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Deshmukh R, Harwansh RK, Garg A, Mishra S, Agrawal R, Jangde R. COVID-19: Recent Insight in Genomic Feature, Pathogenesis, Immunological Biomarkers, Treatment Options and Clinical Updates on SARS-CoV-2. Curr Genomics 2024; 25:69-87. [PMID: 38751601 PMCID: PMC11092912 DOI: 10.2174/0113892029291098240129113500] [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: 12/04/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 05/18/2024] Open
Abstract
SARS-CoV-2 is a highly contagious and transmissible viral infection that first emerged in 2019 and since then has sparked an epidemic of severe respiratory problems identified as "coronavirus disease 2019" (COVID-19) that causes a hazard to human life and safety. The virus developed mainly from bats. The current epidemic has presented a significant warning to life across the world by showing mutation. There are different tests available for testing Coronavirus, and RT-PCR is the best, giving more accurate results, but it is also time-consuming. There are different options available for treating n-CoV-19, which include medications such as Remdesivir, corticosteroids, plasma therapy, Dexamethasone therapy, etc. The development of vaccines such as BNT126b2, ChAdOX1, mRNA-1273 and BBIBP-CorV has provided great relief in dealing with the virus as they decreased the mortality rate. BNT126b2 and ChAdOX1 are two n-CoV vaccines found to be most effective in controlling the spread of infection. In the future, nanotechnology-based vaccines and immune engineering techniques can be helpful for further research on Coronavirus and treatment of this deadly virus. The existing knowledge about the existence of SARS-CoV-2, along with its variants, is summarized in this review. This review, based on recently published findings, presents the core genetics of COVID-19, including heritable characteristics, pathogenesis, immunological biomarkers, treatment options and clinical updates on the virus, along with patents.
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Affiliation(s)
- Rohitas Deshmukh
- Department of Pharmaceutics, Institute of Pharmaceutical Research, GLA University, Mathura, 281406, Uttar Pradesh, India
| | - Ranjit Kumar Harwansh
- Department of Pharmaceutics, Institute of Pharmaceutical Research, GLA University, Mathura, 281406, Uttar Pradesh, India
| | - Akash Garg
- Department of Pharmaceutics, Rajiv Academy for Pharmacy, NH-2, Mathura, Delhi Road, Chhatikara, 281001, Uttar Pradesh, India
| | - Sakshi Mishra
- Department of Pharmaceutics, Institute of Pharmaceutical Research, GLA University, Mathura, 281406, Uttar Pradesh, India
| | - Rutvi Agrawal
- Department of Pharmaceutics, Rajiv Academy for Pharmacy, NH-2, Mathura, Delhi Road, Chhatikara, 281001, Uttar Pradesh, India
| | - Rajendra Jangde
- Institute of Pharmacy, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, 492010, India
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Liu W, Huang Z, Xiao J, Wu Y, Xia N, Yuan Q. Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness. Viruses 2024; 16:184. [PMID: 38399960 PMCID: PMC10893260 DOI: 10.3390/v16020184] [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: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Over the last three years, the pandemic of COVID-19 has had a significant impact on people's lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19.
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Affiliation(s)
- Wenhao Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Yangtao Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [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] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
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Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [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: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
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Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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Dhaka P, Singh A, Choudhary S, Peddinti RK, Kumar P, Sharma GK, Tomar S. Mechanistic and thermodynamic characterization of antiviral inhibitors targeting nucleocapsid N-terminal domain of SARS-CoV-2. Arch Biochem Biophys 2023; 750:109820. [PMID: 37956938 DOI: 10.1016/j.abb.2023.109820] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 plays a pivotal role in encapsulating the viral genome. Developing antiviral treatments for SARS-CoV-2 is imperative due to the diminishing immunity of the available vaccines. This study targets the RNA-binding site located in the N-terminal domain (NTD) of the N-protein to identify the potential antiviral molecules against SARS-CoV-2. A structure-based repurposing approach identified the twelve high-affinity molecules from FDA-approved drugs, natural products, and the LOPAC1280 compound libraries that precisely bind to the RNA binding site within the NTD. The interaction of these potential antiviral agents with the purified NTD protein was thermodynamically characterized using isothermal titration calorimetry (ITC). A fluorescence-based plate assay to assess the RNA binding inhibitory activity of small molecules against the NTD has been employed, and the selected compounds exhibited significant RNA binding inhibition with calculated IC50 values ranging from 8.8 μM to 15.7 μM. Furthermore, the antiviral efficacy of these compounds was evaluated using in vitro cell-based assays targeting the replication of SARS-CoV-2. Remarkably, two compounds, Telmisartan and BMS-189453, displayed potential antiviral activity against SARS-CoV-2, with EC50 values of approximately 1.02 μM and 0.98 μM, and a notable selective index of >98 and > 102, respectively. This study gives valuable insight into developing therapeutic interventions against SARS-CoV-2 by targeting the N-protein, a significant effort given the global public health concern posed due to the virus re-emergence and long COVID-19 disease.
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Affiliation(s)
- Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Rama Krishna Peddinti
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
| | - Gaurav Kumar Sharma
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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Aloise C, Schipper JG, van Vliet A, Oymans J, Donselaar T, Hurdiss DL, de Groot RJ, van Kuppeveld FJM. SARS-CoV-2 nucleocapsid protein inhibits the PKR-mediated integrated stress response through RNA-binding domain N2b. PLoS Pathog 2023; 19:e1011582. [PMID: 37607209 PMCID: PMC10473545 DOI: 10.1371/journal.ppat.1011582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/01/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), purportedly by interacting with stress granule (SG) assembly factors G3BP1 and 2, and inhibits type I interferon responses. To elucidate its mode of action, we systematically deleted and over-expressed distinct regions and domains. We show that N via domain N2b blocks PKR-mediated ISR activation, as measured by suppression of ISR-induced translational arrest and SG formation. N2b mutations that prevent dsRNA binding abrogate these activities also when introduced in the intact N protein. Substitutions reported to block post-translation modifications of N or its interaction with G3BP1/2 did not have a detectable additive effect. In an encephalomyocarditis virus-based infection model, N2b - but not a derivative defective in RNA binding-prevented PKR activation, inhibited β-interferon expression and promoted virus replication. Apparently, SARS-CoV-2 N inhibits innate immunity by sequestering dsRNA to prevent activation of PKR and RIG-I-like receptors. Similar observations were made for the N protein of human coronavirus 229E, suggesting that this may be a general trait conserved among members of other orthocoronavirus (sub)genera.
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Affiliation(s)
- Chiara Aloise
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jelle G. Schipper
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Arno van Vliet
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Judith Oymans
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Tim Donselaar
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniel L. Hurdiss
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Raoul J. de Groot
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J. M. van Kuppeveld
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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Ndiaye MDB, Rasoloharimanana LT, Razafimahatratra SL, Ratovoson R, Rasolofo V, Ranaivomanana P, Raskine L, Hoffmann J, Randremanana R, Rakotosamimanana N, Schoenhals M. Using a multiplex serological assay to estimate time since SARS-CoV-2 infection and past clinical presentation in malagasy patients. Heliyon 2023; 9:e17264. [PMID: 37332901 PMCID: PMC10263216 DOI: 10.1016/j.heliyon.2023.e17264] [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: 05/23/2022] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023] Open
Abstract
Background The world is facing a 2019 coronavirus (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this context, efficient serological assays are needed to accurately describe the humoral responses against the virus. These tools could potentially provide temporal and clinical characteristics and are thus paramount in developing-countries lacking sufficient ongoing COVID-19 epidemic descriptions. Methods We developed and validated a Luminex xMAP® multiplex serological assay targeting specific IgM and IgG antibodies against the SARS-CoV-2 Spike subunit 1 (S1), Spike subunit 2 (S2), Spike Receptor Binding Domain (RBD) and the Nucleocapsid protein (N). Blood samples collected periodically for 12 months from 43 patients diagnosed with COVID-19 in Madagascar were tested for these antibodies. A random forest algorithm was used to build a predictive model of time since infection and symptom presentation. Findings The performance of the multiplex serological assay was evaluated for the detection of SARS-CoV-2 anti-IgG and anti-IgM antibodies. Both sensitivity and specificity were equal to 100% (89.85-100) for S1, RBD and N (S2 had a lower specificity = 95%) for IgG at day 14 after enrolment. This multiplex assay compared with two commercialized ELISA kits, showed a higher sensitivity. Principal Component Analysis was performed on serologic data to group patients according to time of sample collection and clinical presentations. The random forest algorithm built by this approach predicted symptom presentation and time since infection with an accuracy of 87.1% (95% CI = 70.17-96.37, p-value = 0.0016), and 80% (95% CI = 61.43-92.29, p-value = 0.0001) respectively. Interpretation This study demonstrates that the statistical model predicts time since infection and previous symptom presentation using IgM and IgG response to SARS-CoV2. This tool may be useful for global surveillance, discriminating recent- and past- SARS-CoV-2 infection, and assessing disease severity. Fundings This study was funded by the French Ministry for Europe and Foreign Affairs through the REPAIR COVID-19-Africa project coordinated by the Pasteur International Network association. WANTAI reagents were provided by WHO AFRO as part of a Sero-epidemiological "Unity" Study Grant/Award Number: 2020/1,019,828-0 P·O 202546047 and Initiative 5% grant n°AP-5PC-2018-03-RO.
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Affiliation(s)
| | | | | | - Rila Ratovoson
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | | | - Laurent Raskine
- Medical and Scientific Department, Fondation Mérieux, Lyon, France
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Vidal LEL, Figueira-Mansur J, Jurgilas PB, Argondizzo APC, Pestana CP, Martins FO, da Silva Junior HC, Miguez M, Loureiro BO, Marques CDFS, Trinta KS, da Silva LBR, de Mello MB, da Silva ED, Bastos RC, Esteves G. Process development and characterization of recombinant nucleocapsid protein for its application on COVID-19 diagnosis. Protein Expr Purif 2023; 207:106263. [PMID: 36921810 PMCID: PMC10012136 DOI: 10.1016/j.pep.2023.106263] [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: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
COVID-19 pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2). The nucleocapsid (N) protein from Sars-CoV-2 is a highly immunogenic antigen and responsible for genome packing. Serological assays are important tools to detect previous exposure to SARS-CoV-2, complement epidemiological studies, vaccine evaluation and also in COVID-19 surveillance. SARS-CoV-2 N (r2N) protein was produced in Escherichia coli, characterized, and the immunological performance was evaluated by enzyme-linked immunosorbent assay (ELISA) and beads-based array immunoassay. r2N protein oligomers were evidenced when it is associated to nucleic acid. Benzonase treatment reduced host nucleic acid associated to r2N protein, but crosslinking assay still demonstrates the presence of higher-order oligomers. Nevertheless, after RNase treatment the higher-order oligomers reduced, and dimer form increased, suggesting RNA contributes to the oligomer formation. Structural analysis revealed nucleic acid did not interfere with the thermal stability of the recombinant protein. Interestingly, nucleic acid was able to prevent r2N protein aggregation even with increasing temperature while the protein benzonase treated begin aggregation process above 55 °C. In immunological characterization, ELISA performed with 233 serum samples presented a sensitivity of 97.44% (95% Confidence Interval, CI, 91.04%, 99.69%) and a specificity of 98.71% (95% CI, 95.42%, 99.84%) while beads-based array immunoassay carried out with 217 samples showed 100% sensitivity and 98.6% specificity. The results exhibited an excellent immunological performance of r2N protein in serologic assays showing that, even in presence of nucleic acid, it can be used as a component of an immunoassay for the sensitive and specific detection of SARS-CoV-2 antibodies.
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Affiliation(s)
- Luãnna Elisa Liebscher Vidal
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil.
| | - Janaina Figueira-Mansur
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Patrícia Barbosa Jurgilas
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Ana Paula Correa Argondizzo
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Cristiane Pinheiro Pestana
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Fernanda Otaviano Martins
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Haroldo Cid da Silva Junior
- Immunological Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Mariana Miguez
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Bernardo Oliveira Loureiro
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Christiane de Fátima Silva Marques
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Karen Soares Trinta
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Leila Botelho Rodrigues da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Marcelle Bral de Mello
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Edimilson Domingos da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Renata Chagas Bastos
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Gabriela Esteves
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
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Che X, Wu J, Liu H, Su J, Chen X. Cellular liquid-liquid phase separation: Concept, functions, regulations, and detections. J Cell Physiol 2023; 238:847-865. [PMID: 36870067 DOI: 10.1002/jcp.30980] [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: 06/06/2022] [Revised: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023]
Abstract
Liquid-liquid phase separation is a multicomponent system separated into phases with different compositions and structures. It has been identified and explored in organisms after being introduced from the thermodynamic field. Condensate, the product of phase separation, exists in different scales of cellular structures, such as nucleolus, stress granules, and other organelles in nuclei or cytoplasm. And also play critical roles in different cellular behaviors. Here, we review the concept, thermodynamical and biochemical principles of phase separation. We summarized the main functions including the adjustment of biochemical reaction rates, the regulation of macromolecule folding state, subcellular structural support, the mediation of subcellular location, and intimately linked to different kinds of diseases, such as cancer and neurodegeneration. Advanced detection methods to investigate phase separation are collected and analyzed. We conclude with the discussion of anxiety of phase separation, and thought about how progress can be made to develop precise detection methods and disclose the potential application of condensates.
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Affiliation(s)
- Xuanlin Che
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Jiajun Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
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10
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Abstract
The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.
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Key Words
- bcov, bovine coronavirus
- ccov, canine coronavirus
- cov(s), coronavirus(es)
- covid-19, coronavirus disease 2019
- crcov, canine respiratory coronavirus
- e, coronaviral envelope protein
- ecov, equine coronavirus
- fcov, feline coronavirus
- fipv, feline infectious peritonitis virus
- gfcov, guinea fowl coronavirus
- hcov, human coronavirus
- ibv, infectious bronchitis virus
- m, coronaviral membrane protein
- mers, middle east respiratory syndrome-coronavirus
- mhv, mouse hepatitis virus
- pedv, porcine epidemic diarrhea virus
- pdcov, porcine deltacoronavirus
- phcov, pheasant coronavirus
- phev, porcine hemagglutinating encephalomyelitis virus
- prcov, porcine respiratory coronavirus
- rt-pcr, reverse transcriptase polymerase chain reaction
- s, coronaviral spike protein
- sads-cov, swine acute diarrhea syndrome-coronavirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- sars-cov-2, severe acute respiratory syndrome–coronavirus–2
- tcov, turkey coronavirus
- tgev, transmissible gastroenteritis virus
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;,
| | - Tannia S Clark
- Office of Laboratory Animal Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
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11
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Zhou L, Mo C, Yang Y, Zhou Z, You A, Fan Y, Liu W, Li X, Zhou R, Tian X. Characterization and application of a series of monoclonal antibodies against SARS-CoV-2 nucleocapsid protein. J Med Virol 2023; 95:e28225. [PMID: 36238992 PMCID: PMC9874425 DOI: 10.1002/jmv.28225] [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: 06/07/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 01/27/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has a significant global social and economic impact, and the emergence of new and more destructive mutant strains highlights the need for accurate virus detection. Here, 90 monoclonal antibodies (MAbs) that exclusively reacted with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (NP) were generated. These MAbs did not cross-react with NPs of common human coronaviruses (HCoVs, i.e., 229E, OC43, HKU1, and NL63) and Middle East Respiratory Syndrome Coronavirus. Subsequently, overlapped peptides in individual fragments (N1-N4) of NP were synthesized. N1-3 (25-GSNQNGERSGARSKQ-39), N3-1 (217-AALALLLLDRLNQL-230), and N4-8 (393-TLLPAADLDDFSKQL-407) were identified as major epitopes using enzyme-linked immunoassay (ELISA) and recognized by 47, 1, and 18 MAbs, respectively. The 24 remaining MAbs exhibited no reactivity with all synthetic peptides. Among MAb-epitope pairs, only MAbs targeting epitope N1-3 displayed no cross-reaction with NPs of SARS-CoV-1 and other SARS-related CoVs. All Omicron variants contained a three-amino acid deletion (31ERS33) in the N1-3 region. Thus, MAbs targeting N1-3 failed to recognize these variants. Furthermore, a double-antibody sandwich ELISA for antigen detection was established using the optimal MAbs. Overall, a series of MAbs targeting SARS-CoV-2 NP was prepared, characterized with epitope mapping, and applied for the detection of SARS-CoV-2 antigens, and some novel B-cell epitopes of the viral NP were identified.
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Affiliation(s)
- Liling Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Chuncong Mo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
| | - Yujie Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Aiping You
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Ye Fan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Xiao Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina
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12
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Carlson CR, Adly AN, Bi M, Howard CJ, Frost A, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. J Biol Chem 2022; 298:102560. [PMID: 36202211 PMCID: PMC9529352 DOI: 10.1016/j.jbc.2022.102560] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.
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Affiliation(s)
| | - Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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13
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Ning L, Liu M, Gou Y, Yang Y, He B, Huang J. Development and application of ribonucleic acid therapy strategies against COVID-19. Int J Biol Sci 2022; 18:5070-5085. [PMID: 35982905 PMCID: PMC9379410 DOI: 10.7150/ijbs.72706] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/16/2022] [Indexed: 11/17/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2), remaining a global health crisis since its outbreak until now. Advanced biotechnology and research findings have revealed many suitable viral and host targets for a wide range of therapeutic strategies. The emerging ribonucleic acid therapy can modulate gene expression by post-transcriptional gene silencing (PTGS) based on Watson-Crick base pairing. RNA therapies, including antisense oligonucleotides (ASO), ribozymes, RNA interference (RNAi), aptamers, etc., were used to treat SARS-CoV whose genome is similar to SARV-CoV-2, and the past experience also applies for the treatment of COVID-19. Several studies against SARS-CoV-2 based on RNA therapeutic strategy have been reported, and a dozen of relevant preclinical or clinical trials are in process globally. RNA therapy has been a very active and important part of COVID-19 treatment. In this review, we focus on the progress of ribonucleic acid therapeutic strategies development and application, discuss corresponding problems and challenges, and suggest new strategies and solutions.
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Affiliation(s)
- Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Sichuan, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Mujiexin Liu
- Ineye Hospital of Chengdu University of TCM, Sichuan, China
| | - Yushu Gou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Yue Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Bifang He
- Medical College, Guizhou University, Guizhou, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
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14
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Singh VK, Chaurasia H, Mishra R, Srivastava R, Yadav AK, Dwivedi J, Singh P, Singh RK. COVID-19: Pathophysiology, transmission, and drug development for therapeutic treatment and vaccination strategies. Curr Pharm Des 2022; 28:2211-2233. [PMID: 35909276 DOI: 10.2174/1381612828666220729093340] [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: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 11/22/2022]
Abstract
COVID-19, a dreaded and highly contagious pandemic, is flagrantly known for its rapid prevalence across the world. Till date, none of the treatments are distinctly accessible for this life-threatening disease. Under the prevailing conditions of medical emergency, one creative strategy for the identification of novel and potential antiviral agents gaining momentum in research institutions and progressively being leveraged by pharmaceutical companies is target-based drug repositioning/repurposing. A continuous monitoring and recording of results offer an anticipation that this strategy may help to reveal new medications for viral infections. This review recapitulates the neoteric illation of COVID-19, its genomic dispensation, molecular evolution via phylogenetic assessment, drug targets, the most frequently worldwide used repurposed drugs and their therapeutic applications, and a recent update on vaccine management strategies. The available data from solidarity trials exposed that the treatment with several known drugs, viz. lopinavir-ritonavir, chloroquine, hydroxychloroquine, etc had displayed various antagonistic effects along with no impactful result in diminution of mortality rate. The drugs like remdesivir, favipiravir, and ribavirin proved to be quite safer therapeutic options for treatment against COVID-19. Similarly, dexamethasone, convalescent plasma therapy and oral administration of 2DG are expected to reduce the mortality rate of COVID-19 patients.
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Affiliation(s)
- Vishal Kumar Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Himani Chaurasia
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Richa Mishra
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Ritika Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Aditya K Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Jayati Dwivedi
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Prashant Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj- 211002, India
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15
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Andrade SA, Batalha-Carvalho JV, Curi R, Wen FH, Covas DT, Chudzinski-Tavassi AM, Moro AM. Equine Anti-SARS-CoV-2 Serum (ECIG) Binds to Mutated RBDs and N Proteins of Variants of Concern and Inhibits the Binding of RBDs to ACE-2 Receptor. Front Immunol 2022; 13:871874. [PMID: 35898497 PMCID: PMC9310548 DOI: 10.3389/fimmu.2022.871874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID-19 pandemic caused by the severe acute syndrome virus 2 (SARS-CoV-2) has been around since November 2019. As of early June 2022, more than 527 million cases were diagnosed, with more than 6.0 million deaths due to this disease. Coronaviruses accumulate mutations and generate greater diversity through recombination when variants with different mutations infect the same host. Consequently, this virus is predisposed to constant and diverse mutations. The SARS-CoV-2 variants of concern/interest (VOCs/VOIs) such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (B.1.1.28/P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) have quickly spread across the world. These VOCs and VOIs have accumulated mutations within the spike protein receptor-binding domain (RBD) which interacts with the angiotensin-2 converting enzyme (ACE-2) receptor, increasing cell entry and infection. The RBD region is the main target for neutralizing antibodies; however, other notable mutations have been reported to enhance COVID-19 infectivity and lethality. Considering the urgent need for alternative therapies against this virus, an anti-SARS-CoV-2 equine immunoglobulin F(ab’)2, called ECIG, was developed by the Butantan Institute using the whole gamma-irradiated SARS-CoV-2 virus. Surface plasmon resonance experiments revealed that ECIG binds to wild-type and mutated RBD, S1+S2 domains, and nucleocapsid proteins of known VOCs, including Alpha, Gamma, Beta, Delta, Delta Plus, and Omicron. Additionally, it was observed that ECIG attenuates the binding of RBD (wild-type, Beta, and Omicron) to human ACE-2, suggesting that it could prevent viral entry into the host cell. Furthermore, the ability to concomitantly bind to the wild-type and mutated nucleocapsid protein likely enhances its neutralizing activity of SARS-CoV-2. We postulate that ECIG benefits COVID-19 patients by reducing the infectivity of the original virus and existing variants and may be effective against future ones. Impacting the course of the disease, mainly in the more vulnerable, reduces infection time and limits the appearance of new variants by new recombination.
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Affiliation(s)
| | | | - Rui Curi
- Cruzeiro do Sul University, São Paulo, Brazil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | - Fan Hui Wen
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | | | - Ana Marisa Chudzinski-Tavassi
- Center of Excellence in New Target Discovery (CENTD), Instituto Butantan, São Paulo, Brazil
- Innovation and Development Laboratory, Instituto Butantan, São Paulo, Brazil
- *Correspondence: Ana Marisa Chudzinski-Tavassi, ; Ana Maria Moro,
| | - Ana Maria Moro
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo, Brazil
- Center for Research and Development in Immunobiologicals (CeRDI), Instituto Butantan, São Paulo, Brazil
- *Correspondence: Ana Marisa Chudzinski-Tavassi, ; Ana Maria Moro,
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16
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Carlson CR, Adly AN, Bi M, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.23.493138. [PMID: 35664996 PMCID: PMC9164447 DOI: 10.1101/2022.05.23.493138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The nucleocapsid (N) protein of coronaviruses is responsible for compaction of the ∼30-kb RNA genome in the ∼100-nm virion. Cryo-electron tomography suggests that each virion contains 35-40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined with viral RNA fragments in vitro, forms cylindrical 15-nm particles similar to the vRNP structures observed within coronavirus virions. These vRNPs form in the presence of stem-loop-containing RNA and depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine (SR) region weakens these interactions and disrupts vRNP assembly. We propose that unmodified N binds stem-loop-rich regions in genomic RNA to form compact vRNP complexes within the nucleocapsid, while phosphorylated N maintains uncompacted viral RNA to promote the protein's transcriptional function.
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Affiliation(s)
| | - Armin N. Adly
- Department of Physiology, University of California, San Francisco CA 94143
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - David O. Morgan
- Department of Physiology, University of California, San Francisco CA 94143
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17
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Nwagwu CS, Ugwu CN, Ogbonna JDN, Onugwu AL, Agbo CP, Echezona AC, Ezeibe EN, Uzondu S, Kenechukwu FC, Akpa PA, Momoh MA, Nnamani PO, Tarirai C, Ofokansi KC, Attama AA. Recent and advanced nano-technological strategies for COVID-19 vaccine development. METHODS IN MICROBIOLOGY 2022; 50:151-188. [PMID: 38620863 PMCID: PMC9015106 DOI: 10.1016/bs.mim.2022.03.001] [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: 12/15/2022]
Abstract
The outbreak of the COVID-19 pandemic in 2019 has been one of the greatest challenges modern medicine and science has ever faced. It has affected millions of people around the world and altered human life and activities as we once knew. The high prevalence as well as an extended period of incubations which usually does not present with symptoms have played a formidable role in the transmission and infection of millions. A lot of research has been carried out on developing suitable treatment and effective preventive measures for the control of the pandemic. Preventive strategies which include social distancing, use of masks, washing of hands, and contact tracing have been effective in slowing the spread of the virus; however, the infectious nature of the SARS-COV-2 has made these strategies unable to eradicate its spread. In addition, the continuous increase in the number of cases and death, as well as the appearance of several variants of the virus, has necessitated the development of effective and safe vaccines in a bid to ensure that human activities can return to normalcy. Nanotechnology has been of great benefit in the design of vaccines as nano-sized materials have been known to aid the safe and effective delivery of antigens as well as serve as suitable adjuvants to potentiate responses to vaccines. There are only four vaccine candidates currently approved for use in humans while many other candidates are at various levels of development. This review seeks to provide updated information on the current nano-technological strategies employed in the development of COVID-19 vaccines.
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Affiliation(s)
- Chinekwu Sherridan Nwagwu
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chinenye Nnenna Ugwu
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka, Enugu state, Nigeria
| | - John Dike Nwabueze Ogbonna
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Adaeze Linda Onugwu
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chinazom Precious Agbo
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Adaeze Chidiebere Echezona
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Ezinwanne Nneoma Ezeibe
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka, Enugu state, Nigeria
| | - Samuel Uzondu
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Frankline Chimaobi Kenechukwu
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Paul Achile Akpa
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Mumuni Audu Momoh
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Petra Obioma Nnamani
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Clemence Tarirai
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - Kenneth Chibuzor Ofokansi
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Anthony Amaechi Attama
- Drug Delivery & Nanomedicines Research Laboratory, Department of Pharmaceutics, University of Nigeria, Nsukka, Enugu State, Nigeria
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18
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Lu W, Zhao Z, Huang YW, Wang B. Review: A systematic review of virus-like particles of coronavirus: Assembly, generation, chimerism and their application in basic research and in the clinic. Int J Biol Macromol 2022; 200:487-497. [PMID: 35065135 PMCID: PMC8769907 DOI: 10.1016/j.ijbiomac.2022.01.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/27/2022]
Abstract
Virus-like particles (VLPs) are nano-scale particles that are morphologically similar to a live virus but which lack a genetic component. Since the pandemic spread of COVID-19, much focus has been placed on coronavirus (CoV)-related VLPs. CoVs contain four structural proteins, though the minimum requirement for VLP formation differs among virus species. CoV VLPs are commonly produced in mammalian and insect cell systems, sometimes in the form of chimeric VLPs that enable surface display of CoV epitopes. VLPs are an ideal model for virological research and have been applied as vaccines and diagnostic reagents to aid in clinical disease control. This review summarizes and updates the research progress on the characteristics of VLPs from different known CoVs, mainly focusing on assembly, in vitro expression systems for VLP generation, VLP chimerism, protein-based nanoparticles and their applications in basic research and clinical settings, which may aid in development of novel VLP vaccines against emerging coronavirus diseases such as SARS-CoV-2.
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Affiliation(s)
- Wan Lu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
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19
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Clayton E, Rohaim MA, Bayoumi M, Munir M. The Molecular Virology of Coronaviruses with Special Reference to SARS-CoV-2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1352:15-31. [PMID: 35132592 DOI: 10.1007/978-3-030-85109-5_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Coronaviruses (CoVs) are large, enveloped and positive-sense RNA viruses which are responsible for a range of upper respiratory and digestive tract infections. Interest in coronaviruses has recently escalated due to the identification of a newly emerged coronavirus named severe acute respiratory syndrome 2 (SARS-CoV-2), which is the causative agent of the COVID-19 pandemic. In this chapter, we summarise molecular virological features of coronaviruses and understand their molecular mechanisms of replication in guiding the control of the global COVID-19 pandemic. METHODS We applied a holistic and comparative approach to assess the current understanding of coronavirus molecular virology and identify research gaps among different human coronaviruses. RESULTS Coronaviruses can utilise unique strategies that aid in their pathogenicity, replication and survival in multiple hosts. Replication of coronaviruses involves novel mechanisms such as ribosomal frameshifting and the synthesis of both genomic and sub-genomic RNAs. We summarised the key components in coronavirus molecular biology and molecular determinants of pathogenesis. Focusing largely on SARS-CoV-2 due to its current importance, this review explores the virology of recently emerged coronaviruses to gain an in-depth understanding of these infectious diseases. CONCLUSIONS The presented information provides fundamental bottlenecks to devise future disease control and management strategies to curtail the impact of coronaviruses in human populations.
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Affiliation(s)
- Emily Clayton
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Mohammed A Rohaim
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
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20
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Ranjbar M, Asadi M, Nourigorji M, Sarkari B, Mostafavi‐Pour Z, Zomorodian K, Shabaninejad Z, Taheri‐Anganeh M, Maleksabet A, Moghadami M, Savardashtaki A. Development of a recombinant nucleocapsid protein-based ELISA for the detection of IgM and IgG antibodies to SARS-CoV-2. Biotechnol Appl Biochem 2022; 69:2592-2598. [PMID: 34965611 PMCID: PMC9011413 DOI: 10.1002/bab.2308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2021] [Indexed: 12/27/2022]
Abstract
Coronavirus 2019 (COVID-19) is a global concern for public health. Thus, early and accurate diagnosis is a critical step in management of this infectious disease. Currently, RT-PCR is routine diagnosis test for COVID-19, but it has some limitations and false negative results. enzyme-linked immunosorbent assay (ELISA) against SARS-CoV-2 antigens seems to be an appropriate approach for serodiagnosis of COVID-19. In the current study, an ELISA system, using a recombinant nucleocapsid (N) protein, was developed for the detection of IgM and IgG antibodies to SARS-CoV-2. The related protein was expressed, purified, and used in an ELISA system. Sera samples (67) for COVID-19 patients, as well as sera samples from healthy volunteers (112), along with sera samples from non-COVID-19 patients were examined by the ELISA system. The expression and purity of the recombinant N protein were approved by SDS-PAGE and Western blotting. The sensitivity of ELISA system was 91.04 and 92.53% for the detection of IgG and IgM antibodies, respectively. Moreover, the specificity of the developed ELISA system for IgG and IgM were 98.21 and 97.32%, respectively. Our developed ELISA system showed satisfactory sensitivity and specificity for the detection of antiSARS-CoV-2 IgM and IgG antibodies and could be used as a complementary approach for proper diagnosis of COVID-19.
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Affiliation(s)
- Maryam Ranjbar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Marzieh Asadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Marjan Nourigorji
- Health Research InstituteBabol University of Medical SciencesBabolIran
| | - Bahador Sarkari
- Department of Parasitology and Mycology, School of MedicineShiraz University of Medical SciencesShirazIran,Basic Sciences in Infectious Diseases Research CenterShiraz University of Medical SciencesShirazIran
| | - Zohreh Mostafavi‐Pour
- Recombinant Protein Laboratory, Department of Biochemistry, School of MedicineShiraz University of Medical SciencesShirazIran,Autophagy Research CenterShiraz University of Medical SciencesShirazIran
| | - Kamiar Zomorodian
- Department of Parasitology and Mycology, School of MedicineShiraz University of Medical SciencesShirazIran,Basic Sciences in Infectious Diseases Research CenterShiraz University of Medical SciencesShirazIran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran,Pharmaceutical Sciences Research CenterShiraz University of Medical SciencesShirazIran
| | - Mortaza Taheri‐Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in MedicineMazandaran University of Medical SciencesSariIran
| | - Mohsen Moghadami
- Department of Internal Medicine, School of MedicineShiraz University of Medical SciencesShirazIran,Health Policy Research CenterShiraz University of Medical SciencesShirazIran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran,Infertility Research CenterShiraz University of Medical SciencesShirazIran
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21
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Hasan S, Hossain M. Method for Analysing Protein Structure of SARS-COV-2 M Protein for Possible Clues Regarding Virion Stability, Longevity and Transmission. Bio Protoc 2022. [DOI: 10.21769/bioprotoc.3830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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22
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An outlook on potential protein targets of COVID-19 as a druggable site. Mol Biol Rep 2022; 49:10729-10748. [PMID: 35790657 PMCID: PMC9256362 DOI: 10.1007/s11033-022-07724-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/17/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND SARS-CoV-2 which causes COVID-19 disease has started a pandemic episode all over the world infecting millions of people and has created medical and economic crisis. From December 2019, cases originated from Wuhan city and started spreading at an alarming rate and has claimed millions of lives till now. Scientific studies suggested that this virus showed genomic similarity of about 90% with SARS-CoV and is found to be more contagious as compared to SARS-CoV and MERS-CoV. Since the pandemic, virus has undergone constant mutation and few strains have raised public concern like Delta and Omicron variants of SARS-CoV-2. OBJECTIVE This review focuses on the structural features of SARS-CoV-2 proteins and host proteins as well as their mechanism of action. We have also elucidated the repurposed drugs that have shown potency to inhibit these protein targets in combating COVID-19. Moreover, the article discusses the vaccines approved so far and those under clinical trials for their efficacy against COVID-19. CONCLUSION Using cryo-electron microscopy or X-ray diffraction, hundreds of crystallographic data of SARS-CoV-2 proteins have been published including structural and non-structural proteins. These proteins have a significant role at different aspects in the viral machinery and presented themselves as potential target for drug designing and therapeutic interventions. Also, there are few host cell proteins which helps in SARS-CoV-2 entry and proteolytic cleavage required for viral infection.
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23
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Potential antiviral therapies for coronavirus disease 2019 (COVID-19). DATA SCIENCE FOR COVID-19 2022. [PMCID: PMC8989131 DOI: 10.1016/b978-0-323-90769-9.00036-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The novel coronavirus disease (COVID-2019) caused by severe acute respiratory syndrome coronavirus (called SARS-CoV-2) emerged in China in December 2019 and then spread rapidly to more than 200 countries around the world, including the United States, Spain, Italy, the United Kingdom, Germany, France, Japan, and South Korea, resulting in more than 208,112 deaths worldwide. As there is no approved vaccine or therapeutic available to control the COVID-2019 pandemic, scientists across the world are trying every possible way to find antivirals specific to this virus. In this urgent situation, parallel to the development of new vaccines and drugs, many previously approved antiviral drugs of broad range such as arbidol, interferon alfa, chloroquine, remdesivir, and favipiravir are presently undergoing clinical trials against COVID-19. So far some positive findings have been obtained, and here we present a thorough overview of all possible antiviral medicines that can control this pandemic of SARS-CoV-2.
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24
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Moabelo KL, Martin DR, Fadaka AO, Sibuyi NRS, Meyer M, Madiehe AM. Nanotechnology-Based Strategies for Effective and Rapid Detection of SARS-CoV-2. MATERIALS (BASEL, SWITZERLAND) 2021; 14:7851. [PMID: 34947447 PMCID: PMC8703409 DOI: 10.3390/ma14247851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has gained worldwide attention and has prompted the development of innovative diagnostics, therapeutics, and vaccines to mitigate the pandemic. Diagnostic methods based on reverse transcriptase-polymerase chain reaction (RT-PCR) technology are the gold standard in the fight against COVID-19. However, this test might not be easily accessible in low-resource settings for the early detection and diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The lack of access to well-equipped clinical laboratories, requirement for the high level of technical competence, and the cost of the RT-PCR test are the major limitations. Moreover, RT-PCR is unsuitable for application at the point-of-care testing (PoCT) as it is time-consuming and lab-based. Due to emerging mutations of the virus and the burden it has placed on the health care systems, there is a growing urgency to develop sensitive, selective, and rapid diagnostic devices for COVID-19. Nanotechnology has emerged as a versatile technology in the production of reliable diagnostic tools for various diseases and offers new opportunities for the development of COVID-19 diagnostic systems. This review summarizes some of the nano-enabled diagnostic systems that were explored for the detection of SARS-CoV-2. It highlights how the unique physicochemical properties of nanoparticles were exploited in the development of novel colorimetric assays and biosensors for COVID-19 at the PoCT. The potential to improve the efficiency of the current assays, as well as the challenges associated with the development of these innovative diagnostic tools, are also discussed.
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Affiliation(s)
| | | | | | | | - Mervin Meyer
- Department of Science and Innovation (DSI)/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape (UWC), Bellville 7535, South Africa; (K.L.M.); (D.R.M.); (A.O.F.); (N.R.S.S.)
| | - Abram M. Madiehe
- Department of Science and Innovation (DSI)/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape (UWC), Bellville 7535, South Africa; (K.L.M.); (D.R.M.); (A.O.F.); (N.R.S.S.)
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25
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Koetzner CA, Hurst-Hess KR, Kuo L, Masters PS. Analysis of a crucial interaction between the coronavirus nucleocapsid protein and the major membrane-bound subunit of the viral replicase-transcriptase complex. Virology 2021; 567:1-14. [PMID: 34933176 PMCID: PMC8669624 DOI: 10.1016/j.virol.2021.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022]
Abstract
The coronavirus nucleocapsid (N) protein comprises two RNA-binding domains connected by a central spacer, which contains a serine- and arginine-rich (SR) region. The SR region engages the largest subunit of the viral replicase-transcriptase, nonstructural protein 3 (nsp3), in an interaction that is essential for efficient initiation of infection by genomic RNA. We carried out an extensive genetic analysis of the SR region of the N protein of mouse hepatitis virus in order to more precisely define its role in RNA synthesis. We further examined the N-nsp3 interaction through construction of nsp3 mutants and by creation of an interspecies N protein chimera. Our results indicate a role for the central spacer as an interaction hub of the N molecule that is partially regulated by phosphorylation. These findings are discussed in relation to the recent discovery that nsp3 forms a molecular pore in the double-membrane vesicles that sequester the coronavirus replicase-transcriptase.
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Affiliation(s)
- Cheri A Koetzner
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Kelley R Hurst-Hess
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Lili Kuo
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Paul S Masters
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA; Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY, 12208, USA.
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26
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Alshammary AF, Al-Sulaiman AM. The journey of SARS-CoV-2 in human hosts: a review of immune responses, immunosuppression, and their consequences. Virulence 2021; 12:1771-1794. [PMID: 34251989 PMCID: PMC8276660 DOI: 10.1080/21505594.2021.1929800] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory findings from a significant number of patients with COVID-19 indicate the occurrence of leukocytopenia, specifically lymphocytopenia. Moreover, infected patients can experience contrasting outcomes depending on lymphocytopenia status. Patients with resolved lymphocytopenia are more likely to recover, whereas critically ill patients with signs of unresolved lymphocytopenia develop severe complications, sometimes culminating in death. Why immunodepression manifests in patients with COVID-19 remains unclear. Therefore, the evaluation of clinical symptoms and laboratory findings from infected patients is critical for understanding the disease course and its consequences. In this review, we take a logical approach to unravel the reasons for immunodepression in patients with COVID-19. Following the footprints of the virus within host tissues, from entry to exit, we extrapolate the mechanisms underlying the phenomenon of immunodepression.
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Affiliation(s)
- Amal F. Alshammary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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27
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Dastar S, Gharesouran J, Mortazavi D, Hosseinzadeh H, Kian SJ, Taheri M, Ghafouri-Fard S, Jamali E, Rezazadeh M. COVID-19 pandemic: Insights into genetic susceptibility to SARS-CoV-2 and host genes implications on virus spread, disease severity and outcomes. Hum Antibodies 2021; 30:1-14. [PMID: 34864654 DOI: 10.3233/hab-211506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The outbreak of the newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) all over the world has caused global public health emergencies, international concern and economic crises. The systemic SARS-CoV-2 disease (COVID-19) can lead to death through causing unrestrained cytokines-storm and subsequent pulmonary shutdown among the elderly and patients with pre-existing comorbidities. Additionally, in comparison with poor nations without primary health care services, in developed countries with advanced healthcare system we can witness higher number of infections per one million people. In this review, we summarize the latest studies on genes associated with SARS-CoV-2 pathogenesis and propose possible mechanisms of the virus replication cycle and its triggered signaling pathways to encourage researchers to investigate genetic and immune profiles of the disease and try strategies for its treatment. Our review shows that immune response in people with different genetic background might vary as African and then Asian populations have lowest number of affected cases compared with European and American nations. Considering SARS-CoV-2 pathogenesis, we put forward some potentially important genetic gateways to COVID-19 infection including genes involved in the entry and replication of SARS-CoV-2 and the regulation of host immune response which might represent explanation for its spread, severity, and morality. Finally, we suggest that genetic alterations within these gateways could be critical factors in influencing geographical discrepancies of the virus, so it is essential to fully study them and design appropriated and reliable therapeutic agents against COVID-19.
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Affiliation(s)
- Saba Dastar
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Fatih, Istanbul, Turkey
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Deniz Mortazavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Jalal Kian
- Department of Virology, Iran University of Medical Sciences, School of Medicine, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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28
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Mohammad T, Choudhury A, Habib I, Asrani P, Mathur Y, Umair M, Anjum F, Shafie A, Yadav DK, Hassan MI. Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach. Front Cell Infect Microbiol 2021; 11:765039. [PMID: 34722346 PMCID: PMC8548870 DOI: 10.3389/fcimb.2021.765039] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
A continual rise in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease (COVID-19) has become a global threat. The main problem comes when SARS-CoV-2 gets mutated with the rising infection and becomes more lethal for humankind than ever. Mutations in the structural proteins of SARS-CoV-2, i.e., the spike surface glycoprotein (S), envelope (E), membrane (M) and nucleocapsid (N), and replication machinery enzymes, i.e., main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) creating more complexities towards pathogenesis and the available COVID-19 therapeutic strategies. This study analyzes how a minimal variation in these enzymes, especially in S protein at the genomic/proteomic level, affects pathogenesis. The structural variations are discussed in light of the failure of small molecule development in COVID-19 therapeutic strategies. We have performed in-depth sequence- and structure-based analyses of these proteins to get deeper insights into the mechanism of pathogenesis, structure-function relationships, and development of modern therapeutic approaches. Structural and functional consequences of the selected mutations on these proteins and their association with SARS-CoV-2 virulency and human health are discussed in detail in the light of our comparative genomics analysis.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arunabh Choudhury
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Insan Habib
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Yash Mathur
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Dharmendra Kumar Yadav
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Incheon, South Korea
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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29
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Maghsood F, Hassani D, Salimi V, Kardar GA, Khoshnoodi J, Ghaderi A, Raeeskarami SR, Rostamian A, Seyyedsalehi MS, Ahmadi Fesharaki R, Jeddi-Tehrani M, Zarnani AH, Amiri MM, Shokri F. Differential Antibody Response to SARS-CoV-2 Antigens in Recovered and Deceased Iranian COVID-19 Patients. Viral Immunol 2021; 34:708-713. [PMID: 34534012 DOI: 10.1089/vim.2021.0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The coronavirus infectious disease 2019 (COVID-19), which is initiated by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has imposed critical challenges to global health. Understanding the kinetic of SARS-CoV-2-specific IgM and IgG responses in different subsets of COVID-19 patients is crucial to get insight into the humoral immune response elicited against the virus. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and receptor-binding domain (RBD) of spike protein in two groups of recovered and deceased COVID-19 patients. The levels of IgM and IgG specific to N and RBD proteins were detected by ELISA. N- and RBD-specific IgM was higher in deceased patients in comparison with recovered patients, while there was no significant difference in N- and RBD-specific IgG between the two groups. A significant correlation was observed between IgG and IgM titers against RBD and N, in both groups of patients. These results argue against impaired antibody response in deceased COVID-19 patients.
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Affiliation(s)
- Faezeh Maghsood
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Danesh Hassani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Ali Kardar
- Immunology Asthma and Allergy Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalal Khoshnoodi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Ghaderi
- Cancer Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Reza Raeeskarami
- Department of Pediatrics, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdorrahman Rostamian
- Department of Rheumatology, Valiasr Hospital, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Raoufeh Ahmadi Fesharaki
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Amir-Hassan Zarnani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Amiri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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30
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Chen SC, Olsthoorn RCL, Yu CH. Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evol 2021; 7:veab021. [PMID: 34141447 PMCID: PMC8206606 DOI: 10.1093/ve/veab021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - René C L Olsthoorn
- Department of Supramolecular Biomaterials Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden,The Netherlands
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
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31
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Improved diagnosis of SARS-CoV-2 by using nucleoprotein and spike protein fragment 2 in quantitative dual ELISA tests. Epidemiol Infect 2021; 149:e140. [PMID: 34099081 PMCID: PMC8207563 DOI: 10.1017/s0950268821001308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The novel coronavirus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), is the causative agent of the 2020 worldwide coronavirus pandemic. Antibody testing is useful for diagnosing historic infections of a disease in a population. These tests are also a helpful epidemiological tool for predicting how the virus spreads in a community, relating antibody levels to immunity and for assessing herd immunity. In the present study, SARS-CoV-2 viral proteins were recombinantly produced and used to analyse serum from individuals previously exposed, or not, to SARS-CoV-2. The nucleocapsid (Npro) and spike subunit 2 (S2Frag) proteins were identified as highly immunogenic, although responses to the former were generally greater. These two proteins were used to develop two quantitative enzyme-linked immunosorbent assays (ELISAs) that when used in combination resulted in a highly reliable diagnostic test. Npro and S2Frag-ELISAs could detect at least 10% more true positive coronavirus disease-2019 (COVID-19) cases than the commercially available ARCHITECT test (Abbott). Moreover, our quantitative ELISAs also show that specific antibodies to SARS-CoV-2 proteins tend to wane rapidly even in patients who had developed severe disease. As antibody tests complement COVID-19 diagnosis and determine population-level surveillance during this pandemic, the alternative diagnostic we present in this study could play a role in controlling the spread of the virus.
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32
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Sajid M, Moazzam M, Cho Y, Kato S, Xu A, Way JJ, Lohan S, Tiwari RK. siRNA Therapeutics for the Therapy of COVID-19 and Other Coronaviruses. Mol Pharm 2021; 18:2105-2121. [PMID: 33945284 PMCID: PMC9896947 DOI: 10.1021/acs.molpharmaceut.0c01239] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ongoing pandemic of global concern has killed about three million humans and affected around 151 million people worldwide, as of April 30, 2021. Although recently approved vaccines for COVID-19 are engendering hope, finding new ways to cure the viral pandemic is still a quest for researchers worldwide. Major pandemics in history have been of viral origin, such as SARS, MERS, H1NI, Spanish flu, and so on. A larger emphasis has been on discovering potential vaccines, novel antiviral drugs, and agents that can mitigate the viral infection symptoms; however, a relatively new area, RNA interference (RNAi), has proven effective as an antiviral agent. The RNAi phenomenon has been largely exploited to cure cancer, neurodegenerative diseases, and some rare diseases. The U.S. Food and Drug Administration has recently approved three siRNA products for human use that garner significant hope in siRNA therapeutics for coronaviruses. There have been some commentaries and communications addressing this area. We have summarized and illustrated the significance and the potential of the siRNA therapeutics available as of April 30, 2021 to combat the ongoing viral pandemic and the emerging new variants such as B.1.1.7 and B.1.351. Numerous successful in vitro studies and several investigations to address the clinical application of siRNA therapeutics provide great hope in this field. This seminal Review describes the significance of siRNA-based therapy to treat diverse viral infections in addition to the current coronavirus challenge. In addition, we have thoroughly reviewed the patents approved for coronaviruses, the major challenges in siRNA therapy, and the potential approaches to address them, followed by innovation and prospects.
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Affiliation(s)
- Muhammad
Imran Sajid
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Faculty
of Pharmacy, University of Central Punjab, Lahore 54700, Pakistan
| | - Muhammad Moazzam
- Faculty
of Pharmacy, University of Central Punjab, Lahore 54700, Pakistan
| | - Yeseom Cho
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Department
of Biochemistry and Molecular Biology, Schmid College of Science and
Technology, Chapman University, Orange, California 92866, United States
| | - Shun Kato
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Department
of Biochemistry and Molecular Biology, Schmid College of Science and
Technology, Chapman University, Orange, California 92866, United States
| | - Ava Xu
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - J. J. Way
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Sandeep Lohan
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Rakesh K. Tiwari
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
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Raghav PK, Kalyanaraman K, Kumar D. Human cell receptors: potential drug targets to combat COVID-19. Amino Acids 2021; 53:813-842. [PMID: 33950300 PMCID: PMC8097256 DOI: 10.1007/s00726-021-02991-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 04/21/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19). The World Health Organization (WHO) has announced that COVID-19 is a pandemic having a higher spread rate rather than the mortality. Identification of a potential approach or therapy against COVID-19 is still under consideration. Therefore, it is essential to have an insight into SARS-CoV-2, its interacting partner, and domains for an effective treatment. The present study is divided into three main categories, including SARS-CoV-2 prominent receptor and its expression levels, other interacting partners, and their binding domains. The first section focuses primarily on coronaviruses' general aspects (SARS-CoV-2, SARS-CoV, and the Middle East Respiratory Syndrome Coronaviruses (MERS-CoV)) their structures, similarities, and mode of infections. The second section discusses the host receptors which includes the human targets of coronaviruses like dipeptidyl peptidase 4 (DPP4), CD147, CD209L, Angiotensin-Converting Enzyme 2 (ACE2), and other miscellaneous targets (type-II transmembrane serine proteases (TTSPs), furin, trypsin, cathepsins, thermolysin, elastase, phosphatidylinositol 3-phosphate 5-kinase, two-pore segment channel, and epithelium sodium channel C-α subunit). The human cell receptor, ACE2 plays an essential role in the Renin-Angiotensin system (RAS) pathway and COVID-19. Thus, this section also discusses the ACE2 expression and risk of COVID-19 infectivity in various organs and tissues such as the liver, lungs, intestine, heart, and reproductive system in the human body. Absence of ACE2 protein expression in immune cells could be used for limiting the SARS-CoV-2 infection. The third section covers the current available approaches for COVID-19 treatment. Overall, this review focuses on the critical role of human cell receptors involved in coronavirus pathogenesis, which would likely be used in designing target-specific drugs to combat COVID-19.
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Affiliation(s)
| | - Keerthana Kalyanaraman
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh, India
| | - Dinesh Kumar
- ICMR-National Institute of Cancer Prevention & Research, Noida, 201301, India.
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Sakr MM, Elsayed NS, El-Housseiny GS. Latest updates on SARS-CoV-2 genomic characterization, drug, and vaccine development; a comprehensive bioinformatics review. Microb Pathog 2021; 154:104809. [PMID: 33647446 PMCID: PMC7910145 DOI: 10.1016/j.micpath.2021.104809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023]
Abstract
Amid the COVID-19 outbreak, several bioinformatic analyses have been conducted on SARS-CoV-2 virus genome. Numerous studies rushed to fill the gap about this novel virus. Comparison with other related sequences, structural predictions of the produced proteins, determination of variations in amino acid residues and depiction of possible drug and vaccine targets have been the focus of scientific research from the beginning of this year. In addition to discussing the viral taxonomy, clinical features, life cycle, and genome organization, this review will focus on the recent updates in genome and viral proteins characterization and potential therapeutic and vaccine candidates developed so far. Comparative studies with related genomes and proteins provide understanding for the viral molecular mechanisms and suggest targets for therapeutics and vaccinology trials to stop the escalation of this new virus. This pandemic, with its resulting social and economic afflictions, will definitely have significant marks on our lives in the following years.
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Affiliation(s)
- Masarra M Sakr
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt
| | - Noha S Elsayed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt.
| | - Ghadir S El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt
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35
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Mehta A, Michler T, Merkel OM. siRNA Therapeutics against Respiratory Viral Infections-What Have We Learned for Potential COVID-19 Therapies? Adv Healthc Mater 2021; 10:e2001650. [PMID: 33506607 PMCID: PMC7995229 DOI: 10.1002/adhm.202001650] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/06/2021] [Indexed: 12/30/2022]
Abstract
Acute viral respiratory tract infections (AVRIs) are a major burden on human health and global economy and amongst the top five causes of death worldwide resulting in an estimated 3.9 million lives lost every year. In addition, new emerging respiratory viruses regularly cause outbreaks such as SARS-CoV-1 in 2003, the "Swine flu" in 2009, or most importantly the ongoing SARS-CoV-2 pandemic, which intensely impact global health, social life, and economy. Despite the prevalence of AVRIs and an urgent need, no vaccines-except for influenza-or effective treatments were available at the beginning of the COVID-19 pandemic. However, the innate RNAi pathway offers the ability to develop nucleic acid-based antiviral drugs. siRNA sequences against conserved, essential regions of the viral genome can prevent viral replication. In addition, viral infection can be averted prophylactically by silencing host genes essential for host-viral interactions. Unfortunately, delivering siRNAs to their target cells and intracellular site of action remains the principle hurdle toward their therapeutic use. Currently, siRNA formulations and chemical modifications are evaluated for their delivery. This progress report discusses the selection of antiviral siRNA sequences, delivery techniques to the infection sites, and provides an overview of antiviral siRNAs against respiratory viruses.
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Affiliation(s)
- Aditi Mehta
- Department of PharmacyPharmaceutical Technology and BiopharmaceuticsLudwig‐Maximilians‐Universität MünchenButenandtstraße 5Munich81377Germany
| | - Thomas Michler
- Institute of VirologyTechnische Universität MünchenTrogerstr. 30Munich81675Germany
| | - Olivia M. Merkel
- Department of PharmacyPharmaceutical Technology and BiopharmaceuticsLudwig‐Maximilians‐Universität MünchenButenandtstraße 5Munich81377Germany
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36
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Current Understanding of Novel Coronavirus: Molecular Pathogenesis, Diagnosis, and Treatment Approaches. IMMUNO 2021. [DOI: 10.3390/immuno1010004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
An outbreak of “Pneumonia of Unknown Etiology” occurred in Wuhan, China, in late December 2019. Later, the agent factor was identified and coined as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease was named coronavirus disease 2019 (COVID-19). In a shorter period, this newly emergent infection brought the world to a standstill. On 11 March 2020, the WHO declared COVID-19 as a pandemic. Researchers across the globe have joined their hands to investigate SARS-CoV-2 in terms of pathogenicity, transmissibility, and deduce therapeutics to subjugate this infection. The researchers and scholars practicing different arts of medicine are on an extensive quest to come up with safer ways to curb the pathological implications of this viral infection. A huge number of clinical trials are underway from the branch of allopathy and naturopathy. Besides, a paradigm shift on cellular therapy and nano-medicine protocols has to be optimized for better clinical and functional outcomes of COVID-19-affected individuals. This article unveils a comprehensive review of the pathogenesis mode of spread, and various treatment modalities to combat COVID-19 disease.
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37
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Khan MT, Ali S, Khan AS, Muhammad N, Khalil F, Ishfaq M, Irfan M, Al-Sehemi AG, Muhammad S, Malik A, Khan TA, Wei DQ. SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. ACS OMEGA 2021; 6:6588-6599. [PMID: 33748571 PMCID: PMC7944396 DOI: 10.1021/acsomega.0c05163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Among viral outbreaks, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest ones, and it has triggered the global COVID-19 pandemic. In Pakistan, until 5th September 2020, a total of 6342 deaths have been reported, of which 1255 were from the Khyber Pakhtunkhwa (KPK) province. To understand the disease progression and control and also to produce vaccines and therapeutic efforts, whole genome sequence analysis is important. In the current investigation, we sequenced a single sample of SARS-CoV-2 genomes (accession no. MT879619) from a male suspect from Peshawar, the KPK capital city, during the first wave of infection. The local SARS-CoV-2 strain shows some unique characteristics compared to neighboring Iranian and Chinese isolates in phylogenetic tree and mutations. The circulating strains of SARS-CoV-2 represent an intermediate evolution from China and Iran. Furthermore, eight complete whole genome sequences, including the current Pakistani isolates which have been submitted to Global Initiative on Sharing All Influenza Data (GSAID), were also investigated for specific mutations and characters. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. The computational modeling revealed that a majority of these mutations may have a stabilizing effect on the viral protein structure. In conclusion, the genome sequencing of local strains is important for better understanding the pathogenicity, immunogenicity, and epidemiology of causative agents.
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Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad 45320, Pakistan
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Noor Muhammad
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Faiza Khalil
- Department of Biochemistry, Khyber Medical
College, Peshawar 25160, Pakistan
- University
of Peshawar, Road No.
2, Rahat Abad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ishfaq
- Centre for Omic Sciences, Islamia
College Peshawar. Grand Trunk Road, Rahat Abad, Peshawar 25120, Pakistan
| | - Muhammad Irfan
- Department
of Oral Biology, College of Dentistry, University
of Florida, Gainesville, Florida 32611, United States
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shabbir Muhammad
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Arif Malik
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Phase V, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
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Abstract
The worldwide novel coronavirus SARS-CoV‑2 pandemic is ongoing. SARS-CoV‑2 belongs to the coronavirus family, the first representatives of which have been known since the 1960s. Coronaviruses are present in animals and humans and show similarities as well as differences in their biology and pathology regarding each genus. Besides mild flu-like and gastroenterological symptoms, SARS-CoV‑2 can lead to dysfunctions of the lungs and other organs including the heart as already observed during SARS and MERS infections.
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Bhat EA, Khan J, Sajjad N, Ali A, Aldakeel FM, Mateen A, Alqahtani MS, Syed R. SARS-CoV-2: Insight in genome structure, pathogenesis and viral receptor binding analysis - An updated review. Int Immunopharmacol 2021; 95:107493. [PMID: 33721758 PMCID: PMC7904465 DOI: 10.1016/j.intimp.2021.107493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/11/2022]
Abstract
The novel coronavirus disease (COVID-19) a global pandemic outbreak is an emerging new virus accountable for respiratory illness caused by SARS-CoV-2, originated in Wuhan city, Hubei province China, urgently calls to adopt prevention and intervention strategies. Several viral epidemics such as severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 to 2003 and H1N1 influenza in 2009 were reported since last two decades. Moreover, the Saudi Arabia was the epicenter for Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012. The CoVs are large family with single-stranded RNA viruses (+ssRNA). Genome sequence of 2019-nCoV, shows relatively different homology from other coronavirus subtypes, categorized in betacoronavirus and possibly found from strain of bats. The COVID-19 composed of exposed densely glycosylated spike protein (S) determines virus binding and infiltrate into host cells as well as initiate protective host immune response. Recently published reviews on the emerging SARS-CoV-2 have mainly focused on its structure, development of the outbreak, relevant precautions and management trials. Currently, there is an urgency of pharmacological intervention to combat this deadly infectious disease. Elucidation of molecular mechanism of COVID-19 becomes necessary. Based on the current literature and understanding, the aim of this review is to provide current genome structure, etiology, clinical prognosis as well as to explore the viral receptor binding together functional insight of SARS-CoV-2 infection (COVID-19) with treatment and preventive measures.
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Affiliation(s)
- Eijaz Ahmed Bhat
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia.
| | - Nasreena Sajjad
- Department of Biochemistry, University of Kashmir, Hazratbal, Jammu and Kashmir, India
| | - Ahmad Ali
- Department of Life Sciences, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400098, India
| | - Fahad M Aldakeel
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ayesha Mateen
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed S Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Rabbani Syed
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Zarandi PK, Zinatizadeh MR, Zinatizadeh M, Yousefi MH, Rezaei N. SARS-CoV-2: From the pathogenesis to potential anti-viral treatments. Biomed Pharmacother 2021; 137:111352. [PMID: 33550050 PMCID: PMC7969672 DOI: 10.1016/j.biopha.2021.111352] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction The world is witnessing the spread of one of the members of Coronaviruses (CoVs) family, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the 21st century. Considering the short time spent after its prevalence, limited information is known about the effect of the virus mechanism on different organs of the body; meanwhile the lack of specific treatment and vaccine for this virus has exposed millions of people to a big challenge. Areas covered The review article aims to describe the general and particular characteristics of CoVs, their classification, genome structure, host cell infection, cytokine storm, anti-viral treatments, and inhibition of COVID-19-related ER-mitochondrial stress. In addition, it refers to drugs such as Chloroquine/Hydroxychloroquine, Lopinavir/Ritonavir, darunavir, ribavirin, remdesivir, and favipiravir, which have undergone clinical trials for coronavirus disease 2019 (COVID-19) treatment. This analysis was derived from an extensive scientific literature search including Pubmed, ScienceDirect, and Google Scholar performed. Expert opinion The effectiveness rate and complications of these drugs can reveal new insights into the potential therapeutic goals for the disease. Moreover, lifestyle change can effectively prevent SARS-CoV-2 infection.
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Affiliation(s)
- Peyman Kheirandish Zarandi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran; Cancer Biology Signaling Pathway Interest Group (CBSPIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mohammad Reza Zinatizadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran; Cancer Biology Signaling Pathway Interest Group (CBSPIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Maryam Zinatizadeh
- Department of Anesthesiology, Semnan Branch, Islamic Azad University, Shahrood, Iran
| | - Mohammad Hadi Yousefi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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Bhattacharya R, Dev K, Sourirajan A. Antiviral activity of bioactive phytocompounds against coronavirus: An update. J Virol Methods 2021; 290:114070. [PMID: 33497729 PMCID: PMC7826042 DOI: 10.1016/j.jviromet.2021.114070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/25/2020] [Accepted: 01/16/2021] [Indexed: 12/28/2022]
Abstract
Viral infections are one of the main cause of diseases worldwide due to the rising trends of migration, urbanization and global mobility of humans. The outbreak of corona virus diseases caused by SARS-CoV (year 2003), MERS-CoV (year 2012) and SARS-CoV-2 (year 2019) raised global health concerns. The side effects associated with the conventional drugs and increase in cases of anti-microbial resistance have led the researchers to switch to natural sources, especially plants, as they have immense potential to be used as antiviral agents. The aim of the article is to summarize the evidences of the bioactive phytocompounds from different plants as an effective alternative for the treatment of infections caused by coronaviruses. However, the use of most plant compounds succumbs to limitations due to lack of experimental evidences and safety studies. Therefore, further research and studies are required to validate their therapeutic uses for wide application of plant-based medicine, including anti-virals.
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Affiliation(s)
- Riya Bhattacharya
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, PO Sultanpur, District Solan, 173229, Himachal Pradesh, India.
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, PO Sultanpur, District Solan, 173229, Himachal Pradesh, India.
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, PO Sultanpur, District Solan, 173229, Himachal Pradesh, India.
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Marei HE, Althani A, Afifi N, Pozzoli G, Caceci T, Angelini F, Cenciarelli C. Pandemic COVID-19 caused by SARS-CoV-2: genetic structure, vaccination, and therapeutic approaches. Mol Biol Rep 2021; 48:6513-6524. [PMID: 34398427 PMCID: PMC8365286 DOI: 10.1007/s11033-021-06630-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023]
Abstract
We give a summary of SARS-genetic CoV-2's structure and evolution, as well as current attempts to develop efficient vaccine and treatment methods for SARS-CoV-2 infection, in this article. Most therapeutic strategies are based on repurposing of existing therapeutic agents used against various virus infections and focused mainly on inhibition of the virus replication cycle, enhancement of innate immunity, and alleviation of CRS caused by COVID-19. Currently, more than 100 clinical trials on COVID-19 aim to provide robust evidence on the efficacy of the currently available anti-SARS-CoV-2 antiviral substances, such as the nucleotide analogue remdesivir, the antimalarial drug chloroquine, and drugs directed against docking of SARS-CoV-2 to the membrane-associated angiotensin-converting enzyme 2 (ACE2) such as transmembrane protease serine 2 (TMPRSS2). The current vaccination campaign is ongoing worldwide using different types of vaccines such as Pfizer-BioNTech and Moderna, Johnson & Johnson, Oxford-AstraZeneca, Novavax, and others with efficacy ranging from 72-95%. In March 2021 Germany limited the use of the Oxford-AstraZeneca COVID-19 vaccine to people 60 years of age and older due to concerns that it may be causing blood clots. Further study and more data are needed to confirm the safety of different available vaccines.
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Affiliation(s)
- Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
| | - Asmaa Althani
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | - Giacomo Pozzoli
- Pharmacology Unit, Fondazione Policlinico A. Gemelli, IRCCS, Rome, Italy
| | - Thomas Caceci
- Biomedical Sciences, Virginia Maryland College of Veterinary Medicine, Blacksburg, VA, USA
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Petrović T, Lauc G, Trbojević-Akmačić I. The Importance of Glycosylation in COVID-19 Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1325:239-264. [PMID: 34495539 DOI: 10.1007/978-3-030-70115-4_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently one of the major health problems worldwide. SARS-CoV-2 survival and virulence are shown to be impacted by glycans, covalently attached to proteins in a process of glycosylation, making glycans an area of interest in SARS-CoV-2 biology and COVID-19 infection. The SARS-CoV-2 uses its highly glycosylated spike (S) glycoproteins to bind to the cell surface receptor angiotensin-converting enzyme 2 (ACE2) glycoprotein and facilitate host cell entry. Viral glycosylation has wide-ranging roles in viral pathobiology, including mediating protein folding and stability, immune evasion, host receptor attachment, and cell entry. Modification of SARS-CoV-2 envelope membrane with glycans is important in host immune recognition and interaction between S and ACE2 glycoproteins. On the other hand, immunoglobulin G, a key molecule in immune response, shows a distinct glycosylation profile in COVID-19 infection and with increased disease severity. Hence, further studies on the role of glycosylation in SARS-CoV-2 infectivity and COVID-19 infection are needed for its successful prevention and treatment. This chapter focuses on recent findings on the importance of glycosylation in COVID-19 infection.
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Affiliation(s)
- Tea Petrović
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
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44
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Zhang Y, Tang LV. Overview of Targets and Potential Drugs of SARS-CoV-2 According to the Viral Replication. J Proteome Res 2021; 20:49-59. [PMID: 33347311 PMCID: PMC7770889 DOI: 10.1021/acs.jproteome.0c00526] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Indexed: 01/18/2023]
Abstract
Since the novel coronavirus pandemic, people around the world have been touched in varying degrees, and this pandemic has raised a major global health concern. As there is no effective drug or vaccine, it is urgent to find therapeutic drugs that can serve to deal with the current epidemic situation in all countries and regions. We searched drugs and response measures for SARS-CoV-2 in the PubMed database, and then updated the potential targets and therapeutic drugs from the perspective of the viral replication cycle. The drug research studies of the viral replication cycle are predominantly focused on the process of the virus entering cells, proteases, and RdRp. The inhibitors of the virus entry to cells and RdRp, such as Arbidol, remdesivir, favipiravir, EIDD-2081, and ribavirin, are in clinical trials, while most of the protease inhibitors are mainly calculated by molecular docking technology, which needs in vivo and in vitro experiments to prove the effect for SARS-CoV-2. This review summarizes the drugs targeting the viral replication process and provides a basis and directions for future drug development and reuse on the protein level of COVID-19.
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Affiliation(s)
- Yi Zhang
- Institute
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Liang V. Tang
- Institute
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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45
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Carlson CR, Asfaha JB, Ghent CM, Howard CJ, Hartooni N, Safari M, Frankel AD, Morgan DO. Phosphoregulation of Phase Separation by the SARS-CoV-2 N Protein Suggests a Biophysical Basis for its Dual Functions. Mol Cell 2020; 80:1092-1103.e4. [PMID: 33248025 PMCID: PMC7677695 DOI: 10.1016/j.molcel.2020.11.025] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/02/2020] [Accepted: 11/10/2020] [Indexed: 12/20/2022]
Abstract
The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription. It is not clear how the N protein mediates such distinct functions. The N protein contains two RNA-binding domains surrounded by regions of intrinsic disorder. Phosphorylation of the central disordered region promotes the protein's transcriptional function, but the underlying mechanism is not known. Here, we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates. Unmodified N protein forms partially ordered gel-like condensates and discrete 15-nm particles based on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces these interactions, generating a more liquid-like droplet. We propose that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing.
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Affiliation(s)
- Christopher R Carlson
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathan B Asfaha
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chloe M Ghent
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nairi Hartooni
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maliheh Safari
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan D Frankel
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA.
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46
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Inhibition of SARS-CoV-2 Entry into Host Cells Using Small Molecules. Pharmaceuticals (Basel) 2020; 13:ph13120447. [PMID: 33302344 PMCID: PMC7762362 DOI: 10.3390/ph13120447] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a virus belonging to the Coronavirus family, is now known to cause Coronavirus Disease (Covid-19) which was first recognized in December 2019. Covid-19 leads to respiratory illnesses ranging from mild infections to pneumonia and lung failure. Strikingly, within a few months of its first report, Covid-19 has spread worldwide at an exceptionally high speed and it has caused enormous human casualties. As yet, there is no specific treatment for Covid-19. Designing inhibitory drugs that can interfere with the viral entry process constitutes one of the main preventative therapies that could combat SARS-CoV-2 infection at an early stage. In this review, we provide a brief introduction of the main features of coronaviruses, discuss the entering mechanism of SARS-CoV-2 into human host cells and review small molecules that inhibit SARS-CoV-2 entry into host cells. Specifically, we focus on small molecules, identified by experimental validation and/or computational prediction, that target the SARS-CoV-2 spike protein, human angiotensin converting enzyme 2 (ACE2) receptor and the different host cell proteases that activate viral fusion. Given the persistent rise in Covid-19 cases to date, efforts should be directed towards validating the therapeutic effectiveness of these identified small molecule inhibitors.
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47
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Simabuco FM, Tamura RE, Pavan ICB, Morale MG, Ventura AM. Molecular mechanisms and pharmacological interventions in the replication cycle of human coronaviruses. Genet Mol Biol 2020; 44:e20200212. [PMID: 33237152 PMCID: PMC7731901 DOI: 10.1590/1678-4685-gmb-2020-0212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), as well as SARS-CoV from 2003 along with MERS-CoV from 2012, is a member of the Betacoronavirus genus of the Nidovirales order and is currently the cause of the pandemic called COVID-19 (or Coronavirus disease 2019). COVID-19, which is characterized by cough, fever, fatigue, and severe cases of pneumonia, has affected more than 23 million people worldwide until August 25th, 2020. Here, we present a review of the cellular mechanisms associated with human coronavirus replication, including the unique molecular events related to the replication transcription complex (RTC) of coronaviruses. We also present information regarding the interactions between each viral protein and cellular proteins associated to known host-pathogen implications for the coronavirus biology. Finally, a specific topic addresses the current attempts for pharmacological interventions against COVID-19, highlighting the possible effects of each drug on the molecular events of viral replication. This review intends to aid future studies for a better understanding of the SARS-CoV-2 replication cycle and the development of pharmacological approaches targeting COVID-19.
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Affiliation(s)
- Fernando Moreira Simabuco
- Universidade Estadual de Campinas, Faculdade de Ciências Aplicadas (FCA), Laboratório Multidisciplinar em Alimentos e Saúde (LABMAS), Limeira, SP, Brazil
| | - Rodrigo Esaki Tamura
- Universidade Federal de São Paulo (UNIFESP), Departmento de Ciências Biológicas, Diadema, SP, Brazil
| | - Isadora Carolina Betim Pavan
- Universidade Estadual de Campinas, Faculdade de Ciências Aplicadas (FCA), Laboratório Multidisciplinar em Alimentos e Saúde (LABMAS), Limeira, SP, Brazil.,Universidade Estadual de Campinas, Faculdade de Ciências Farmacêuticas (FCF), Campinas, SP, Brazil
| | - Mirian Galliote Morale
- Universidade de São Paulo (USP), Departamento de Radiologia e Oncologia, Faculdade de Medicina, Centro de Oncologia Translacional, Instituto do Câncer do Estado de São Paulo (ICESP), São Paulo, SP, Brazil
| | - Armando Morais Ventura
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas (ICB), Departamento de Microbiologia, São Paulo, SP, Brazil
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48
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Gupta SP. Progress in Studies on Structural and Remedial Aspects of Newly Born Coronavirus, SARS-CoV-2. Curr Top Med Chem 2020; 20:2362-2378. [PMID: 32962613 DOI: 10.2174/1568026620666200922112300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/10/2020] [Accepted: 09/01/2020] [Indexed: 01/12/2023]
Abstract
The article highlights an up-to-date progress in studies on structural and the remedial aspects of novel coronavirus 2019-nCoV, renamed as SARS-CoV-2, leading to the disease COVID-19, a pandemic. In general, all CoVs including SARS-CoV-2 are spherical positive single-stranded RNA viruses containing spike (S) protein, envelope (E) protein, nucleocapsid (N) protein, and membrane (M) protein, where S protein has a Receptor-binding Domain (RBD) that mediates the binding to host cell receptor, Angiotensin Converting Enzyme 2 (ACE2). The article details the repurposing of some drugs to be tried for COVID-19 and presents the status of vaccine development so far. Besides drugs and vaccines, the role of Convalescent Plasma (CP) therapy to treat COVID-19 is also discussed.
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Affiliation(s)
- Satya P Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut-250005, India
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49
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Lang Y, Chen K, Li Z, Li H. The nucleocapsid protein of zoonotic betacoronaviruses is an attractive target for antiviral drug discovery. Life Sci 2020; 282:118754. [PMID: 33189817 PMCID: PMC7658559 DOI: 10.1016/j.lfs.2020.118754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/10/2020] [Indexed: 12/02/2022]
Abstract
Betacoronaviruses are in one genera of coronaviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV), etc. These viruses threaten public health and cause dramatic economic losses. The nucleocapsid (N) protein is a structural protein of betacoronaviruses with multiple functions such as forming viral capsids with viral RNA, interacting with viral membrane protein to form the virus core with RNA, binding to several cellular kinases for signal transductions, etc. In this review, we highlighted the potential of the N protein as a suitable antiviral target from different perspectives, including structure, functions, and antiviral strategies for combatting betacoronaviruses.
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Affiliation(s)
- Yuekun Lang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Ke Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, 1 University Place, Rensselaer, NY 12144, USA.
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50
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Wang QJ, Yao YZ, Song JS, Wang Q, Xu LY, Bao ZJ, Mao DW, Zhou JH, Zhang ZE, Wang Y, Li YW, Wang HP, Li L, Pan HY, Zhang GQ, Li SB. Kinetic changes in virology, specific antibody response and imaging during the clinical course of COVID-19: a descriptive study. BMC Infect Dis 2020; 20:818. [PMID: 33167900 PMCID: PMC7652587 DOI: 10.1186/s12879-020-05549-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Background To explore the kinetic changes in virology, specific antibody response and imaging during the clinical course of COVID-19. Methods This observational study enrolled 20 patients with COVID-19, who were hospitalized between January 20–April 6, 2020, in the two COVID-19 designated hospitals of Zhoushan, Zhejiang and Rushan, Shandong, China, The laboratory findings, imaging, serum response to viral infection, and viral RNA level in the throat and stool samples were assessed from onset to recovery phase in patients with COVID-19. Results SARS-COV-2 RNA was positive as early as day four. It remained positive until day 55 post-onset in the sputum-throat swabs and became negative in most cases (55%) within 14 days after onset. Lymphocytopenia occurred in 40% (8/20) of patients during the peak infection period and returned to normal at week five. The most severe inflammation in the lungs appeared in week 2 or 3 after onset, and this was completely absorbed between week 6 and 8 in 85.7% of patients. All patients had detectable antibodies to the receptor binding domain (RBD), and 95% of these patients had IgG to viral N proteins. The antibody titer peaked at week four. Anti-S IgM was positive in 7 of 20 patients after week three. Conclusions All COVID-19 patients in this study were self-limiting and recovered well though it may take as long as 6–8 weeks. Our findings on the kinetic changes in imaging, serum response to viral infection and viral RNA level may help understand pathogenesis and define clinical course of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05549-8.
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Affiliation(s)
- Qiu-Jing Wang
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, NO.739 Dingshen Road, Zhoushan City, 316021, Zhejiang, China
| | - Yan-Zhen Yao
- Department of Clinical Laboratory, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - Jun-Shuai Song
- Department of Emergency, Rushan People's Hospital, Shandong, 264500, Rushan, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Li-Yun Xu
- Cell and Molecular Biology Laboratory, Zhoushan Hospital, Wenzhou medical University, Zhoushan, 316021, Zhejiang, China
| | - Zhou-Jun Bao
- Department of Clinical Laboratory, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - Dai-Wen Mao
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, NO.739 Dingshen Road, Zhoushan City, 316021, Zhejiang, China
| | - Ji-Hang Zhou
- Cell and Molecular Biology Laboratory, Zhoushan Hospital, Wenzhou medical University, Zhoushan, 316021, Zhejiang, China
| | - Zhe-En Zhang
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, NO.739 Dingshen Road, Zhoushan City, 316021, Zhejiang, China
| | - Yan Wang
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, NO.739 Dingshen Road, Zhoushan City, 316021, Zhejiang, China
| | - Yi-Wei Li
- Department of Clinical Laboratory, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - He-Ping Wang
- Department of Radiology Diagnostic Center, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - Lue Li
- Department of Respiratory Medicine, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - Hai-Yan Pan
- Department of Gastroenterology, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - Guo-Qiang Zhang
- Department of Gastrointestinal Surgery, Zhoushan Hospital, WenZhou Medical University, Zhoushan, 316021, Zhejiang, China
| | - Shi-Bo Li
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, NO.739 Dingshen Road, Zhoushan City, 316021, Zhejiang, China.
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