in which both host and antiviral therapies could be targeted to block the viral cycle. Lastly, we discuss the development of adaptive immunity against various structural proteins, indicating specific vulnerable regions in the proteins. We discuss current CoV vaccine development approaches with purified proteins, attenuated viruses and DNA vaccines.
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Affiliation(s)
- Nicholas A. Wong
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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21
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Rabaan AA, Al-Ahmed SH, Sah R, Alqumber MA, Haque S, Patel SK, Pathak M, Tiwari R, Yatoo MI, Haq AU, Bilal M, Dhama K, Rodriguez-Morales AJ. MERS-CoV: epidemiology, molecular dynamics, therapeutics, and future challenges. Ann Clin Microbiol Antimicrob 2021; 20:8. [PMID: 33461573 PMCID: PMC7812981 DOI: 10.1186/s12941-020-00414-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
| | - Mohammed A Alqumber
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shuhama, Alusteng Srinagar, Shalimar, Srinagar, Jammu and Kashmir, 190006, India
| | - Abrar Ul Haq
- Division of Clinical Veterinary Medicine Ethics & Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Sher E Kashmir University of Agricultural Sciences and Technology, Kashmir, Shuhama, Srinagar, 190006, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India.
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia. .,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia. .,School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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22
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de Breyne S, Vindry C, Guillin O, Condé L, Mure F, Gruffat H, Chavatte L, Ohlmann T. Translational control of coronaviruses. Nucleic Acids Res 2020; 48:12502-12522. [PMID: 33264393 PMCID: PMC7736815 DOI: 10.1093/nar/gkaa1116] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.
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Affiliation(s)
- Sylvain de Breyne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Caroline Vindry
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Olivia Guillin
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Lionel Condé
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Fabrice Mure
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Henri Gruffat
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Laurent Chavatte
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Théophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007, Lyon, France
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23
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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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24
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Alexander SP, Armstrong JF, Davenport AP, Davies JA, Faccenda E, Harding SD, Levi‐Schaffer F, Maguire JJ, Pawson AJ, Southan C, Spedding M. A rational roadmap for SARS-CoV-2/COVID-19 pharmacotherapeutic research and development: IUPHAR Review 29. Br J Pharmacol 2020; 177:4942-4966. [PMID: 32358833 PMCID: PMC7267163 DOI: 10.1111/bph.15094] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
In this review, we identify opportunities for drug discovery in the treatment of COVID-19 and, in so doing, provide a rational roadmap whereby pharmacology and pharmacologists can mitigate against the global pandemic. We assess the scope for targeting key host and viral targets in the mid-term, by first screening these targets against drugs already licensed, an agenda for drug repurposing, which should allow rapid translation to clinical trials. A simultaneous, multi-pronged approach using conventional drug discovery methods aimed at discovering novel chemical and biological means of targeting a short list of host and viral entities which should extend the arsenal of anti-SARS-CoV-2 agents. This longer term strategy would provide a deeper pool of drug choices for future-proofing against acquired drug resistance. Second, there will be further viral threats, which will inevitably evade existing vaccines. This will require a coherent therapeutic strategy which pharmacology and pharmacologists are best placed to provide. LINKED ARTICLES: This article is part of a themed issue on The Pharmacology of COVID-19. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.21/issuetoc.
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Affiliation(s)
- Steve P.H. Alexander
- Chair, Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC‐IUPHAR), School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Jane F. Armstrong
- Curator, Guide to PHARMACOLOGY (GtoPdb), Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | | | - Jamie A. Davies
- Principal Investigator, Guide to PHARMACOLOGY (GtoPdb), Executive Committee, NC‐IUPHAR, Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Elena Faccenda
- Curator, Guide to PHARMACOLOGY (GtoPdb), Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Simon D. Harding
- Database Developer, Guide to PHARMACOLOGY (GtoPdb), Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Francesca Levi‐Schaffer
- First Vice‐President and Chair of Immunopharmacology Section, International Union of Basic and Clinical Pharmacology (IUPHAR)Hebrew University of JerusalemJerusalemIsrael
| | | | - Adam J. Pawson
- Senior Curator, Guide to PHARMACOLOGY (GtoPdb), Executive Committee, NC‐IUPHAR, Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Christopher Southan
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
- TW2Informatics LtdGothenburgSweden
| | - Michael Spedding
- Secretary‐General, International Union of Basic and Clinical Pharmacology (IUPHAR) and Spedding Research Solutions SASLe VesinetFrance
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25
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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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26
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Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PLoS Biol 2020; 18:e3000849. [PMID: 32898168 PMCID: PMC7478592 DOI: 10.1371/journal.pbio.3000849] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/05/2020] [Indexed: 01/12/2023] Open
Abstract
Despite limited genomic diversity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA sequencing profiles of nasopharyngeal (NP) swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with up-regulation of antiviral factors such as OAS1-3 and IFIT1-3 and T helper type 1 (Th1) chemokines CXCL9/10/11, as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial (HAE) cultures replicated the in vivo antiviral host response 7 days post infection, with no induction of interferon-stimulated genes after 3 days. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2, increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of the Th1 chemokines CXCL9/10/11 and their cognate receptor CXCR3, as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B cell-specific and NK cell-specific transcripts and an increase in inhibitors of nuclear factor kappa-B (NF-κB) signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Vikas Peddu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Megan C. Mears
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maria N. Cajimat
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dennis A. Bente
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Francesca Bovier
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anne Moscona
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York, United States of America
- Department of Physiology & Cellular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - Matteo Porotto
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Columbia University Medical Center, New York, New York, United States of America
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” Caserta, Italy
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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27
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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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28
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de Lima Menezes G, da Silva RA. Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1). J Biomol Struct Dyn 2020; 39:5657-5667. [PMID: 32657643 PMCID: PMC7443570 DOI: 10.1080/07391102.2020.1792992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Non-structural protein 1 (nsp1) is found in all Betacoronavirus genus, an important viral group that causes severe respiratory
human diseases. This protein has significant role in pathogenesis and it is considered a
probably major virulence factor. As it is absent in humans, it becomes an interesting
target of study, especially when it comes to the rational search for drugs, since it
increases the specificity of the target and reduces possible adverse effects that may be
caused to the patient. Using approaches in silico we seek to
study the behavior of nsp1 in solution to obtain its most stable conformation and find
possible drugs with affinity to all of them. For this purpose, complete model of nsp1 of
SARS-CoV-2 were predicted and its stability analyzed by molecular dynamics simulations in
five different replicas. After main pocket validation using two control drugs and the main
conformations of nsp1, molecular docking based on virtual screening were performed to
identify novel potential inhibitors from DrugBank database. It has been found 16 molecules
in common to all five nsp1 replica conformations. Three of them was ranked as the best
compounds among them and showed better energy score than control molecules that have
in vitro activity against nsp1 from SARS-CoV-2. The
results pointed out here suggest new potential drugs for therapy to aid the rational drug
search against COVID-19. Communicated by Ramaswamy H. Sarma
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29
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Maranon DG, Anderson JR, Maranon AG, Wilusz J. The interface between coronaviruses and host cell RNA biology: Novel potential insights for future therapeutic intervention. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1614. [PMID: 32638509 PMCID: PMC7361139 DOI: 10.1002/wrna.1614] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022]
Abstract
Coronaviruses, including SARS-Cov-2, are RNA-based pathogens that interface with a large variety of RNA-related cellular processes during infection. These processes include capping, polyadenylation, localization, RNA stability, translation, and regulation by RNA binding proteins or noncoding RNA effectors. The goal of this article is to provide an in-depth perspective on the current state of knowledge of how various coronaviruses interact with, usurp, and/or avoid aspects of these cellular RNA biology machineries. A thorough understanding of how coronaviruses interact with RNA-related posttranscriptional processes in the cell should allow for new insights into aspects of viral pathogenesis as well as identify new potential avenues for the development of anti-coronaviral therapeutics. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- David G Maranon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Abril G Maranon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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30
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Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165225. [PMID: 32607510 PMCID: PMC7325176 DOI: 10.1101/2020.06.22.165225] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Despite limited genomic diversity, SARS-CoV-2 has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with upregulation of antiviral factors such as OAS1-3 and IFIT1-3 , and Th1 chemokines CXCL9/10/11 , as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial cultures replicated the in vivo antiviral host response. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2 , increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of Th1 chemokines CXCL9/10/11 and their cognate receptor, CXCR3 , as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B and NK cell-specific transcripts and an increase in inhibitors of NF-κB signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
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31
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Chen B, Tian EK, He B, Tian L, Han R, Wang S, Xiang Q, Zhang S, El Arnaout T, Cheng W. Overview of lethal human coronaviruses. Signal Transduct Target Ther 2020; 5:89. [PMID: 32533062 PMCID: PMC7289715 DOI: 10.1038/s41392-020-0190-2] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 02/05/2023] Open
Abstract
Coronavirus infections of multiple origins have spread to date worldwide, causing severe respiratory diseases. Seven coronaviruses that infect humans have been identified: HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2. Among them, SARS-CoV and MERS-CoV caused outbreaks in 2002 and 2012, respectively. SARS-CoV-2 (COVID-19) is the most recently discovered. It has created a severe worldwide outbreak beginning in late 2019, leading to date to over 4 million cases globally. Viruses are genetically simple, yet highly diverse. However, the recent outbreaks of SARS-CoV and MERS-CoV, and the ongoing outbreak of SARS-CoV-2, indicate that there remains a long way to go to identify and develop specific therapeutic treatments. Only after gaining a better understanding of their pathogenic mechanisms can we minimize viral pandemics. This paper mainly focuses on SARS-CoV, MERS-CoV, and SARS-CoV-2. Here, recent studies are summarized and reviewed, with a focus on virus-host interactions, vaccine-based and drug-targeted therapies, and the development of new approaches for clinical diagnosis and treatment.
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Affiliation(s)
- Bin Chen
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Er-Kang Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lejin Tian
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ruiying Han
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Shuangwen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qianrong Xiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Shu Zhang
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | | | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China.
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32
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[Basis of coronavirus infection, and SARS-CoV-2]. Uirusu 2020; 70:155-166. [PMID: 34544930 DOI: 10.2222/jsv.70.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Choudhry H, Bakhrebah MA, Abdulaal WH, Zamzami MA, Baothman OA, Hassan MA, Zeyadi M, Helmi N, Alzahrani F, Ali A, Zakaria MK, Kamal MA, Warsi MK, Ahmed F, Rasool M, Jamal MS. Middle East respiratory syndrome: pathogenesis and therapeutic developments. Future Virol 2019; 14:237-246. [PMID: 32201499 PMCID: PMC7080179 DOI: 10.2217/fvl-2018-0201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/15/2019] [Indexed: 12/13/2022]
Abstract
The first case of Middle East respiratory syndrome coronavirus (MERS-CoV) was identified in the year 2012, which spread rapidly and increased to more than 2200 in 2018. This highly pathogenic virus with high mortality rate is among one of the major public health concerns. Saudi Arabia remains to be the most affected region with the majority of MERS-CoV cases, and currently, no effective drugs and vaccines are available for prevention and treatment. A large amount of information is now available regarding the virus, its structure, route of transmission and its pathophysiology. Therefore, this review summarizes the current understanding of MERS-CoV's pathogenesis, treatment options and recent scientific advancements in vaccine and other therapeutic developments, and the major steps taken for MERS prevention control.
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Affiliation(s)
- Hani Choudhry
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammed A Bakhrebah
- Life Science & environment Research Institute, National Center for Genome Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12371, Saudi Arabia.,Life Science & environment Research Institute, National Center for Genome Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12371, Saudi Arabia
| | - Wesam H Abdulaal
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Othman A Baothman
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed A Hassan
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Basic Medical Sciences, College of Medicine & Health Sciences, Hadhramout University, Yemen.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Basic Medical Sciences, College of Medicine & Health Sciences, Hadhramout University, Yemen
| | - Mustafa Zeyadi
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Nawal Helmi
- Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Biochemistry, Cancer Metabolism & Epigenetic Unit, Faculty of Science, Cancer & Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Faisal Alzahrani
- Hematology Lab Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Hematology Lab Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ashraf Ali
- Hematology Lab Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Science of Agriculture, Food and Environment (SAFE), University of Foggia, Via Napoli, 25 - 71122, Foggia, Italy.,Hematology Lab Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Science of Agriculture, Food and Environment (SAFE), University of Foggia, Via Napoli, 25 - 71122, Foggia, Italy
| | - Mohammad Khalid Zakaria
- The Pirbright Institute, Ash Road, GU240NF, Surrey, United Kingdom.,The Pirbright Institute, Ash Road, GU240NF, Surrey, United Kingdom
| | - Mohammad Azhar Kamal
- Department of Biochemistry, University of Jeddah, Jeddah 23890, Saudi Arabia.,Department of Biochemistry, University of Jeddah, Jeddah 23890, Saudi Arabia
| | - Mohiuddin Khan Warsi
- The Pirbright Institute, Ash Road, GU240NF, Surrey, United Kingdom.,The Pirbright Institute, Ash Road, GU240NF, Surrey, United Kingdom
| | - Firoz Ahmed
- The Pirbright Institute, Ash Road, GU240NF, Surrey, United Kingdom.,The Pirbright Institute, Ash Road, GU240NF, Surrey, United Kingdom
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Sarwar Jamal
- Hematology Lab Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Hematology Lab Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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34
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Widagdo W, Sooksawasdi Na Ayudhya S, Hundie GB, Haagmans BL. Host Determinants of MERS-CoV Transmission and Pathogenesis. Viruses 2019; 11:E280. [PMID: 30893947 PMCID: PMC6466079 DOI: 10.3390/v11030280] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 01/01/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen that causes respiratory infection in humans, ranging from asymptomatic to severe pneumonia. In dromedary camels, the virus only causes a mild infection but it spreads efficiently between animals. Differences in the behavior of the virus observed between individuals, as well as between humans and dromedary camels, highlight the role of host factors in MERS-CoV pathogenesis and transmission. One of these host factors, the MERS-CoV receptor dipeptidyl peptidase-4 (DPP4), may be a critical determinant because it is variably expressed in MERS-CoV-susceptible species as well as in humans. This could partially explain inter- and intraspecies differences in the tropism, pathogenesis, and transmissibility of MERS-CoV. In this review, we explore the role of DPP4 and other host factors in MERS-CoV transmission and pathogenesis-such as sialic acids, host proteases, and interferons. Further characterization of these host determinants may potentially offer novel insights to develop intervention strategies to tackle ongoing outbreaks.
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Affiliation(s)
- W Widagdo
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| | | | - Gadissa B Hundie
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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35
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Zhou Y, Yang Y, Huang J, Jiang S, Du L. Advances in MERS-CoV Vaccines and Therapeutics Based on the Receptor-Binding Domain. Viruses 2019; 11:v11010060. [PMID: 30646569 PMCID: PMC6357101 DOI: 10.3390/v11010060] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 12/28/2022] Open
Abstract
Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) is an infectious virus that was first reported in 2012. The MERS-CoV genome encodes four major structural proteins, among which the spike (S) protein has a key role in viral infection and pathogenesis. The receptor-binding domain (RBD) of the S protein contains a critical neutralizing domain and is an important target for development of MERS vaccines and therapeutics. In this review, we describe the relevant features of the MERS-CoV S-protein RBD, summarize recent advances in the development of MERS-CoV RBD-based vaccines and therapeutic antibodies, and illustrate potential challenges and strategies to further improve their efficacy.
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Affiliation(s)
- Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.
| | - Yang Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Jingwei Huang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
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