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Jaganathan R, Kumaradhas P. Structural insights into Furin enzyme inhibition to block SARS-CoV-2 spike protein cleavage: an in-silico approach. 3 Biotech 2024; 14:213. [PMID: 39193012 PMCID: PMC11345345 DOI: 10.1007/s13205-024-04054-y] [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: 06/08/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024] Open
Abstract
This study investigates the binding affinity and interactions of the Furin enzyme with two inhibitors, Naphthofluorescein and decanoyl-RVKR-chloromethylketone (CMK), using molecular docking and molecular dynamics (MD) simulations. Molecular docking results showed binding affinities of - 9.18 kcal/mol for CMK and - 5.39 kcal/mol for Naphthofluorescein. To further understand the stability and conformational changes of these complexes, MD simulations were performed. Despite CMK's favorable docking score, MD simulations revealed that its binding interactions at the Furin-active site were unstable, with significant changes observed during the simulation. In contrast, Naphthofluorescein maintained strong and stable interactions throughout the MD simulation, as confirmed by RMSD and RMSF analyses. The binding-free-energy analysis also supported the stability of Naphthofluorescein. These findings indicate that Naphthofluorescein exhibits greater stability and binding affinity as a Furin inhibitor compared to CMK. The results of this in-silico study suggest that Naphthofluorescein, along with CMK, holds the potential for repurposing as a treatment for COVID-19, subject to further validation through clinical studies.
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Affiliation(s)
- Ramakrishnan Jaganathan
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 602 105 India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011 India
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2
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Chen X, Kalyar F, Chughtai AA, MacIntyre CR. Use of a risk assessment tool to determine the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2024; 44:1896-1906. [PMID: 38488186 DOI: 10.1111/risa.14291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/28/2023] [Indexed: 08/07/2024]
Abstract
The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is contentious. Most studies have focused on a zoonotic origin, but definitive evidence such as an intermediary animal host is lacking. We used an established risk analysis tool for differentiating natural and unnatural epidemics, the modified Grunow-Finke assessment tool (mGFT) to study the origin of SARS-COV-2. The mGFT scores 11 criteria to provide a likelihood of natural or unnatural origin. Using published literature and publicly available sources of information, we applied the mGFT to the origin of SARS-CoV-2. The mGFT scored 41/60 points (68%), with high inter-rater reliability (100%), indicating a greater likelihood of an unnatural than natural origin of SARS-CoV-2. This risk assessment cannot prove the origin of SARS-CoV-2 but shows that the possibility of a laboratory origin cannot be easily dismissed.
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Affiliation(s)
- Xin Chen
- Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Fatema Kalyar
- Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Abrar Ahmad Chughtai
- School of Population Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Chandini Raina MacIntyre
- Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- College of Public Service & Community Solutions, Arizona State University, Tempe, Arizona, USA
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3
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Jiang X, Li D, Maghsoudloo M, Zhang X, Ma W, Fu J. Targeting furin, a cellular proprotein convertase, for COVID-19 prevention and therapeutics. Drug Discov Today 2024; 29:104026. [PMID: 38762086 DOI: 10.1016/j.drudis.2024.104026] [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: 12/22/2023] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
SARS-CoV-2 has triggered an international outbreak of the highly contagious acute respiratory disease known as COVID-19. Identifying key targets in the virus infection lifecycle is crucial for developing effective prevention and therapeutic strategies against it. Furin is a serine endoprotease that belongs to the family of proprotein convertases and plays a critical role in the entry of host cells by SARS-CoV-2. Furin can cleave a specific S1/S2 site, PRRAR, on the spike protein of SARS-CoV-2, which promotes viral transmission by facilitating membrane fusion. Hence, targeting furin could hold clinical implications for the prevention and treatment of COVID-19. This review offers an overview of furin's structure, substrates, function, and inhibitors, with a focus on its potential role in SARS-CoV-2 infection.
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Affiliation(s)
- Xia Jiang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau
| | - Dabing Li
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Mazaher Maghsoudloo
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Xinghai Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Wenzhe Ma
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau.
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China.
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4
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Zhang Y, Chen S, Tian Y, Fu X. Host factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects. Front Cell Infect Microbiol 2024; 14:1407261. [PMID: 38846354 PMCID: PMC11155306 DOI: 10.3389/fcimb.2024.1407261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
SARS-CoV-2 is the causative virus of the devastating COVID-19 pandemic that results in an unparalleled global health and economic crisis. Despite unprecedented scientific efforts and therapeutic interventions, the fight against COVID-19 continues as the rapid emergence of different SARS-CoV-2 variants of concern and the increasing challenge of long COVID-19, raising a vast demand to understand the pathomechanisms of COVID-19 and its long-term sequelae and develop therapeutic strategies beyond the virus per se. Notably, in addition to the virus itself, the replication cycle of SARS-CoV-2 and clinical severity of COVID-19 is also governed by host factors. In this review, we therefore comprehensively overview the replication cycle and pathogenesis of SARS-CoV-2 from the perspective of host factors and host-virus interactions. We sequentially outline the pathological implications of molecular interactions between host factors and SARS-CoV-2 in multi-organ and multi-system long COVID-19, and summarize current therapeutic strategies and agents targeting host factors for treating these diseases. This knowledge would be key for the identification of new pathophysiological aspects and mechanisms, and the development of actionable therapeutic targets and strategies for tackling COVID-19 and its sequelae.
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Affiliation(s)
| | | | - Yan Tian
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
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Rodriguez Galvan JJ, de Vries M, Belblidia S, Fisher A, Prescott RA, Crosse KM, Mangel WF, Duerr R, Dittmann M. In-silico docking platform with serine protease inhibitor (SERPIN) structures identifies host cysteine protease targets with significance for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.11.18.517133. [PMID: 36415456 PMCID: PMC9681043 DOI: 10.1101/2022.11.18.517133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Serine Protease Inhibitors (SERPINs) regulate protease activity in various physiological processes such as inflammation, cancer metastasis, angiogenesis, and neurodegenerative diseases. However, their potential in combating viral infections, where proteases are also crucial, remains underexplored. This is due to our limited understanding of SERPIN expression during viral-induced inflammation and of the SERPINs' full spectrum of target proteases. Here, we demonstrate widespread expression of human SERPINs in response to respiratory virus infections, both in vitro and in vivo , alongside classical antiviral effectors. Through comprehensive in-silico docking with full-length SERPIN and protease 3D structures, we confirm known inhibitors of specific proteases; more importantly, the results predict novel SERPIN-protease interactions. Experimentally, we validate the direct inhibition of key proteases essential for viral life cycles, including the SERPIN PAI-1's capability to inhibit select cysteine proteases such as cathepsin L, and the serine protease TMPRSS2. Consequently, PAI-1 suppresses spike maturation and multi-cycle SARS-CoV-2 replication. Our findings challenge conventional notions of SERPIN selectivity, underscore the power of in-silico docking for SERPIN target discovery, and offer potential therapeutic interventions targeting host proteolytic pathways to combat viruses with urgent unmet therapeutic needs. SIGNIFICANCE Serine protease inhibitors (SERPINs) play crucial roles in various physiological processes, including viral infections. However, our comprehension of the full array of proteases targeted by the SERPIN family has traditionally been limited, hindering a comprehensive understanding of their regulatory potential. We developed an in-silico docking platform to identify new SERPIN target proteases expressed in the respiratory tract, a critical viral entry portal. The platform confirmed known and predicted new targets for every SERPIN examined, shedding light on previously unrecognized patterns in SERPIN selectivity. Notably, both key proteases for SARS-CoV-2 maturation were among the newly predicted targets, which we validated experimentally. This underscores the platform's potential in uncovering targets with significance in viral infections, paving the way to define the full potential of the SERPIN family in infectious disease and beyond.
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Behboudi E, Nooreddin Faraji S, Daryabor G, Mohammad Ali Hashemi S, Asadi M, Edalat F, Javad Raee M, Hatam G. SARS-CoV-2 mechanisms of cell tropism in various organs considering host factors. Heliyon 2024; 10:e26577. [PMID: 38420467 PMCID: PMC10901034 DOI: 10.1016/j.heliyon.2024.e26577] [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: 05/02/2023] [Revised: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
A critical step in the drug design for SARS-CoV-2 is to discover its molecular targets. This study comprehensively reviewed the molecular mechanisms of SARS-CoV-2, exploring host cell tropism and interaction targets crucial for cell entry. The findings revealed that beyond ACE2 as the primary entry receptor, alternative receptors, co-receptors, and several proteases such as TMPRSS2, Furin, Cathepsin L, and ADAM play critical roles in virus entry and subsequent pathogenesis. Additionally, SARS-CoV-2 displays tropism in various human organs due to its diverse receptors. This review delves into the intricate details of receptors, host proteases, and the involvement of each organ. Polymorphisms in the ACE2 receptor and mutations in the spike or its RBD region contribute to the emergence of variants like Alpha, Beta, Gamma, Delta, and Omicron, impacting the pathogenicity of SARS-CoV-2. The challenge posed by mutations raises questions about the effectiveness of existing vaccines and drugs, necessitating consideration for updates in their formulations. In the urgency of these critical situations, repurposed drugs such as Camostat Mesylate and Nafamostat Mesylate emerge as viable pharmaceutical options. Numerous drugs are involved in inhibiting receptors and host factors crucial for SARS-CoV-2 entry, with most discussed in this review. In conclusion, this study may provide valuable insights to inform decisions in therapeutic approaches.
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Affiliation(s)
- Emad Behboudi
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
| | - Seyed Nooreddin Faraji
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Daryabor
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Maryam Asadi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fahime Edalat
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Li M, Wang Y, Wang Y, Li R, Wang S, Ding P, Zhang G. Accurate location of two conserved linear epitopes of PEDV utilizing monoclonal antibodies induced by S1 protein nanoparticles. Int J Biol Macromol 2023; 253:127276. [PMID: 37804887 DOI: 10.1016/j.ijbiomac.2023.127276] [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: 08/16/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Porcine Epidemic diarrhea virus (PEDV), which can result in severe vomiting, diarrhea, dehydration and death in newborn piglets, poses a great threat to the pig industry around the world. The S1 subunit of S protein is crucial for triggering neutralizing antibodies binding to the receptor. Based on the advantages of high immunogenicity and precise assembly of nanoparticles, the mi3 nanoparticles and truncated S1 protein were assembled by the SpyTag/SpyCatcher system and then expressed in HEK293F cells, whereafter high-efficiency monoclonal antibodies (mAbs) were produced and identified. The obtained five mAbs can bind to various genotypes of PEDV, including a mAb (12G) which can neutralize G1 and G2 genotypes of PEDV in vitro. By further identification of monoclonal antibody target sequences, 507FNDHSF512 and 553LFYNVTNSYG562 were first identified as B-cell linear epitopes, in which 553LFYNVTNSYG562 was a neutralizing epitope. Alanine scans identified the key amino acid sites of two epitopes. Moreover, the results of multiple sequence alignment analysis showed that these two epitopes were highly conserved in various subtype variants. In brief, these findings can serve as a basis for additional research of PEDV and prospective resources for the creation of later detection and diagnostic techniques.
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Affiliation(s)
- Minghui Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yue Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yanan Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ruiqi Li
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Siqiao Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Peiyang Ding
- College of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Longhu Laboratory, Zhengzhou, China.
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; College of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Longhu Laboratory, Zhengzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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Wells EW, Parker MT. Regulating Select Agent Chimeras: Defining the Problem(s) Through the Lens of SARS-CoV-1/SARS-CoV-2 Chimeric Viruses. Health Secur 2023; 21:392-406. [PMID: 37703547 DOI: 10.1089/hs.2023.0008] [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] [Indexed: 09/15/2023] Open
Abstract
In late 2021, the US Centers for Disease Control and Prevention (CDC) posted an interim final rule (86 FR 64075) to the federal register regulating the possession, use, and transfer of SARS-CoV-1/SARS-CoV-2 chimeric viruses. In doing so, the CDC provided the reasoning that viral chimeras combining the transmissibility of SARS-CoV-2 with the pathogenicity and lethality of SARS-CoV-1 pose a significant risk to public health and should thus be placed on the select agents and toxins list. However, 86 FR 64075 lacked clarity in its definitions and scope, some of which the CDC addressed in response to public comments in the final rule, 88 FR 13322, in early 2023. To evaluate these regulatory actions, we reviewed the existing select agent regulations to understand the landscape of chimeric virus regulation. Based on our findings, we first present clear definitions for the terms "chimeric virus," "viral chimera," and "virulence factor" and provide a list of SARS-CoV-1 virulence factors in an effort to aid researchers and federal rulemaking for these agents moving forward. We then provide suggestions for a combination of similarity and functional characteristic cutoffs that the government could use to enable researchers to distinguish between regulated and nonregulated chimeras. Finally, we discuss current select agent regulations and their overlaps with 86 FR 64075 and 88 FR 13322 and make suggestions for how to address chimera concerns within and/or without these regulations. Collectively, we believe that our findings fill important gaps in current federal regulations and provide forward-looking philosophical and practical analysis that can guide future decisionmaking.
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Affiliation(s)
- Elizabeth W Wells
- Elizabeth W. Wells is a Student, Department of Biology, Georgetown College of Arts & Sciences, Georgetown University, Washington, DC
| | - Michael T Parker
- Michael T. Parker, PhD, is Assistant Dean, Georgetown College of Arts & Sciences, Georgetown University, Washington, DC
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Sengar A, Cervantes M, Bondalapati ST, Hess T, Kasson PM. Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry. J Virol 2023; 97:e0199222. [PMID: 37133381 PMCID: PMC10231210 DOI: 10.1128/jvi.01992-22] [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: 01/05/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to cell surface receptors and is activated for membrane fusion and cell entry via proteolytic cleavage. Phenomenological data have shown that SARS-CoV-2 can be activated for entry at either the cell surface or in endosomes, but the relative roles in different cell types and mechanisms of entry have been debated. Here, we used single-virus fusion experiments and exogenously controlled proteases to probe activation directly. We found that plasma membrane and an appropriate protease are sufficient to support SARS-CoV-2 pseudovirus fusion. Furthermore, fusion kinetics of SARS-CoV-2 pseudoviruses are indistinguishable no matter which of a broad range of proteases is used to activate the virus. This suggests that the fusion mechanism is insensitive to protease identity or even whether activation occurs before or after receptor binding. These data support a model for opportunistic fusion by SARS-CoV-2 in which the subcellular location of entry likely depends on the differential activity of airway, cellsurface, and endosomal proteases, but all support infection. Inhibition of any single host protease may thus reduce infection in some cells but may be less clinically robust. IMPORTANCE SARS-CoV-2 can use multiple pathways to infect cells, as demonstrated recently when new viral variants switched dominant infection pathways. Here, we used single-virus fusion experiments together with biochemical reconstitution to show that these multiple pathways coexist simultaneously and specifically that the virus can be activated by different proteases in different cellular compartments with mechanistically identical effects. The consequences of this are that the virus is evolutionarily plastic and that therapies targeting viral entry should address multiple pathways at once to achieve optimal clinical effects.
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Affiliation(s)
- Anjali Sengar
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Marcos Cervantes
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Sai T. Bondalapati
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Tobin Hess
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Peter M. Kasson
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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López-Andreo MJ, Vicente-Romero MR, Bernal E, Navarro-González I, Salazar-Martínez F, Cánovas-Cánovas V, Gil-Ortuño C, Riquelme-Rocamora MG, Solano F, Ibáñez-López FJ, Tomás C, Candel-Pérez C, Pérez-Parra S, Flores-Flores C. Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications. Diseases 2023; 11:diseases11020054. [PMID: 37092436 PMCID: PMC10123601 DOI: 10.3390/diseases11020054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
During the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging to samples taken from COVID-19 patients from October 2020 to April 2021 at the “Reina Sofía” Hospital (Murcia, Spain) focused to variant appeared later. The results at the mentioned stage show the turning point since the 20E (EU1) variant was still prevalent (71.6%), but Alpha was bursting to 14.8%. Concern mutations have been found in 5 genomes classified as 20E (EU1), which were not characteristic of this still little evolved variant. Most of those mutations are found in the spike protein, namely Δ69–70, E484K, Q675H and P681H. However, a relevant deletion in ORF1a at positions 3675–3677 was also identified. These mutations have been reported in many later SARS-CoV-2 lineages, including Omicron. Taken together, our data suggest that preferential emergence mutations could already be present in the early converging evolution. Aside from this, the molecular information has been contrasted with clinical data. Statistical analyses suggest that the correlation between age and severity criteria is significantly higher in the viral samples with more accumulated changes.
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Affiliation(s)
- María José López-Andreo
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | | | - Enrique Bernal
- Laboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, Spain
- Correspondence: (E.B.); (F.S.)
| | - Inmaculada Navarro-González
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | - Francisco Salazar-Martínez
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | - Vanesa Cánovas-Cánovas
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | - Cristina Gil-Ortuño
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | - María Gema Riquelme-Rocamora
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | - Francisco Solano
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Universidad de Murcia, 30100 Murcia, Spain
- Correspondence: (E.B.); (F.S.)
| | - Francisco Javier Ibáñez-López
- Sección de Apoyo Estadístico, Servicio de Investigación Biosanitaria, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
| | - Cristina Tomás
- Laboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, Spain
| | - Carmen Candel-Pérez
- Laboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, Spain
| | | | - César Flores-Flores
- Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, Spain
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11
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Wang Z, Zhong K, Wang G, Lu Q, Li H, Wu Z, Zhang Z, Yang N, Zheng M, Wang Y, Nie C, Zhou L, Tong A. Loss of furin site enhances SARS-CoV-2 spike protein pseudovirus infection. Gene X 2023; 856:147144. [PMID: 36577450 PMCID: PMC9790109 DOI: 10.1016/j.gene.2022.147144] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND SARS-CoV-2 has a significant impact on healthcare systems all around the world. Due to its high pathogenicity, live SARS-CoV-2 must be handled under biosafety level 3 conditions. Pseudoviruses are useful virological tools because of their safety and versatility, but the low titer of these viruses remains a limitation for their more comprehensive applications. METHOD Here, we constructed a Luc/eGFP based on a pseudotyped lentiviral HIV-1 system to transduce SARS-CoV-2 S glycoprotein to detect cell entry properties and cellular tropism. RESULTS The furin cleavage site deletion of the S protein removed (SFko) can help SARS-CoV-2 S to be cleaved during viral packaging to improve infection efficiency. The furin cleavage site in SARS-CoV-2-S mediates membrane fusion and SFko leads to an increased level of S protein and limits S1/S2 cleavage to enhance pseudovirus infection in cells. Full-length S (SFL) pseudotyped with N, M, and E helper packaging can effectively help SFL infect cells. Finally, pseudotyped SFko particles were successfully used to detect neutralizing antibodies in RBD protein-immunized mouse serum. CONCLUSION Overall, our study indicates a series of modifications that result in the production of relatively high-titer SARS-COV-2 pseudo-particles that may be suitable for the detection of neutralizing antibodies from COVID-19 patients.
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Affiliation(s)
- Zeng Wang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kunhong Zhong
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guoqing Wang
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qizhong Lu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hexian Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiguo Wu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zongliang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Nian Yang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Meijun Zheng
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuelong Wang
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chunlai Nie
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Liangxue Zhou
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
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Intensive critical care and management of asthmatic and smoker patients in COVID-19 infection. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:29-42. [PMID: 36692461 DOI: 10.2478/acph-2023-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 01/25/2023]
Abstract
This century's most serious catastrophe, COVID-19, has been dubbed "the most life-threatening disaster ever". Asthmatic persons are even more prone to COVID-19's complex interplay with the underlying inflammatory condition. In order to protect themselves against COVID-19, asthmatic patients must be very vigilant in their usage of therapeutic techniques and drugs (e.g., bronchodilators, 5-lipoxygenase inhibitors), which may be accessed to deal with mild, moderate, and severe COVID-19 indications. People with asthma may have more severe COVID-19 symptoms, which may lead to a worsening of their condition. Several cytokines were found to be elevated in the bronchial tracts of patients with acute instances of COVID-19, suggesting that this ailment may aggravate asthma episodes by increasing inflammation. The intensity of COVID-19 symptoms is lessened in patients with asthma who have superior levels of T-cells. Several antibiotics, antivirals, antipyretics, and anti-inflammatory drugs have been suggested to suppress COVID-19 symptoms in asthmatic persons. Furthermore, smokers are more likely to have aggravated repercussions in COVID-19 infection. Being hospitalized to critical care due to COVID-19, needing mechanical breathing, and suffering from serious health repercussions, are all possible outcomes for someone who has previously smoked. Smoking damages airways and alveoli, which significantly raises the risk of COVID-19-related health complications. Patients with a previous record of smoking are predisposed to severe COVID-19 disease symptoms that essentially require a combination of bronchodilators, mucolytics, antivirals, and antimuscarinic drugs, to cope with the situation. The present review discusses the care and management of asthmatic and smoker patients in COVID-19 infection.
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13
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Lee CY, Nguyen AT, Doan LH, Chu LW, Chang CH, Liu HK, Lee IL, Wang TH, Lai JM, Tsao SM, Liao HJ, Ping YH, Huang CYF. Repurposing Astragalus Polysaccharide PG2 for Inhibiting ACE2 and SARS-CoV-2 Spike Syncytial Formation and Anti-Inflammatory Effects. Viruses 2023; 15:641. [PMID: 36992350 PMCID: PMC10054482 DOI: 10.3390/v15030641] [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: 12/29/2022] [Revised: 02/05/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious threat to global public health. In an effort to develop novel anti-coronavirus therapeutics and achieve prophylactics, we used gene set enrichment analysis (GSEA) for drug screening and identified that Astragalus polysaccharide (PG2), a mixture of polysaccharides purified from Astragalus membranaceus, could effectively reverse COVID-19 signature genes. Further biological assays revealed that PG2 could prevent the fusion of BHK21-expressing wild-type (WT) viral spike (S) protein and Calu-3-expressing ACE2. Additionally, it specifically prevents the binding of recombinant viral S of WT, alpha, and beta strains to ACE2 receptor in our non-cell-based system. In addition, PG2 enhances let-7a, miR-146a, and miR-148b expression levels in the lung epithelial cells. These findings speculate that PG2 has the potential to reduce viral replication in lung and cytokine storm via these PG2-induced miRNAs. Furthermore, macrophage activation is one of the primary issues leading to the complicated condition of COVID-19 patients, and our results revealed that PG2 could regulate the activation of macrophages by promoting the polarization of THP-1-derived macrophages into an anti-inflammatory phenotype. In this study, PG2 stimulated M2 macrophage activation and increased the expression levels of anti-inflammatory cytokines IL-10 and IL-1RN. Additionally, PG2 was recently used to treat patients with severe COVID-19 symptoms by reducing the neutrophil-to-lymphocyte ratio (NLR). Therefore, our data suggest that PG2, a repurposed drug, possesses the potential to prevent WT SARS-CoV-2 S-mediated syncytia formation with the host cells; it also inhibits the binding of S proteins of WT, alpha, and beta strains to the recombinant ACE2 and halts severe COVID-19 development by regulating the polarization of macrophages to M2 cells.
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Affiliation(s)
- Chia-Yin Lee
- Taiwan National Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112304, Taiwan
| | - Anh Thuc Nguyen
- Taiwan National Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112304, Taiwan
| | - Ly Hien Doan
- Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Li-Wei Chu
- Department and Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chih-Hung Chang
- Department of Orthopedic Surgery, Far Eastern Memorial Hospital, New Taipei City 220216, Taiwan
| | - Hui-Kang Liu
- Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine (NRICM), Ministry of Health and Welfare, Taipei 112304, Taiwan
| | - I-Lin Lee
- PhytoHeath Corporation, Taipei 105403, Taiwan
| | | | - Jin-Mei Lai
- Department of Life Science, College of Science and Engineering, Fu Jen Catholic University, New Taipei City 242062, Taiwan
| | - Shih-Ming Tsao
- Division of Pulmonary Medicine, School of Medicine, Chung Shan Medical University Hospital, Chung Shan Medical University, Taichung 402306, Taiwan
| | - Hsiu-Jung Liao
- Department of Medical Research, Far Eastern Memorial Hospital, New Taipei City 220216, Taiwan
| | - Yueh-Hsin Ping
- Department and Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chi-Ying F. Huang
- Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
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14
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Production and characterization of lentivirus vector-based SARS-CoV-2 pseudoviruses with dual reporters: Evaluation of anti-SARS-CoV-2 viral effect of Korean Red Ginseng. J Ginseng Res 2023; 47:123-132. [PMID: 35855181 PMCID: PMC9283196 DOI: 10.1016/j.jgr.2022.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/09/2023] Open
Abstract
Background Pseudotyped virus systems that incorporate viral proteins have been widely employed for the rapid determination of the effectiveness and neutralizing activity of drug and vaccine candidates in biosafety level 2 facilities. We report an efficient method for producing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus with dual luciferase and fluorescent protein reporters. Moreover, using the established method, we also aimed to investigate whether Korean Red Ginseng (KRG), a valuable Korean herbal medicine, can attenuate infectivity of the pseudotyped virus. Methods A pseudovirus of SARS-CoV-2 (SARS-2pv) was constructed and efficiently produced using lentivirus vector systems available in the public domain by the introduction of critical mutations in the cytoplasmic tail of the spike protein. KRG extract was dose-dependently treated to Calu-3 cells during SARS2-pv treatment to evaluate the protective activity against SARS-CoV-2. Results The use of Calu-3 cells or the expression of angiotensin-converting enzyme 2 (ACE2) in HEK293T cells enabled SARS-2pv infection of host cells. Coexpression of transmembrane protease serine subtype 2 (TMPRSS2), which is the activator of spike protein, with ACE2 dramatically elevated luciferase activity, confirming the importance of the TMPRSS2-mediated pathway during SARS-CoV-2 entry. Our pseudovirus assay also revealed that KRG elicited resistance to SARS-CoV-2 infection in lung cells, suggesting its beneficial health effect. Conclusion The method demonstrated the production of SARS-2pv for the analysis of vaccine or drug candidates. When KRG was assessed by the method, it protected host cells from coronavirus infection. Further studies will be followed for demonstrating this potential benefit.
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Dong B, Zhang X, Bai J, Zhang G, Li C, Lin W. Epidemiological investigation of canine coronavirus infection in Chinese domestic dogs: A systematic review and data synthesis. Prev Vet Med 2022; 209:105792. [DOI: 10.1016/j.prevetmed.2022.105792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022]
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16
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Zhang Y, Zhang L, Wu J, Yu Y, Liu S, Li T, Li Q, Ding R, Wang H, Nie J, Cui Z, Wang Y, Huang W, Wang Y. A second functional furin site in the SARS-CoV-2 spike protein. Emerg Microbes Infect 2022; 11:182-194. [PMID: 34856891 PMCID: PMC8741242 DOI: 10.1080/22221751.2021.2014284] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ubiquitously-expressed proteolytic enzyme furin is closely related to the pathogenesis of SARS-CoV-2 and therefore represents a key target for antiviral therapy. Based on bioinformatic analysis and pseudovirus tests, we discovered a second functional furin site located in the spike protein. Furin still increased the infectivity of mutated SARS-CoV-2 pseudovirus in 293T-ACE2 cells when the canonical polybasic cleavage site (682-686) was deleted. However, K814A mutation eliminated the enhancing effect of furin on virus infection. Furin inhibitor prevented infection by 682-686-deleted SARS-CoV-2 in 293T-ACE2-furin cells, but not the K814A mutant. K814A mutation did not affect the activity of TMPRSS2 and cathepsin L but did impact the cleavage of S2 into S2' and cell-cell fusion. Additionally, we showed that this functional furin site exists in RaTG13 from bat and PCoV-GD/GX from pangolin. Therefore, we discovered a new functional furin site that is pivotal in promoting SARS-CoV-2 infection.
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Affiliation(s)
- Yue Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
- National Vaccine & Serum Institute, Beijing, People's Republic of China
| | - Li Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jiajing Wu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Yuanling Yu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Tao Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Qianqian Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Ruxia Ding
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Haixin Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Zhimin Cui
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Yulin Wang
- National Vaccine & Serum Institute, Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
- Lead Contact
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17
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Jose AM. Analyzing the Impermeable Structure and Myriad of Antiviral Therapies for SARS-CoV-2. JOURNAL OF THE ASSOCIATION OF PHYSICIANS OF INDIA 2022. [DOI: 10.5005/japi-11001-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Hao Y, Wang Y, Wang M, Zhou L, Shi J, Cao J, Wang D. The origins of COVID-19 pandemic: A brief overview. Transbound Emerg Dis 2022; 69:3181-3197. [PMID: 36218169 PMCID: PMC9874793 DOI: 10.1111/tbed.14732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.
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Affiliation(s)
- Ying‐Jian Hao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Yu‐Lan Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Mei‐Yue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Lan Zhou
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Jian‐Yun Shi
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Ji‐Min Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - De‐Ping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
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Sachs JD, Karim SSA, Aknin L, Allen J, Brosbøl K, Colombo F, Barron GC, Espinosa MF, Gaspar V, Gaviria A, Haines A, Hotez PJ, Koundouri P, Bascuñán FL, Lee JK, Pate MA, Ramos G, Reddy KS, Serageldin I, Thwaites J, Vike-Freiberga V, Wang C, Were MK, Xue L, Bahadur C, Bottazzi ME, Bullen C, Laryea-Adjei G, Ben Amor Y, Karadag O, Lafortune G, Torres E, Barredo L, Bartels JGE, Joshi N, Hellard M, Huynh UK, Khandelwal S, Lazarus JV, Michie S. The Lancet Commission on lessons for the future from the COVID-19 pandemic. Lancet 2022; 400:1224-1280. [PMID: 36115368 PMCID: PMC9539542 DOI: 10.1016/s0140-6736(22)01585-9] [Citation(s) in RCA: 262] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 02/03/2023]
Affiliation(s)
- Jeffrey D Sachs
- Center for Sustainable Development, Columbia University, New York, NY, United States.
| | - Salim S Abdool Karim
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lara Aknin
- Department of Psychology, Simon Fraser University, Burnaby, BC, Canada
| | - Joseph Allen
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, United States
| | | | - Francesca Colombo
- Health Division, Organisation for Economic Co-operation and Development, Paris, France
| | | | | | - Vitor Gaspar
- Fiscal Affairs Department, International Monetary Fund, Washington, DC, United States
| | | | - Andy Haines
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, UK; Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Peter J Hotez
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Phoebe Koundouri
- Department of International and European Economic Studies, Athens University of Economics and Business, Athens, Greece; Department of Technology, Management and Economics, Technical University of Denmark, Kongens Lyngby, Denmark; European Association of Environmental and Resource Economists, Athens, Greece
| | - Felipe Larraín Bascuñán
- Department of Economics and Administration, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jong-Koo Lee
- National Academy of Medicine of Korea, Seoul, Republic of Korea
| | - Muhammad Ali Pate
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, United States
| | | | | | | | - John Thwaites
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | | | - Chen Wang
- National Clinical Research Center for Respiratory Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China; National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | | | - Lan Xue
- Schwarzman College, Tsinghua University, Beijing, China
| | - Chandrika Bahadur
- The Lancet COVID-19 Commission Regional Task Force: India, New Delhi, India
| | - Maria Elena Bottazzi
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Chris Bullen
- National Institute for Health Innovation, University of Auckland, Auckland, New Zealand
| | | | - Yanis Ben Amor
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | - Ozge Karadag
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | | | - Emma Torres
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | - Lauren Barredo
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | - Juliana G E Bartels
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | - Neena Joshi
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | | | | | | | - Jeffrey V Lazarus
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Susan Michie
- Centre for Behaviour Change, University College London, London, UK
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20
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Kim J, Yoon J, Park JE. Furin cleavage is required for swine acute diarrhea syndrome coronavirus spike protein-mediated cell-cell fusion. Emerg Microbes Infect 2022; 11:2176-2183. [PMID: 35976165 PMCID: PMC9518401 DOI: 10.1080/22221751.2022.2114850] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) was reported in China in 2017 and is a causative agent of porcine enteric disease. Recent studies indicate that cells from various hosts are susceptible to SADS-CoV, suggesting the zoonotic potential of this virus. However, little is known about the mechanisms through which this virus enters cells. In this study, we investigated the role of furin in SADS-CoV spike (S)-mediated cell-cell fusion and entry. We found that the SADS-CoV S protein induced the fusion of various cells. Cell-cell fusion was inhibited by the proprotein convertase inhibitor dec-RVKR-cmk, and between cells transfected with mutant S proteins resistant to furin cleavage. These findings revealed that furin-induced cleavage of the SADS-CoV S protein is required for cell-cell fusion. Using mutagenesis analysis, we demonstrated that furin cleaves the SADS-CoV S protein near the S1/S2 cleavage site, 446RYVR449 and 543AVRR546. We used pseudotyped viruses to determine whether furin-induced S cleavage is also required for viral entry. Pseudotyped viruses expressing S proteins with a mutated furin cleavage site could be transduced into target cells, indicating that furin-induced cleavage is not required for pseudotyped virus entry. Our data indicate that S cleavage is critical for SADS-CoV S-mediated cell-cell fusion and suggest that furin might be a host target for SADS-CoV antivirals.
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Affiliation(s)
- Jinman Kim
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jaewon Yoon
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jung-Eun Park
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea.,Research Institute of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
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21
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Study of protease-mediated processes initiating viral infection and cell-cell viral spreading of SARS-CoV-2. J Mol Model 2022; 28:224. [PMID: 35854129 PMCID: PMC9296015 DOI: 10.1007/s00894-022-05206-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
Abstract
Viral-cell entry and cell-cell viral spreading processes of SARS-CoV-2 are subjected to fast evolutionary optimization because of its worldwide spreading, requiring the need for new drug developments. However, this task is still challenging, because a detailed understanding of the underlying molecular processes, mediated by the key cellular proteases TMPRSS2 and furin, is still lacking. Here, we show by large-scale atomistic calculations that binding of the ACE2 cell receptor at one of the heteromers of the SARS-CoV-2 spike leads to a release of its furin cleavage site (S1/S2), enabling an enhanced furin binding, and that this latter process promotes the binding of TMPRSS2 through the release of the TMPRSS2 cleavage site (S2') out of the ACE2-binding heteromer. Moreover, we find that, after proteolytic cleavage, improved furin binding causes that parts of the S2 subunit dissociate from the complex, suggesting that furin promotes the fusion of the S2 subunit with the cell membrane before transfer of the viral RNA. Here we show by computational means that binding of the ACE2-cell receptor at one of the heteromers of the SARS-CoV-2 spike leads to an enhanced binding of the protease furin, promoting the binding of the protease TMPRSS2. Moreover, we show that, after proteolytic cleavage, improved furin binding causes that parts of the heteromer dissociate from the spike.
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22
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A call for an independent inquiry into the origin of the SARS-CoV-2 virus. Proc Natl Acad Sci U S A 2022; 119:e2202769119. [PMID: 35588448 PMCID: PMC9173817 DOI: 10.1073/pnas.2202769119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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23
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Gonçalves RL, Leite TCR, Dias BDP, Caetano CCDS, de Souza ACG, Batista UDS, Barbosa CC, Reyes-Sandoval A, Coelho LFL, Silva BDM. SARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein. J Biomol Struct Dyn 2022; 40:3336-3346. [DOI: 10.1080/07391102.2020.1844052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ricardo Lemes Gonçalves
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Biotecnologia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Túlio César Rodrigues Leite
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Biotecnologia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Bruna de Paula Dias
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Biotecnologia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Camila Carla da Silva Caetano
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Ana Clara Gomes de Souza
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Ubiratan da Silva Batista
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Camila Cavadas Barbosa
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Arturo Reyes-Sandoval
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luiz Felipe Leomil Coelho
- Laboratório de Vacinas, Departamento de Microbiologia e Imunologia, Universidade Federal de Alfenas, Alfenas, Brazil
| | - Breno de Mello Silva
- Laboratório de Biologia e Tecnologia de Micro-organismos, Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Biotecnologia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Programa de pós-graduação em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
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Yépez Y, Marcano-Ruiz M, Bezerra RS, Fam B, Ximenez JPB, Silva WA, Bortolini MC. Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Genet Mol Biol 2022; 45:e20210309. [PMID: 35266951 PMCID: PMC8908351 DOI: 10.1590/1678-4685-gmb-2021-0309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
Abstract
Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses.
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Affiliation(s)
- Yuri Yépez
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Mariana Marcano-Ruiz
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Rafael S Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Bibiana Fam
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - João PB Ximenez
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Wilson A Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Departamento de Genética, Ribeirão Preto, SP, Brazil
- Instituto de Pesquisa do Câncer de Guarapuava, Guarapuava, PR,
Brazil
| | - Maria Cátira Bortolini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
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25
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A highly immunogenic live-attenuated vaccine candidate prevents SARS-CoV-2 infection and transmission in hamsters. Innovation (N Y) 2022; 3:100221. [PMID: 35252935 PMCID: PMC8888354 DOI: 10.1016/j.xinn.2022.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/28/2022] [Indexed: 01/08/2023] Open
Abstract
The highly pathogenic and readily transmissible SARS-CoV-2 has caused a global coronavirus pandemic, urgently requiring effective countermeasures against its rapid expansion. All available vaccine platforms are being used to generate safe and effective COVID-19 vaccines. Here, we generated a live-attenuated candidate vaccine strain by serial passaging of a SARS-CoV-2 clinical isolate in Vero cells. Deep sequencing revealed the dynamic adaptation of SARS-CoV-2 in Vero cells, resulting in a stable clone with a deletion of seven amino acids (N679SPRRAR685) at the S1/S2 junction of the S protein (named VAS5). VAS5 showed significant attenuation of replication in multiple human cell lines, human airway epithelium organoids, and hACE2 mice. Viral fitness competition assays demonstrated that VAS5 showed specific tropism to Vero cells but decreased fitness in human cells compared with the parental virus. More importantly, a single intranasal injection of VAS5 elicited a high level of neutralizing antibodies and prevented SARS-CoV-2 infection in mice as well as close-contact transmission in golden Syrian hamsters. Structural and biochemical analysis revealed a stable and locked prefusion conformation of the S trimer of VAS5, which most resembles SARS-CoV-2-3Q-2P, an advanced vaccine immunogen (NVAX-CoV2373). Further systematic antigenic profiling and immunogenicity validation confirmed that the VAS5 S trimer presents an enhanced antigenic mimic of the wild-type S trimer. Our results not only provide a potent live-attenuated vaccine candidate against COVID-19 but also clarify the molecular and structural basis for the highly attenuated and super immunogenic phenotype of VAS5. Passaging of a protype SARS-CoV-2 in Vero cells generates a live-attenuated VAS5 A 7 amino acids deletion of the S protein contributes to the attenuated phenotype VAS5 immunization prevents SARS-CoV-2 infection and transmission in Syrian hamsters The VAS5 S protein forms a locked prefusion conformation with enhanced immunogenicity
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26
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Mohamed ME, Tawfeek N, Elbaramawi SS, Fikry E. Agathis robusta Bark Essential Oil Effectiveness against COVID-19: Chemical Composition, In Silico and In Vitro Approaches. PLANTS (BASEL, SWITZERLAND) 2022; 11:663. [PMID: 35270131 PMCID: PMC8912836 DOI: 10.3390/plants11050663] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), the causative agent of Coronavirus Disease 2019 (COVID-19), has seriously threatened global health. Alongside the approved vaccines, the discovery of prospective anti-COVID-19 drugs has been progressively targeted. Essential oils (EOs) provide a rich source of compounds with valuable antiviral activities that may contribute as effective agents against COVID-19. In this study, the EO of Agathus robusta bark was investigated for its chemical composition and its antiviral activity against SARS-CoV2. Overall, 26 constituents were identified by gas chromatography-mass spectrometry (GC-MS) analysis. α-Pinene, tricyclene, α-terpineol, limonene, d-camphene, trans-pinocarveol, α-phellandren-8-ol, L-β-pinene and borneol were the major components. In silico docking of these constituents against viral key enzymes, spike receptor-binding domain (RBD), main protease (Mpro) and RNA-dependent RNA polymerase (RdRp), using Molecular Operating Environment (MOE) software revealed good binding affinities of the components to the active site of the selected targets, especially, the RBD. In Vitro antiviral MTT and cytopathic effect inhibition assays demonstrated a promising anti SARS-CoV2 for A. robusta bark EO, with a significant selectivity index of 17.5. The results suggested using this EO or its individual components for the protection against or treatment of COVID-19.
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Affiliation(s)
- Maged E. Mohamed
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Nora Tawfeek
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (N.T.); (E.F.)
| | - Samar S. Elbaramawi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt;
| | - Eman Fikry
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (N.T.); (E.F.)
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27
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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28
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Spelios MG, Capanelli JM, Li AW. A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. Immunol Lett 2022; 242:1-7. [PMID: 35007661 PMCID: PMC8739817 DOI: 10.1016/j.imlet.2022.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 harbors a unique S1/S2 furin cleavage site within its spike protein, which can be cleaved by furin and other proprotein convertases. Proteolytic activation of SARS-CoV-2 spike protein at the S1/S2 boundary facilitates interaction with host ACE2 receptor for cell entry. To address this, high titer antibody was generated against the SARS-CoV-2-specific furin motif. Using a series of innovative ELISA-based assays, this furin site blocking antibody displayed high sensitivity and specificity for the S1/S2 furin cleavage site, including with a P681R mutation, and demonstrated effective blockage of both enzyme-mediated cleavage and spike-ACE2 interaction. The results suggest that immunological blocking of the furin cleavage site may afford a suitable approach to stem proteolytic activation of SARS-CoV-2 spike protein and curtail viral infectivity.
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Affiliation(s)
- Michael G Spelios
- EpiGentek Group Inc., 110 Bi County Boulevard, Suite 122, Farmingdale, NY, 11735, United States of America
| | - Jeanne M Capanelli
- EpiGentek Group Inc., 110 Bi County Boulevard, Suite 122, Farmingdale, NY, 11735, United States of America
| | - Adam W Li
- EpiGentek Group Inc., 110 Bi County Boulevard, Suite 122, Farmingdale, NY, 11735, United States of America.
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29
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P N, R. N, B. V, S. R, A. S. COVID-19: Invasion, pathogenesis and possible cure - A review. J Virol Methods 2022; 300:114434. [PMID: 34919978 PMCID: PMC8669942 DOI: 10.1016/j.jviromet.2021.114434] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022]
Abstract
Today, Coronavirus disease (COVID-19) which is believed to be transmitted from bats to humans where the people of Wuhan city, China exposed to the wet animal market is an important international public health anxiety (Xiong et al., 2020). Although, several measures were undertaken to treat the diseases by various medical advancements and by a variety of treatment procedures, still the mortality is higher. Hence, social distancing has been implemented to control the current outburst of this pandemic which spreads through human to human transmission. As a consequence, there is a need to completely understand the route of invasions of the virus into the humans and the target receptors besides the other factors leading to the disease. Several vaccines and drugs have been developed with its own pros and cons. Many are still under the various phase of R&D and clinical trials. Here we highlight the possible entry molecules, pathogenesis, symptomatology, probable cure and the recently developed vaccines for the existing pandemic due to the COVID-19.
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Affiliation(s)
- Nitin P
- Research and Development Section, Verena Haptic & VR Systems, Bhuvaneswari Nagar, Velachery, Chennai, 600042, Tamil Nadu, India
| | - Nandhakumar R.
- Department of Applied Chemistry, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, 641114, Tamil Nadu, India,Corresponding author at: Professor, Department of Applied Chemistry, Karunya Institute of Technology and Sciences(deemed to be University), Coimbatore - 641114, Tamil Nadu, India
| | - Vidhya B.
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, 641114, Tamil Nadu, India,Corresponding author
| | - Rajesh S.
- Department of Applied Physics, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, 641114, Tamil Nadu, India
| | - Sakunthala A.
- Department of Applied Physics, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, 641114, Tamil Nadu, India
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30
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Saravanan UB, Namachivayam M, Jeewon R, Huang JD, Durairajan SSK. Animal models for SARS-CoV-2 and SARS-CoV-1 pathogenesis, transmission and therapeutic evaluation. World J Virol 2022; 11:40-56. [PMID: 35117970 PMCID: PMC8788210 DOI: 10.5501/wjv.v11.i1.40] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/22/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
There is a critical need to develop animal models to alleviate vaccine and drug development difficulties against zoonotic viral infections. The coronavirus family, which includes severe acute respiratory syndrome coronavirus 1 and severe acute respiratory syndrome coronavirus 2, crossed the species barrier and infected humans, causing a global outbreak in the 21st century. Because humans do not have pre-existing immunity against these viral infections and with ethics governing clinical trials, animal models are therefore being used in clinical studies to facilitate drug discovery and testing efficacy of vaccines. The ideal animal models should reflect the viral replication, clinical signs, and pathological responses observed in humans. Different animal species should be tested to establish an appropriate animal model to study the disease pathology, transmission and evaluation of novel vaccine and drug candidates to treat coronavirus disease 2019. In this context, the present review summarizes the recent progress in developing animal models for these two pathogenic viruses and highlights the utility of these models in studying SARS-associated coronavirus diseases.
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Affiliation(s)
- Udhaya Bharathy Saravanan
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Mayurikaa Namachivayam
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit 80837, Mauritius
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong Province, China
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31
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Lubinski B, Fernandes MH, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. iScience 2022; 25:103589. [PMID: 34909610 PMCID: PMC8662955 DOI: 10.1016/j.isci.2021.103589] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern first identified in the United Kingdom in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7, or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that, although the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage, this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Maureen H.V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
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32
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Goc A, Niedzwiecki A, Ivanov V, Ivanova S, Rath M. Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants. Eur J Microbiol Immunol (Bp) 2022; 11:87-94. [PMID: 35060921 PMCID: PMC8830412 DOI: 10.1556/1886.2021.00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Despite vaccine availability, the global spread of COVID-19 continues, largely facilitated by emerging SARS-CoV-2 mutations. Our earlier research documented that a specific combination of plant-derived compounds can inhibit SARS-CoV-2 binding to its ACE2 receptor and controlling key cellular mechanisms of viral infectivity. In this study, we evaluated the efficacy of a defined mixture of plant extracts and micronutrients against original SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants. The composition containing vitamin C, N-acetylcysteine, resveratrol, theaflavin, curcumin, quercetin, naringenin, baicalin, and broccoli extract demonstrated a highest efficacy by inhibiting the receptor-binding domain (RBD) binding of SARS-CoV-2 to its cellular ACE2 receptor by 90%. In vitro exposure of test pseudo-typed variants to this formula for 1 h before or simultaneously administrated to human pulmonary cells resulted in up to 60% inhibition in their cellular entry. Additionally, this composition significantly inhibited other cellular mechanisms of viral infectivity, including the activity of viral RdRp, furin, and cathepsin L. These findings demonstrate the efficacy of natural compounds against SARS-CoV-2 including its mutated forms through pleiotropic mechanisms. Our results imply that simultaneous inhibition of multiple mechanisms of viral infection of host cells could be an effective strategy to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Anna Goc
- Dr. Rath Research Institute, 5941 Optical Ct., San Jose, CA 95138,USA
| | | | - Vadim Ivanov
- Dr. Rath Research Institute, 5941 Optical Ct., San Jose, CA 95138,USA
| | - Svetlana Ivanova
- Dr. Rath Research Institute, 5941 Optical Ct., San Jose, CA 95138,USA
| | - Matthias Rath
- Dr. Rath Research Institute, 5941 Optical Ct., San Jose, CA 95138,USA
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33
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Yu W, Zhong N, Li X, Ren J, Wang Y, Li C, Yao G, Zhu R, Wang X, Jia Z, Wu C, Chen R, Zheng W, Liao H, Wu X, Yuan X. Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches. Viruses 2022; 14:v14020186. [PMID: 35215781 PMCID: PMC8875849 DOI: 10.3390/v14020186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/25/2022] Open
Abstract
The COVID-19 epidemic is raging around the world. Neutralizing antibodies are powerful tools for the prevention and treatment of SARS-CoV-2 infection. Antibody CR3022, a SARS-CoV neutralizing antibody, was found to cross-react with SARS-CoV-2, but its affinity was lower than that of its binding with SARS-CoV, which greatly limited the further development of CR3022 against SARS-CoV-2. Therefore, it is necessary to improve its affinity to SARS-CoV-2 in vitro. In this study, the structure-based molecular simulations were utilized to virtually mutate the possible key residues in the complementarity-determining regions (CDRs) of the CR3022 antibody. According to the criteria of mutation energy, the mutation sites that have the potential to impact the antibody affinity were then selected. Then optimized CR3022 mutants with the enhanced affinity were further identified and verified by enzyme-linked immunosorbent assay (ELISA), surface plasma resonance (SPR) and autoimmune reactivity experiments. Finally, molecular dynamics (MD) simulation and binding free energy calculation (MM/PBSA) were performed on the wild-type CR3022 and its two double-site mutants to understand in more detail the contribution of these sites to the higher affinity. It was found that the binding affinity of the CR3022 antibody could be significantly enhanced more than ten times after the introduction of the S103F/Y mutation in HCDR–3 and the S33R mutation in LCDR–1. The additional hydrogen-bonding, hydrophobic interactions, as well as salt-bridges formed between the modified double-site mutated antibody and SARS-CoV-2 RBD were identified. The computational and experimental results clearly demonstrated that the affinity of the modified antibody has been greatly enhanced. This study indicates that CR3022 as a neutralizing antibody recognizing the conserved region of RBD against SARS-CoV with cross-reactivity with SARS-CoV-2, a different member in a large family of coronaviruses, could be improved by the computational and experimental approaches which provided insights for developing antibody drugs against SARS-CoV-2.
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Affiliation(s)
- Wei Yu
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Nan Zhong
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Xin Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
| | - Jiayi Ren
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- School of Health, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Yueming Wang
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Chengming Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Rui Zhu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Xiaoli Wang
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Zhenxing Jia
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Changwen Wu
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Rongfeng Chen
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Weihong Zheng
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Huaxin Liao
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
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Abstract
Compared with other SARS-related coronaviruses (SARSr-CoVs), SARS-CoV-2 possesses a unique furin cleavage site (FCS) in its spike. This has stimulated discussion pertaining to the origin of SARS-CoV-2 because the FCS has been observed to be under strong selective pressure in humans and confers the enhanced ability to infect some cell types and induce cell-cell fusion. Furthermore, scientists have demonstrated interest in studying novel cleavage sites by introducing them into SARSr-CoVs. We review what is known about the SARS-CoV-2 FCS in the context of its pathogenesis, origin, and how future wildlife coronavirus sampling may alter the interpretation of existing data.
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Affiliation(s)
- Yujia Alina Chan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shing Hei Zhan
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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35
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Abstract
The field of molecular epidemiology responded to the SARS-CoV-2 pandemic with an unrivaled amount of whole viral genome sequencing. By the time this sentence is published we will have well surpassed 1.5 million whole genomes, more than 4 times the number of all microbial whole genomes deposited in GenBank and 35 times the total number of viral genomes. This extraordinary dataset that accrued in near real time has also given us an opportunity to chart the global and local evolution of a virus as it moves through the world population. The data itself presents challenges that have never been dealt with in molecular epidemiology, and tracking a virus that is changing so rapidly means that we are often running to catch up. Here we review what is known about the evolution of the virus, and the critical impact that whole genomes have had on our ability to trace back and track forward the spread of lineages of SARS-CoV-2. We then review what whole genomes have told us about basic biological properties of the virus such as transmissibility, virulence, and immune escape with a special emphasis on pediatric disease. We couch this discussion within the framework of systematic biology and phylogenetics, disciplines that have proven their worth again and again for identifying and deciphering the spread of epidemics, though they were largely developed in areas far removed from infectious disease and medicine.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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36
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Perez-Gomez R. The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. J Dev Biol 2021; 9:58. [PMID: 34940505 PMCID: PMC8705434 DOI: 10.3390/jdb9040058] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
A novel coronavirus (SARS-CoV-2) emerged towards the end of 2019 that caused a severe respiratory disease in humans called COVID-19. It led to a pandemic with a high rate of morbidity and mortality that is ongoing and threatening humankind. Most of the mutations occurring in SARS-CoV-2 are synonymous or deleterious, but a few of them produce improved viral functions. The first known mutation associated with higher transmissibility, D614G, was detected in early 2020. Since then, the virus has evolved; new mutations have occurred, and many variants have been described. Depending on the genes affected and the location of the mutations, they could provide altered infectivity, transmissibility, or immune escape. To date, mutations that cause variations in the SARS-CoV-2 spike protein have been among the most studied because of the protein's role in the initial virus-cell contact and because it is the most variable region in the virus genome. Some concerning mutations associated with an impact on viral fitness have been described in the Spike protein, such as D614G, N501Y, E484K, K417N/T, L452R, and P681R, among others. To understand the impact of the infectivity and antigenicity of the virus, the mutation landscape of SARS-CoV-2 has been under constant global scrutiny. The virus variants are defined according to their origin, their genetic profile (some characteristic mutations prevalent in the lineage), and the severity of the disease they produce, which determines the level of concern. If they increase fitness, new variants can outcompete others in the population. The Alpha variant was more transmissible than previous versions and quickly spread globally. The Beta and Gamma variants accumulated mutations that partially escape the immune defenses and affect the effectiveness of vaccines. Nowadays, the Delta variant, identified around March 2021, has spread and displaced the other variants, becoming the most concerning of all lineages that have emerged. The Delta variant has a particular genetic profile, bearing unique mutations, such as T478K in the spike protein and M203R in the nucleocapsid. This review summarizes the current knowledge of the different mutations that have appeared in SARS-CoV-2, mainly on the spike protein. It analyzes their impact on the protein function and, subsequently, on the level of concern of different variants and their importance in the ongoing pandemic.
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Affiliation(s)
- Raquel Perez-Gomez
- Translational Genomics Group, Institut Universitari de Biotecnologia y Biomedicina BIOTECMED, Universitat de Valencia, 46100 Valencia, Spain
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37
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Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Viruses 2021; 13:v13122511. [PMID: 34960779 PMCID: PMC8705554 DOI: 10.3390/v13122511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. This finding highlights that VOCs are still evolving to enhance viral fitness and to adapt to the human host. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution.
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38
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Host Manipulation Mechanisms of SARS-CoV-2. Acta Biotheor 2021; 70:4. [PMID: 34902063 PMCID: PMC8667538 DOI: 10.1007/s10441-021-09425-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/16/2021] [Indexed: 10/28/2022]
Abstract
Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to bind to the host receptor neuropilin-1 in order to gain entry into the cell. To do this, the virus utilizes its spike protein polybasic cleavage site (PCS), which mimics the CendR motif of neuropilin-1's endogenous ligands. In addition to facilitating cell entry, binding to neuropilin-1 has analgesic effects. We discuss the potential impact of neuropilin-1 binding by SARS-CoV-2 in ameliorating sickness behavior of the host, and identify a convergent evolutionary strategy of PCS cleavage and subsequent neuropilin binding in other human viruses. In addition, we discuss the evolutionary leap of the ancestor of SARS-COV-2, which involved acquisition of the PCS thus faciliting binding to the neuropilin-1 receptor. Acquisition of the PCS by the ancestor of SARS-CoV-2 appears to have led to pleiotropic beneficial effects including enhancement of cell entry via binding to ACE2, facilitation of cell entry via binding to neuropilin-1, promotion of analgesia, and potentially the formation of decoy epitopes via enhanced shedding of the S1 subunit. Lastly, other potential neuromanipulation strategies employed by SARS-CoV-2 are discussed, including interferon suppression and the resulting reduction in sickness behavior, enhanced transmission through neurally mediated cough induction, and reduction in sense of smell.
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Lazebnik Y. Cell fusion as a link between the SARS-CoV-2 spike protein, COVID-19 complications, and vaccine side effects. Oncotarget 2021; 12:2476-2488. [PMID: 34917266 PMCID: PMC8664391 DOI: 10.18632/oncotarget.28088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/24/2021] [Indexed: 12/23/2022] Open
Abstract
A distinctive feature of the SARS-CoV-2 spike protein is its ability to efficiently fuse cells, thus producing syncytia found in COVID-19 patients. This commentary proposes how this ability enables spike to cause COVID-19 complications as well as side effects of COVID-19 vaccines, and suggests how these effects can be prevented.
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40
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Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.06.438731. [PMID: 33851153 PMCID: PMC8043443 DOI: 10.1101/2021.04.06.438731] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern (VOC) first identified in the UK in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7 or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that while the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maureen H. V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA
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41
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Rowland R, Brandariz-Nuñez A. Analysis of the Role of N-Linked Glycosylation in Cell Surface Expression, Function, and Binding Properties of SARS-CoV-2 Receptor ACE2. Microbiol Spectr 2021; 9:e0119921. [PMID: 34494876 PMCID: PMC8557876 DOI: 10.1128/spectrum.01199-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Human angiotensin I-converting enzyme 2 (hACE2) is a type I transmembrane glycoprotein that serves as the major cell entry receptor for SARS-CoV and SARS-CoV-2. The viral spike (S) protein is required for the attachment to ACE2 and subsequent virus-host cell membrane fusion. Previous work has demonstrated the presence of N-linked glycans in ACE2. N-glycosylation is implicated in many biological activities, including protein folding, protein activity, and cell surface expression of biomolecules. However, the contribution of N-glycosylation to ACE2 function is poorly understood. Here, we examined the role of N-glycosylation in the activity and localization of two species with different susceptibility to SARS-CoV-2 infection, porcine ACE2 (pACE2) and hACE2. The elimination of N-glycosylation by tunicamycin (TM) treatment, or mutagenesis, showed that N-glycosylation is critical for the proper cell surface expression of ACE2 but not for its carboxiprotease activity. Furthermore, nonglycosylable ACE2 was localized predominantly in the endoplasmic reticulum (ER) and not at the cell surface. Our data also revealed that binding of SARS-CoV or SARS-CoV-2 S protein to porcine or human ACE2 was not affected by deglycosylation of ACE2 or S proteins, suggesting that N-glycosylation does not play a role in the interaction between SARS coronaviruses and the ACE2 receptor. Impairment of hACE2 N-glycosylation decreased cell-to-cell fusion mediated by SARS-CoV S protein but not that mediated by SARS-CoV-2 S protein. Finally, we found that hACE2 N-glycosylation is required for an efficient viral entry of SARS-CoV/SARS-CoV-2 S pseudotyped viruses, which may be the result of low cell surface expression of the deglycosylated ACE2 receptor. IMPORTANCE Understanding the role of glycosylation in the virus-receptor interaction is important for developing approaches that disrupt infection. In this study, we showed that deglycosylation of both ACE2 and S had a minimal effect on the spike-ACE2 interaction. In addition, we found that the removal of N-glycans of ACE2 impaired its ability to support an efficient transduction of SARS-CoV and SARS-CoV-2 S pseudotyped viruses. Our data suggest that the role of deglycosylation of ACE2 on reducing infection is likely due to a reduced expression of the viral receptor on the cell surface. These findings offer insight into the glycan structure and function of ACE2 and potentially suggest that future antiviral therapies against coronaviruses and other coronavirus-related illnesses involving inhibition of ACE2 recruitment to the cell membrane could be developed.
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Affiliation(s)
- Raymond Rowland
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alberto Brandariz-Nuñez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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42
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A Novel Potentially Recombinant Rodent Coronavirus with a Polybasic Cleavage Site in the Spike Protein. J Virol 2021; 95:e0117321. [PMID: 34431700 PMCID: PMC8549509 DOI: 10.1128/jvi.01173-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. Here, we sampled 297 rodents and shrews, representing eight species, from three municipalities of southern China. We report coronavirus prevalences of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalences than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus (rat coronavirus [RCoV] GCCDC3), an Alphacoronavirus (RCoV-GCCDC5), and a novel Betacoronavirus (RCoV-GCCDC4). Recombination analysis suggests that there was a potential recombination event involving RCoV-GCCDC4, murine hepatitis virus (MHV), and Longquan Rl rat coronavirus (LRLV). Furthermore, we uncovered a polybasic cleavage site, RARR, in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery. IMPORTANCE Surveillance of viruses among rodents in rural and urban areas of South China identified three rodent coronaviruses, RCoV-GCCDC3, RCoV-GCCDC4, and RCoV-GCCDC5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription-PCR (RT-PCR) screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in the S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
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43
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Stevens CS, Oguntuyo KY, Lee B. Proteases and variants: context matters for SARS-CoV-2 entry assays. Curr Opin Virol 2021; 50:49-58. [PMID: 34365113 PMCID: PMC8302850 DOI: 10.1016/j.coviro.2021.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/17/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), like other coronaviruses, relies on a flexible array of entry mechanisms, driven by the spike (S) protein. Entry is dependent on proteolytic priming, activation, and receptor binding; all of which can be variable, dependent on context. Here we review the implications of the complexity of SARS-CoV-2 entry pathways on entry assays that then drive our understanding of humoral immunity, therapeutic efficacy, and tissue restriction. We focus especially on the proteolytic activation of SARS-CoV-2 spike and how this constellation of proteases lends deeper insight to our understanding of arising variants and their putative role transmission or variable pathogenicity in vivo. In this review, we argue for better universal standards to assay virus entry as well as suggest best practices for reporting viral passage number, the cell line used, and proteases present, among other important considerations.
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Affiliation(s)
- Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
| | - Kasopefoluwa Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, United States.
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44
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Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. The origins of SARS-CoV-2: A critical review. Cell 2021; 184:4848-4856. [PMID: 34480864 PMCID: PMC8373617 DOI: 10.1016/j.cell.2021.08.017] [Citation(s) in RCA: 272] [Impact Index Per Article: 90.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 01/11/2023]
Abstract
Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.
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Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94704, USA
| | - Joel O Wertheim
- Department of Medicine, University of California-San Diego, La Jolla, CA 92093, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter C Doherty
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | | | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China
| | - Julian L Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX 77807, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Tim Skern
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Zalgen Labs, Germantown, MD 20876, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
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45
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Glotov OS, Chernov AN, Scherbak SG, Baranov VS. Genetic Risk Factors for the Development of COVID-19 Coronavirus Infection. RUSS J GENET+ 2021; 57:878-892. [PMID: 34483599 PMCID: PMC8404752 DOI: 10.1134/s1022795421080056] [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] [Received: 09/14/2020] [Revised: 12/28/2020] [Accepted: 01/18/2021] [Indexed: 01/08/2023]
Abstract
The COVID-19 coronavirus pandemic has spread to 215 countries around the world and caused tens of millions of infections and more than a million deaths worldwide. In the midst of COVID-19 infection, it is extremely important to identify new protein and gene targets that may be highly sensitive diagnostic and prognostic markers of the severity and outcome of the disease for combating this pandemic. Identification of individual genetic predisposition allows personalizing programs of medical rehabilitation and therapy. It has now been shown that the transmissibility and severity of COVID-19 infection can be affected by gene variants in both the human body (ACE2, HLA-B*4601, FcγRIIA, MBL, TMPRSS2, TNFA, IL6, blood group A antigen, etc.) and the virus itself (ORF8 in RNA polymerase, ORF6 in RNA primase, S, N, E proteins). The presence of mutations in the proteins of the virus can change the affinity and specificity for the binding of targeted drugs to them, being the molecular basis of individual differences in the response of the human body to antiviral drugs and/or vaccines. The review summarizes the data on the variants of the genomes of the coronavirus and humans associated with an individual predisposition to an increased or decreased risk of transmission, severity, and outcome of COVID-19 infection. Targeted drugs and vaccines being developed for the therapy of COVID-19 infection are briefly reviewed.
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Affiliation(s)
- O. S. Glotov
- City Hospital no. 40, Sestroretsk, 197706 St. Petersburg, Russia
- Ott Research Institute of Obstetrics, Gynecology, and Reproductology, 199034 St. Petersburg, Russia
| | - A. N. Chernov
- City Hospital no. 40, Sestroretsk, 197706 St. Petersburg, Russia
| | - S. G. Scherbak
- City Hospital no. 40, Sestroretsk, 197706 St. Petersburg, Russia
- St. Petersburg State University, 199034 St. Petersburg, Russia
| | - V. S. Baranov
- Ott Research Institute of Obstetrics, Gynecology, and Reproductology, 199034 St. Petersburg, Russia
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Patiño-Galindo JÁ, Filip I, Chowdhury R, Maranas CD, Sorger PK, AlQuraishi M, Rabadan R. Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2. Genome Med 2021; 13:124. [PMID: 34362430 PMCID: PMC8343217 DOI: 10.1186/s13073-021-00943-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/24/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The emergence of SARS-CoV-2 underscores the need to better understand the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. In the betacoronavirus genus, which also includes SARS-CoV and MERS-CoV, recombination frequently encompasses the receptor binding domain (RBD) of the Spike protein, which is responsible for viral binding to host cell receptors. In this work, we reconstruct the evolutionary events that have accompanied the emergence of SARS-CoV-2, with a special emphasis on the RBD and its adaptation for binding to its receptor, human ACE2. METHODS By means of phylogenetic and recombination analyses, we found evidence of a recombination event in the RBD involving ancestral linages to both SARS-CoV and SARS-CoV-2. We then assessed the effect of this recombination at protein level by reconstructing the RBD of the closest ancestors to SARS-CoV-2, SARS-CoV, and other Sarbecoviruses, including the most recent common ancestor of the recombining clade. The resulting information was used to measure and compare, in silico, their ACE2-binding affinities using the physics-based trRosetta algorithm. RESULTS We show that, through an ancestral recombination event, SARS-CoV and SARS-CoV-2 share an RBD sequence that includes two insertions (positions 432-436 and 460-472), as well as the variants 427N and 436Y. Both 427N and 436Y belong to a helix that interacts directly with the human ACE2 (hACE2) receptor. Reconstruction of ancestral states, combined with protein-binding affinity analyses, suggests that the recombination event involving ancestral strains of SARS-CoV and SARS-CoV-2 led to an increased affinity for hACE2 binding and that alleles 427N and 436Y significantly enhanced affinity as well. CONCLUSIONS We report an ancestral recombination event affecting the RBD of both SARS-CoV and SARS-CoV-2 that was associated with an increased binding affinity to hACE2. Structural modeling indicates that ancestors of SARS-CoV-2 may have acquired the ability to infect humans decades ago. The binding affinity with the human receptor would have been subsequently boosted in SARS-CoV and SARS-CoV-2 through further mutations in RBD.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Ioan Filip
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Ratul Chowdhury
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mohammed AlQuraishi
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA.
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Rynkiewicz P, Lynch ML, Cui F, Hudson AO, Babbitt GA. Functional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains. J Biomol Struct Dyn 2021; 40:10978-10996. [PMID: 34286673 PMCID: PMC8776918 DOI: 10.1080/07391102.2021.1953604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/04/2021] [Indexed: 01/03/2023]
Abstract
Comparative functional analysis of the dynamic interactions between various Betacoronavirus mutant strains and broadly utilized target proteins such as ACE2 and CD26, is crucial for a more complete understanding of zoonotic spillovers of viruses that cause diseases such as COVID-19. Here, we employ machine learning to replicated sets of nanosecond scale GPU accelerated molecular dynamics simulations to statistically compare and classify atom motions of these target proteins in both the presence and absence of different endemic and emergent strains of the viral receptor binding domain (RBD) of the S spike glycoprotein. A multi-agent classifier successfully identified functional binding dynamics that are evolutionarily conserved from bat CoV-HKU4 to human endemic/emergent strains. Conserved dynamics regions of ACE2 involve both the N-terminal helices, as well as a region of more transient dynamics encompassing residues K353, Q325 and a novel motif AAQPFLL 386-92 that appears to coordinate their dynamic interactions with the viral RBD at N501. We also demonstrate that the functional evolution of Betacoronavirus zoonotic spillovers involving ACE2 interaction dynamics are likely pre-adapted from two precise and stable binding sites involving the viral bat progenitor strain's interaction with CD26 at SAMLI 291-5 and SS 333-334. Our analyses further indicate that the human endemic strains hCoV-HKU1 and hCoV-OC43 have evolved more stable N-terminal helix interactions through enhancement of an interfacing loop region on the viral RBD, whereas the highly transmissible SARS-CoV-2 variants (B.1.1.7, B.1.351 and P.1) have evolved more stable viral binding via more focused interactions between the viral N501 and ACE2 K353 alone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Miranda L. Lynch
- Hauptmann-Woodward Medical Research Institute, Buffalo NY, USA 14203
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
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48
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Kumavath R, Barh D, Andrade BS, Imchen M, Aburjaile FF, Ch A, Rodrigues DLN, Tiwari S, Alzahrani KJ, Góes-Neto A, Weener ME, Ghosh P, Azevedo V. The Spike of SARS-CoV-2: Uniqueness and Applications. Front Immunol 2021; 12:663912. [PMID: 34305894 PMCID: PMC8297464 DOI: 10.3389/fimmu.2021.663912] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point-of-care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.
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Affiliation(s)
- Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Flavia Figueira Aburjaile
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Athira Ch
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Diego Lucas Neres Rodrigues
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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49
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Barrett CT, Neal HE, Edmonds K, Moncman CL, Thompson R, Branttie JM, Boggs KB, Wu CY, Leung DW, Dutch RE. Effect of clinical isolate or cleavage site mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion. J Biol Chem 2021; 297:100902. [PMID: 34157282 PMCID: PMC8214756 DOI: 10.1016/j.jbc.2021.100902] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
The trimeric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2-infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. A furin cleavage site at the border between the S1 and S2 subunits (S1/S2) has been identified, along with putative cathepsin L and transmembrane serine protease 2 cleavage sites within S2. We demonstrate that S must be processed at the S1/S2 border in order to mediate cell-cell fusion and that mutations at potential cleavage sites within the S2 subunit alter S processing at the S1/S2 border, thus preventing cell-cell fusion. We also identify residues within the internal fusion peptide and the cytoplasmic tail that modulate S-mediated cell-cell fusion. In addition, we examined S stability and protein cleavage kinetics in a variety of mammalian cell lines, including a bat cell line related to the likely reservoir species for SARS-CoV-2, and provide evidence that proteolytic processing alters the stability of the S trimer. This work therefore offers insight into S stability, proteolytic processing, and factors that mediate S cell-cell fusion, all of which help give a more comprehensive understanding of this high-profile therapeutic target.
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Affiliation(s)
- Chelsea T Barrett
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Hadley E Neal
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Kearstin Edmonds
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Carole L Moncman
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Rachel Thompson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Jean M Branttie
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Kerri Beth Boggs
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Cheng-Yu Wu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Daisy W Leung
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Rebecca E Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA.
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50
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Abstract
COVID-19 pandemic has been a subject of extensive study. However, it is still unclear why it was restricted to higher latitudes during the initial days and later cascaded in the tropics. Here, we analyzed 176 SARS-CoV-2 genomes across different climate zones and Köppen's climate that provided insights about within-species virus evolution and its relation to abiotic factors. Two genetically variant groups, named G1 and G2, were identified, well defined by four mutations. The G1 group (ancestor) is mainly restricted to warm and moist, temperate climate (Köppen's C climate) while its descendent G2 group surpasses the climatic restrictions of G1, initially cascading into neighboring cold climate (D) of higher latitudes and later into the hot climate of the tropics (A). It appears that the gradation of temperate climate (Cfa-Cfb) to cold climate (Dfa-Dfb) drives the evolution of G1 into the G2 variant group, which later adapted to tropical climate (A) as well. It seems this virus followed an inverse latitudinal gradient in the beginning due to its preference towards temperate (C) and cold climate (D). Our work elucidates virus evolutionary studies combined with climatic studies can provide crucial information about the pathogenesis and natural spreading pathways in such outbreaks, which is hard to achieve through individual studies. Mutational insights gained may help design an efficacious vaccine.
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