1
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Sugimoto S, Kawase M, Suwa R, Kume Y, Chishiki M, Ono T, Okabe H, Norito S, Hanaki KI, Hosoya M, Hashimoto K, Shirato K. Comparison of mutations in human parainfluenza viruses during passage in primary human bronchial/tracheal epithelial air-liquid interface cultures and cell lines. Microbiol Spectr 2024:e0116424. [PMID: 39078148 DOI: 10.1128/spectrum.01164-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Human parainfluenza virus (HPIV) causes respiratory infections, which are exacerbated in children and older people. Correct evaluation of viral characteristics is essential for the study of countermeasures. However, adaptation of viruses to cultured cells during isolation or propagation might select laboratory passage-associated mutations that modify the characteristics of the virus. It was previously reported that adaptation of HPIV3, but not other HPIVs, was avoided in human airway epithelia. To examine the influence of laboratory passage on the genomes of HPIV1-HPIV4, we evaluated the occurrence of mutations after passage in primary human bronchial/tracheal epithelial cell air-liquid interface (HBTEC-ALI) culture and conventional cultured cells (Vero cells expressing the transmembrane protease, serine 2, and normal Vero cells). The occurrence of mutations was significantly lower in HBTEC-ALI than in conventional culture. In HBTEC-ALI culture, most of the mutations were silent or remained at low variant frequency, resulting in less impact on the viral consensus sequence. In contrast, passage in conventional culture induced or selected genetic mutations at high frequency with passage-associated unique substitutions. High mutagenesis of hemagglutinin-neuraminidase was commonly observed in all four HPIVs, and mutations even occurred in a single passage. In addition, in HPIV1 and HPIV2, mutations in the large protein were more frequent. These results indicate that passage in HBTEC-ALI culture is more suitable than conventional culture for maintaining the original characteristics of clinical isolates in all four HPIVs, which can help with the understanding of viral pathogenesis. IMPORTANCE Adaptation of viruses to cultured cells can increase the risk of misinterpretation in virological characterization of clinical isolates. In human parainfluenza virus (HPIV) 3, it has been reported that the human airway epithelial and lung organoid models are preferable for the study of viral characteristics of clinical strains without mutations. Therefore, we analyzed clinical isolates of all four HPIVs for the occurrence of mutations after five laboratory passages in human bronchial/tracheal epithelial cell air-liquid interface (HBTEC-ALI) or conventional culture. We found a high risk of hemagglutinin-neuraminidase mutagenesis in all four HPIVs in conventional cultured cells. In addition, in HPIV1 and HPIV2, mutations of the large protein were also more frequent in conventional cultured cells than in HBTEC-ALI culture. HBTEC-ALI culture was useful for maintaining the original sequence and characteristics of clinical isolates in all four HPIVs. The present study contributes to the understanding of HPIV pathogenesis and antiviral strategies.
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Affiliation(s)
- Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Ken-Ichi Hanaki
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
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2
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Xiang Q, Wu J, Zhou Y, Li L, Tian M, Li G, Zhang Z, Fu Y. SARS-CoV-2 Membrane protein regulates the function of Spike by inhibiting its plasma membrane localization and enzymatic activity of Furin. Microbiol Res 2024; 282:127659. [PMID: 38430890 DOI: 10.1016/j.micres.2024.127659] [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: 01/08/2024] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
The presence of a multibasic cleavage site in the Spike protein of SARS-CoV-2 makes it prone to be cleaved by Furin at the S1/S2 junction (aa. 685-686), which enhances the usage of TMPRSS2 to promote cell-cell fusion to form syncytia. Syncytia may contribute to pathology by facilitating viral dissemination, cytopathicity, immune evasion, and inflammation. However, the role of other SARS-CoV-2 encoding viral proteins in syncytia formation remains largely unknown. Here, we report that SARS-CoV-2 M protein effectively inhibits syncytia formation triggered by Spike or its variants (Alpha, Delta, Omicron, etc.) and prevents Spike cleavage into S1 and S2 based on a screen assay of 20 viral proteins. Mechanistically, M protein interacts with Furin and inhibits its enzymatic activity, preventing the cleavage of Spike. In addition, M interacts with Spike independent of its cytoplasmic tail, retaining it within the cytoplasm and reducing cell membrane localization. Our findings offer new insights into M protein's role in regulating Spike's function and underscore the importance of functional interplay among viral proteins, highlighting potential avenues for SARS-CoV-2 therapy development.
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Affiliation(s)
- Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Jie Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518112, China
| | - Linhao Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Guobao Li
- Department of Tuberculosis, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518112, China.
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China.
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3
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Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
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Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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4
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Cai HL, Huang YW. Reverse genetics systems for SARS-CoV-2: Development and applications. Virol Sin 2023; 38:837-850. [PMID: 37832720 PMCID: PMC10786661 DOI: 10.1016/j.virs.2023.10.001] [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: 07/09/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.
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Affiliation(s)
- Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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5
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Adler JM, Martin Vidal R, Voß A, Kunder S, Nascimento M, Abdelgawad A, Langner C, Vladimirova D, Osterrieder N, Gruber AD, Kunec D, Trimpert J. A non-transmissible live attenuated SARS-CoV-2 vaccine. Mol Ther 2023; 31:2391-2407. [PMID: 37263272 PMCID: PMC10214529 DOI: 10.1016/j.ymthe.2023.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/23/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
Live attenuated vaccines (LAVs) administered via the mucosal route may offer better control of the COVID-19 pandemic than non-replicating vaccines injected intramuscularly. Conceptionally, LAVs have several advantages, including presentation of the entire antigenic repertoire of the virus, and the induction of strong mucosal immunity. Thus, immunity induced by LAV could offer superior protection against future surges of COVID-19 cases caused by emerging SARS-CoV-2 variants. However, LAVs carry the risk of unintentional transmission. To address this issue, we investigated whether transmission of a SARS-CoV-2 LAV candidate can be blocked by removing the furin cleavage site (FCS) from the spike protein. The level of protection and immunity induced by the attenuated virus with the intact FCS was virtually identical to the one induced by the attenuated virus lacking the FCS. Most importantly, removal of the FCS completely abolished horizontal transmission of vaccine virus between cohoused hamsters. Furthermore, the vaccine was safe in immunosuppressed animals and showed no tendency to recombine in vitro or in vivo with a SARS-CoV-2 field strain. These results indicate that removal of the FCS from SARS-CoV-2 LAV is a promising strategy to increase vaccine safety and prevent vaccine transmission without compromising vaccine efficacy.
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Affiliation(s)
- Julia M Adler
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Anne Voß
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Sandra Kunder
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany.
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6
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Olivier T, Blomet J, Desmecht D. Central role of lung macrophages in SARS-CoV-2 physiopathology: a cross-model single-cell RNA-seq perspective. Front Immunol 2023; 14:1197588. [PMID: 37350967 PMCID: PMC10282834 DOI: 10.3389/fimmu.2023.1197588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023] Open
Abstract
Cytokine storms are considered a driving factor in coronavirus disease 2019 (COVID-19) severity. However, the triggering and resolution of this cytokine production, as well as the link between this phenomenon and infected cells, are still poorly understood. In this study, a cross-species scRNA-seq analysis showed that cytokine-producing macrophages together with pneumocytes were found to be the main contributors of viral transcripts in both Syrian hamsters and African green monkeys. Whatever the cell type, viral read-bearing cells show an apoptotic phenotype. A comparison of SARS-CoV-2 entry receptor candidates showed that Fc receptors are better correlated with infected cells than ACE2, NRP1, or AXL. Although both species show similar interferon responses, differences in adaptive immunity were highlighted. Lastly, Fc receptor and cytokine upregulation in M1 macrophages was found to correlate with a comprehensive interferon response. Based on these results, we propose a model in which lung macrophages play a central role in COVID-19 severity through antibody-dependent enhancement.
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Affiliation(s)
- Thibaut Olivier
- GAS Department, Prevor Research Laboratories, Valmondois, France
- Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Joël Blomet
- GAS Department, Prevor Research Laboratories, Valmondois, France
| | - Daniel Desmecht
- Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
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7
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Cassari L, Pavan A, Zoia G, Chinellato M, Zeni E, Grinzato A, Rothenberger S, Cendron L, Dettin M, Pasquato A. SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works. Int J Mol Sci 2023; 24:4791. [PMID: 36902222 PMCID: PMC10003014 DOI: 10.3390/ijms24054791] [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: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiological agent responsible for the worldwide pandemic and has now claimed millions of lives. The virus combines several unusual characteristics and an extraordinary ability to spread among humans. In particular, the dependence of the maturation of the envelope glycoprotein S from Furin enables the invasion and replication of the virus virtually within the entire body, since this cellular protease is ubiquitously expressed. Here, we analyzed the naturally occurring variation of the amino acids sequence around the cleavage site of S. We found that the virus grossly mutates preferentially at P positions, resulting in single residue replacements that associate with gain-of-function phenotypes in specific conditions. Interestingly, some combinations of amino acids are absent, despite the evidence supporting some cleavability of the respective synthetic surrogates. In any case, the polybasic signature is maintained and, as a consequence, Furin dependence is preserved. Thus, no escape variants to Furin are observed in the population. Overall, the SARS-CoV-2 system per se represents an outstanding example of the evolution of substrate-enzyme interaction, demonstrating a fast-tracked optimization of a protein stretch towards the Furin catalytic pocket. Ultimately, these data disclose important information for the development of drugs targeting Furin and Furin-dependent pathogens.
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Affiliation(s)
- Leonardo Cassari
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Angela Pavan
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Giulia Zoia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Chinellato
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Elena Zeni
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alessandro Grinzato
- European Synchrotron Radiation Facility, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Sylvia Rothenberger
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Antonella Pasquato
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
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8
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Faizuloev E, Gracheva A, Korchevaya E, Smirnova D, Samoilikov R, Pankratov A, Trunova G, Khokhlova V, Ammour Y, Petrusha O, Poromov A, Leneva I, Svitich O, Zverev V. Cold-adapted SARS-CoV-2 variants with different temperature sensitivity exhibit an attenuated phenotype and confer protective immunity. Vaccine 2023; 41:892-902. [PMID: 36528447 PMCID: PMC9744683 DOI: 10.1016/j.vaccine.2022.12.019] [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: 08/11/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
As novel SARS-CoV-2 Variants of Concern emerge, the efficacy of existing vaccines against COVID-19 is declining. A possible solution to this problem lies in the development of a live attenuated vaccine potentially able of providing cross-protective activity against a wide range of SARS-CoV-2 antigenic variants. Cold-adapted (ca) SARS-CoV-2 variants, Dubrovka-ca-B4 (D-B4) and Dubrovka-ca-D2 (D-D2), were obtained after long-term passaging of the Dubrovka (D) strain in Vero cells at reduced temperatures. Virulence, immunogenicity, and protective activity of SARS-CoV-2 variants were evaluated in experiments on intranasal infection of Syrian golden hamsters (Mesocricetus auratus). In animal model infecting with ca variants, the absence of body weight loss, the significantly lower viral titer and viral RNA concentration in animal tissues, the less pronounced inflammatory lesions in animal lungs as compared with the D strain indicated the reduced virulence of the virus variant. Single intranasal immunization with D-B4 and D-D2 variants induced the production of neutralizing antibodies in hamsters and protected them from infection with the D strain and the development of severe pneumonia. It was shown that for ca SARS-CoV-2 variants, the temperature-sensitive (ts) phenotype was not obligate for virulence reduction. Indeed, the D-B4 variant, which did not possess the ts phenotype but had lost the ability to infect human lung cells Calu-3, exhibited reduced virulence in hamsters. Consequently, the potential phenotypic markers of attenuation of ca SARS-CoV-2 variants are the ca phenotype, the ts phenotype, and the change in species specificity of the virus. This study demonstrates the great potential of SARS-CoV-2 cold adaptation as a strategy to develop a live attenuated COVID-19 vaccine.
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Affiliation(s)
- Evgeny Faizuloev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia; Russian Medical Academy of Continuous Professional Education, Moscow, Russia.
| | | | | | - Daria Smirnova
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Roman Samoilikov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Andrey Pankratov
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Galina Trunova
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Varvara Khokhlova
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Yulia Ammour
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Olga Petrusha
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Artem Poromov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,Peoples' Friendship University of Russia, Department of Biochemistry, Moscow, Russia
| | - Irina Leneva
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,I.M. Sechenov First Moscow State Medical University (Sechenov University), F.F. Erisman Institute of Public Health, Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,I.M. Sechenov First Moscow State Medical University (Sechenov University), F.F. Erisman Institute of Public Health, Moscow, Russia
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9
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Sasaki M, Tabata K, Kishimoto M, Itakura Y, Kobayashi H, Ariizumi T, Uemura K, Toba S, Kusakabe S, Maruyama Y, Iida S, Nakajima N, Suzuki T, Yoshida S, Nobori H, Sanaki T, Kato T, Shishido T, Hall WW, Orba Y, Sato A, Sawa H. S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and ameliorates COVID-19 severity in hamsters. Sci Transl Med 2023; 15:eabq4064. [PMID: 36327352 PMCID: PMC9765455 DOI: 10.1126/scitranslmed.abq4064] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622 (ensitrelvir), an inhibitor of SARS-CoV-2 main protease (Mpro; also known as 3C-like protease), decreases viral load and ameliorates disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to submicromolar concentrations in cells. Oral administration of S-217622 demonstrated favorable pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern, including the highly pathogenic Delta variant and the recently emerged Omicron BA.5 and BA.2.75 variants. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase 3 clinical trial (clinical trial registration no. jRCT2031210350), has remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Corresponding author. (M.S.); (H.S.)
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Hiroko Kobayashi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Takuma Ariizumi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shinsuke Toba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shinji Kusakabe
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Yuki Maruyama
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | | | | | | | | | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,National Virus Reference Laboratory, School of Medicine, University College of Dublin, 4, Ireland.,Global Virus Network, Baltimore, MD, 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Akihiko Sato
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,Global Virus Network, Baltimore, MD, 21201, USA.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan.,One Health Research Center, Hokkaido University, Sapporo, 001-0020, Japan.,Corresponding author. (M.S.); (H.S.)
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10
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Gao Y, Fu Z, Guan J, Liu X, Zhang Q. The role of Notch signaling pathway in metabolic bone diseases. Biochem Pharmacol 2023; 207:115377. [PMID: 36513140 DOI: 10.1016/j.bcp.2022.115377] [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: 09/29/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Metabolic bone diseases is the third most common endocrine diseases after diabetes and thyroid diseases. More than 500 million people worldwide suffer from metabolic bone diseases. The generation and development of bone metabolic diseases is a complex process regulated by multiple signaling pathways, among which the Notch signaling pathway is one of the most important pathways. The Notch signaling pathway regulates the differentiation and function of osteoblasts and osteoclasts, and affects the process of cartilage formation, bone formation and bone resorption. Genetic mutations in upstream and downstream of Notch signaling genes can lead to a series of metabolic bone diseases, such as Alagille syndrome, Adams-Oliver syndrome and spondylocostal dysostosis. In this review, we analyzed the mechanisms of Notch ligands, Notch receptors and signaling molecules in the process of signal transduction, and summarized the progress on the pathogenesis and clinical manifestations of bone metabolic diseases caused by Notch gene mutation. We hope to draw attention to the role of the Notch signaling pathway in metabolic bone diseases and provide new ideas and approaches for the diagnosis and treatment of metabolic bone diseases.
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Affiliation(s)
- Yongguang Gao
- Tangshan Key Laboratory of Green Speciality Chemicals, Department of Chemistry, Tangshan Normal University, Tangshan 063000, China.
| | - Zhanda Fu
- Tangshan Key Laboratory of Green Speciality Chemicals, Department of Chemistry, Tangshan Normal University, Tangshan 063000, China
| | - Junxia Guan
- Tangshan Key Laboratory of Green Speciality Chemicals, Department of Chemistry, Tangshan Normal University, Tangshan 063000, China
| | - Xinhua Liu
- Tangshan Key Laboratory of Green Speciality Chemicals, Department of Chemistry, Tangshan Normal University, Tangshan 063000, China
| | - Qing Zhang
- Tangshan Key Laboratory of Green Speciality Chemicals, Department of Chemistry, Tangshan Normal University, Tangshan 063000, China.
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11
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Lu X, Chen Y, Zhang G. Functional evolution of SARS-CoV-2 spike protein: Maintaining wide host spectrum and enhancing infectivity via surface charge of spike protein. Comput Struct Biotechnol J 2023; 21:2068-2074. [PMID: 36936817 PMCID: PMC10008190 DOI: 10.1016/j.csbj.2023.03.010] [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: 10/09/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The SARS-CoV-2 virus, which causes the COVID-19, is rapidly accumulating mutations to adapt to the hosts. We collected SARS-CoV-2 sequence data from the end of 2019 to January 2023 to analyze for their evolutionary features during the pandemic. We found that most of the SARS-CoV-2 genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection. From the original strain to the alpha, delta and omicron variant types, the Ka/Ks of the S-gene increases, while the Ka/Ks within one variant type decreases over time. During the evolution, the codon usage did not evolve towards optimal translation and protein expression. In contrast, only S-gene mutations showed a remarkable trend on accumulating more positive charges. This facilitates the infection via binding human ACE2 for cell entry and binding furin for cleavage. Such a functional evolution emphasizes the survival strategy of SARS-CoV-2, and indicated new druggable target to contain the viral infection. The nearly fully positively-charged interaction surfaces indicated that the infectivity of SARS-CoV-2 virus may approach a limit.
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Affiliation(s)
- Xiaolong Lu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
- Chi-Biotech Co. Ltd., Shenzhen, China
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12
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Baumgardt M, Hülsemann M, Löwa A, Fatykhova D, Hoffmann K, Kessler M, Mieth M, Hellwig K, Frey D, Langenhagen A, Voss A, Obermayer B, Wyler E, Dökel S, Gruber AD, Tölch U, Hippenstiel S, Hocke AC, Hönzke K. State-of-the-art analytical methods of viral infections in human lung organoids. PLoS One 2022; 17:e0276115. [PMID: 36538516 PMCID: PMC9767351 DOI: 10.1371/journal.pone.0276115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
Human-based organ models can provide strong predictive value to investigate the tropism, virulence, and replication kinetics of viral pathogens. Currently, such models have received widespread attention in the study of SARS-CoV-2 causing the COVID-19 pandemic. Applicable to a large set of organoid models and viruses, we provide a step-by-step work instruction for the infection of human alveolar-like organoids with SARS-CoV-2 in this protocol collection. We also prepared a detailed description on state-of-the-art methodologies to assess the infection impact and the analysis of relevant host factors in organoids. This protocol collection consists of five different sets of protocols. Set 1 describes the protein extraction from human alveolar-like organoids and the determination of protein expression of angiotensin-converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2) and FURIN as exemplary host factors of SARS-CoV-2. Set 2 provides detailed guidance on the extraction of RNA from human alveolar-like organoids and the subsequent qPCR to quantify the expression level of ACE2, TMPRSS2, and FURIN as host factors of SARS-CoV-2 on the mRNA level. Protocol set 3 contains an in-depth explanation on how to infect human alveolar-like organoids with SARS-CoV-2 and how to quantify the viral replication by plaque assay and viral E gene-based RT-qPCR. Set 4 provides a step-by-step protocol for the isolation of single cells from infected human alveolar-like organoids for further processing in single-cell RNA sequencing or flow cytometry. Set 5 presents a detailed protocol on how to perform the fixation of human alveolar-like organoids and guides through all steps of immunohistochemistry and in situ hybridization to visualize SARS-CoV-2 and its host factors. The infection and all subsequent analytical methods have been successfully validated by biological replications with human alveolar-like organoids based on material from different donors.
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Affiliation(s)
- Morris Baumgardt
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Maren Hülsemann
- Berlin Institute of Health at Charité (BIH), BIH QUEST Center for Responsible Research, Berlin, Germany
| | - Anna Löwa
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Diana Fatykhova
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Karen Hoffmann
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Mirjana Kessler
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Department of Gynecology and Obstetrics, University Hospital, LMU, Munich, Germany
| | - Maren Mieth
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Katharina Hellwig
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Doris Frey
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alina Langenhagen
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voss
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) and IRI Life Sciences, Institute for Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Simon Dökel
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Ulf Tölch
- Berlin Institute of Health at Charité (BIH), BIH QUEST Center for Responsible Research, Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Andreas C. Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Katja Hönzke
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
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13
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Liu S, Stauft CB, Selvaraj P, Chandrasekaran P, D’Agnillo F, Chou CK, Wu WW, Lien CZ, Meseda CA, Pedro CL, Starost MF, Weir JP, Wang TT. Intranasal delivery of a rationally attenuated SARS-CoV-2 is immunogenic and protective in Syrian hamsters. Nat Commun 2022; 13:6792. [PMID: 36357440 PMCID: PMC9648440 DOI: 10.1038/s41467-022-34571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Few live attenuated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are in pre-clinical or clinical development. We seek to attenuate SARS-CoV-2 (isolate WA1/2020) by removing the polybasic insert within the spike protein and the open reading frames (ORFs) 6-8, and by introducing mutations that abolish non-structural protein 1 (Nsp1)-mediated toxicity. The derived virus (WA1-ΔPRRA-ΔORF6-8-Nsp1K164A/H165A) replicates to 100- to 1000-fold-lower titers than the ancestral virus and induces little lung pathology in both K18-human ACE2 (hACE2) transgenic mice and Syrian hamsters. Immunofluorescence and transcriptomic analyses of infected hamsters confirm that three-pronged genetic modifications attenuate the proinflammatory pathways more than the removal of the polybasic cleavage site alone. Finally, intranasal administration of just 100 PFU of the WA1-ΔPRRA-ΔORF6-8-Nsp1K164A/H165A elicits robust antibody responses in Syrian hamsters and protects against SARS-CoV-2-induced weight loss and pneumonia. As a proof-of-concept study, we demonstrate that live but sufficiently attenuated SARS-CoV-2 vaccines may be attainable by rational design.
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Affiliation(s)
- Shufeng Liu
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Charles B. Stauft
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Prabhuanand Selvaraj
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Prabha Chandrasekaran
- grid.94365.3d0000 0001 2297 5165Laboratory of Clinical Investigation, National Institutes of Aging, National Institutes of Health, Baltimore, USA
| | - Felice D’Agnillo
- grid.417587.80000 0001 2243 3366Laboratory of Biochemistry and Vascular Biology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Chao-Kai Chou
- grid.417587.80000 0001 2243 3366Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Wells W. Wu
- grid.417587.80000 0001 2243 3366Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Christopher Z. Lien
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Clement A. Meseda
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Cyntia L. Pedro
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Matthew F. Starost
- grid.94365.3d0000 0001 2297 5165Division of Veterinary Resources, Diagnostic and Research Services Branch, National Institutes of Health, Rockville Pike, USA
| | - Jerry P. Weir
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Tony T. Wang
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
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14
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Abdoli M, Shafaati M, Ghamsari LK, Abdoli A. Intranasal administration of cold-adapted live-attenuated SARS-CoV-2 candidate vaccine confers protection against SARS-CoV-2. Virus Res 2022; 319:198857. [PMID: 35820511 PMCID: PMC9270963 DOI: 10.1016/j.virusres.2022.198857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/15/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
With the COVID-19 pandemic globally, the ongoing threat of new challenges of mucosal infections was once again reminded human beings. Hence, access to the next-generation vaccine to elicit mucosal immunity is required to reduce virus shedding. SARS-CoV-2 retains a unique polybasic cleavage motif in its spike protein, recognized by the host furin protease. The proteolytic furin cleavage site at the junction of S1/S2 glycoprotein plays a key role in the pathogenesis of SARS-CoV-2. Here, we examined the protective immunity of a double-deleted PRRA/GTNGTKR motifs cold-adapted live-attenuated candidate vaccines as a called "KaraVac." using a hamster animal model of infected attenuated SARS-CoV-2. The KaraVac vaccinated hamsters were challenged against the wild-type (WT) SARS-CoV-2. No apparent bodyweight loss and histopathological lesions were observed in the hamsters. The establishment of sterilizing immunity was induced via stimulating a robust neutralizing antibody (NAb) response in a hamster model. Consequently, deletions in the spike sequence and inoculation into hamsters provide resistance to the subsequent challenge with WT SARS-CoV-2. We have suggested that deletion of the furin cleavage site and GTNGTKR motifs in the spike sequence attenuates the virus from the parental strain and can be used as a potent immunogen.
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Affiliation(s)
- Mohsen Abdoli
- Amirabad Virology Laboratory, Vaccine Unit, Tehran 1413693341, Iran
| | - Maryam Shafaati
- Department of Microbiology, Faculty Science, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | | | - Asghar Abdoli
- Amirabad Virology Laboratory, Vaccine Unit, Tehran 1413693341, Iran; Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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15
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Yan K, Dumenil T, Tang B, Le TT, Bishop CR, Suhrbier A, Rawle DJ. Evolution of ACE2-Independent SARS-CoV-2 Infection and Mouse Adaption After Passage in Cells Expressing Human and Mouse ACE2. Virus Evol 2022; 8:veac063. [PMID: 35919871 PMCID: PMC9338707 DOI: 10.1093/ve/veac063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022] Open
Abstract
Human ACE2 Human angiotensin converting enzyme 2 (hACE2) is the key cell attachment and entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with the original SARS-CoV-2 isolates unable to use mouse ACE2 (mACE2). Herein we describe the emergence of a SARS-CoV-2 strain capable of ACE2-independent infection and the evolution of mouse-adapted (MA) SARS-CoV-2 by in vitro serial passaging of virus in co-cultures of cell lines expressing hACE2 and mACE2. MA viruses evolved with up to five amino acid changes in the spike protein, all of which have been seen in human isolates. MA viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates and caused characteristic lung histopathology. One MA virus also evolved to replicate efficiently in several ACE2-negative cell lines across several species, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) ACE2 knockout cells. An E484D substitution is likely involved in ACE2-independent entry and has appeared in only ≈0.003 per cent of human isolates globally, suggesting that it provided no significant selection advantage in humans. ACE2-independent entry reveals a SARS-CoV-2 infection mechanism that has potential implications for disease pathogenesis, evolution, tropism, and perhaps also intervention development.
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Affiliation(s)
- Kexin Yan
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
| | - Troy Dumenil
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
| | - Bing Tang
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
| | - Thuy T Le
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
| | - Cameron R Bishop
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
| | - Andreas Suhrbier
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence , Brisbane, Queensland, 4029 and 4072, Australia
| | - Daniel J Rawle
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute , Brisbane, Queensland. 4029, Australia
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16
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Xia S, Wang L, Zhu Y, Lu L, Jiang S. Origin, virological features, immune evasion and intervention of SARS-CoV-2 Omicron sublineages. Signal Transduct Target Ther 2022; 7:241. [PMID: 35853878 PMCID: PMC9295084 DOI: 10.1038/s41392-022-01105-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/26/2022] [Accepted: 07/04/2022] [Indexed: 12/12/2022] Open
Abstract
Recently, a large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continuously emerged and posed a major threat to global public health. Among them, particularly, Omicron variant (B.1.1.529), first identified in November 2021, carried numerous mutations in its spike protein (S), and then quickly spread around the world. Currently, Omicron variant has expanded into more than one hundred sublineages, such as BA.1, BA.2, BA.2.12.1, BA.4 and BA.5, which have already become the globally dominant variants. Different from other variants of concern (VOCs) of SARS-CoV-2, the Omicron variant and its sublineages exhibit increased transmissibility and immune escape from neutralizing antibodies generated through previous infection or vaccination, and have caused numerous re-infections and breakthrough infections. In this prospective, we have focused on the origin, virological features, immune evasion and intervention of Omicron sublineages, which will benefit the development of next-generation vaccines and therapeutics, including pan-sarbecovirus and universal anti-CoV therapeutics, to combat currently circulating and future emerging Omicron sublineages as well as other SARS-CoV-2 variants.
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Affiliation(s)
- Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Lijue Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China.
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China.
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17
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Pászti-Gere E, Szentkirályi-Tóth A, Szabó P, Steinmetzer T, Fliszár-Nyúl E, Poór M. In vitro characterization of the furin inhibitor MI-1851: Albumin binding, interaction with cytochrome P450 enzymes and cytotoxicity. Biomed Pharmacother 2022; 151:113124. [PMID: 35594709 PMCID: PMC9110138 DOI: 10.1016/j.biopha.2022.113124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023] Open
Abstract
The substrate-analog furin inhibitor MI-1851 can suppress the cleavage of SARS-CoV-2 spike protein and consequently produces significant antiviral effect on infected human airway epithelial cells. In this study, the interaction of inhibitor MI-1851 was examined with human serum albumin using fluorescence spectroscopy and ultrafiltration techniques. Furthermore, the impacts of MI-1851 on human microsomal hepatic cytochrome P450 (CYP) 1A2, 2C9, 2C19, 2D6 and 3A4 activities were assessed based on fluorometric assays. The inhibitory action was also examined on human recombinant CYP3A4 enzyme and on hepatocytes. In addition, microsomal stability (60 min) and cytotoxicity were tested as well. MI-1851 showed no relevant interaction with human serum albumin and was significantly depleted by human microsomes. Furthermore, it did not inhibit CYP1A2, 2C9, 2C19 and 2D6 enzymes. In human hepatocytes, CYP3A4 was significantly suppressed by MI-1851 and weak inhibition was noticed in regard to human microsomes and human recombinant CYP3A4. Finally, MI-1851 did not impair the viability and the oxidative status of primary human hepatocytes (up to 100 μM concentration). Based on these observations, furin inhibitor MI-1851 appears to be potential drug candidates in the treatment of COVID-19, due to the involvement of furin in S protein priming and thus activation of the pandemic SARS-CoV-2.
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Affiliation(s)
- Erzsébet Pászti-Gere
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary.
| | - Anna Szentkirályi-Tóth
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | - Pál Szabó
- MS Metabolomics Laboratory, Center for Structural Study, Research Center for Natural Sciences, Budapest, Hungary
| | - Torsten Steinmetzer
- Faculty of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Eszter Fliszár-Nyúl
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Pécs, Hungary
| | - Miklós Poór
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Pécs, Hungary; Lab-on-a-Chip Research Group, János Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
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18
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Akaishi T. Comparison of Insertion, Deletion, and Point Mutations in the Genomes of Human Adenovirus HAdvC-2 and SARS-CoV-2. TOHOKU J EXP MED 2022; 258:23-27. [PMID: 35705320 DOI: 10.1620/tjem.2022.j049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Tetsuya Akaishi
- Division of General Internal Medicine, Tohoku University Hospital.,Department of Education and Support for Regional Medicine, Tohoku University Hospital.,COVID-19 Screening Test Center, Tohoku University
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19
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Mezger MC, Conzelmann C, Weil T, von Maltitz P, Albers DPJ, Münch J, Stamminger T, Schilling EM. Inhibitors of Activin Receptor-like Kinase 5 Interfere with SARS-CoV-2 S-Protein Processing and Spike-Mediated Cell Fusion via Attenuation of Furin Expression. Viruses 2022; 14:v14061308. [PMID: 35746781 PMCID: PMC9228453 DOI: 10.3390/v14061308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/18/2023] Open
Abstract
Screening of a protein kinase inhibitor library identified SB431542, targeting activin receptor-like kinase 5 (ALK5), as a compound interfering with SARS-CoV-2 replication. Since ALK5 is implicated in transforming growth factor β (TGF-β) signaling and regulation of the cellular endoprotease furin, we pursued this research to clarify the role of this protein kinase for SARS-CoV-2 infection. We show that TGF-β1 induces the expression of furin in a broad spectrum of cells including Huh-7 and Calu-3 that are permissive for SARS-CoV-2. The inhibition of ALK5 by incubation with SB431542 revealed a dose-dependent downregulation of both basal and TGF-β1 induced furin expression. Furthermore, we demonstrate that the ALK5 inhibitors SB431542 and Vactosertib negatively affect the proteolytic processing of the SARS-CoV-2 Spike protein and significantly reduce spike-mediated cell-cell fusion. This correlated with an inhibitory effect of ALK5 inhibition on the production of infectious SARS-CoV-2. Altogether, our study shows that interference with ALK5 signaling attenuates SARS-CoV-2 infectivity and cell-cell spread via downregulation of furin which is most pronounced upon TGF-β stimulation. Since a TGF-β dominated cytokine storm is a hallmark of severe COVID-19, ALK5 inhibitors undergoing clinical trials might represent a potential therapy option for COVID-19.
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Affiliation(s)
- Maja C. Mezger
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (M.C.M.); (E.-M.S.)
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Dan P. J. Albers
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Thomas Stamminger
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (M.C.M.); (E.-M.S.)
- Correspondence: ; Tel.: +49-731-50065100
| | - Eva-Maria Schilling
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (M.C.M.); (E.-M.S.)
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20
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Kircheis R, Planz O. Could a Lower Toll-like Receptor (TLR) and NF-κB Activation Due to a Changed Charge Distribution in the Spike Protein Be the Reason for the Lower Pathogenicity of Omicron? Int J Mol Sci 2022; 23:ijms23115966. [PMID: 35682644 PMCID: PMC9180620 DOI: 10.3390/ijms23115966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023] Open
Abstract
The novel SARS-CoV-2 Omicron variant B.1.1.529, which emerged in late 2021, is currently active worldwide, replacing other variants, including the Delta variant, due to an enormously increased infectivity. Multiple substitutions and deletions in the N-terminal domain (NTD) and the receptor binding domain (RBD) in the spike protein collaborate with the observed increased infectivity and evasion from therapeutic monoclonal antibodies and vaccine-induced neutralizing antibodies after primary/secondary immunization. In contrast, although three mutations near the S1/S2 furin cleavage site were predicted to favor cleavage, observed cleavage efficacy is substantially lower than in the Delta variant and also lower compared to the wild-type virus correlating with significantly lower TMPRSS2-dependent replication in the lungs, and lower cellular syncytium formation. In contrast, the Omicron variant shows high TMPRSS2-independent replication in the upper airway organs, but lower pathogenicity in animal studies and clinics. Based on recent data, we present here a hypothesis proposing that the changed charge distribution in the Omicron’s spike protein could lead to lower activation of Toll-like receptors (TLRs) in innate immune cells, resulting in lower NF-κB activation, furin expression, and viral replication in the lungs, and lower immune hyper-activation.
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Affiliation(s)
- Ralf Kircheis
- Syntacoll GmbH, 93342 Saal an der Donau, Germany
- Correspondence: ; Tel.: +49-151-167-90606
| | - Oliver Planz
- Interfaculty Institute for Cell Biology, Department of Immunology, Eberhard Karls University Tuebingen, 72076 Tübingen, Germany;
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21
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Goławski M, Lewandowski P, Jabłońska I, Delijewski M. The Reassessed Potential of SARS-CoV-2 Attenuation for COVID-19 Vaccine Development—A Systematic Review. Viruses 2022; 14:v14050991. [PMID: 35632736 PMCID: PMC9146402 DOI: 10.3390/v14050991] [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: 03/30/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Live-attenuated SARS-CoV-2 vaccines received relatively little attention during the COVID-19 pandemic. Despite this, several methods of obtaining attenuated coronaviruses are known. In this systematic review, the strategies of coronavirus attenuation, which may potentially be applied to SARS-CoV-2, were identified. PubMed, Scopus, Web of Science and Embase databases were searched to identify relevant articles describing attenuating mutations tested in vivo. In case of coronaviruses other than SARS-CoV-2, sequence alignment was used to exclude attenuating mutations that cannot be applied to SARS-CoV-2. Potential immunogenicity, safety and efficacy of the attenuated SARS-CoV-2 vaccine were discussed based on animal studies data. A total of 27 attenuation strategies, used to create 101 different coronaviruses, have been described in 56 eligible articles. The disruption of the furin cleavage site in the SARS-CoV-2 spike protein was identified as the most promising strategy. The replacement of core sequences of transcriptional regulatory signals, which prevents recombination with wild-type viruses, also appears particularly advantageous. Other important attenuating mutations encompassed mostly the prevention of evasion of innate immunity. Sufficiently attenuated coronaviruses typically caused no meaningful disease in susceptible animals and protected them from challenges with virulent virus. This indicates that attenuated COVID-19 vaccines may be considered as a potential strategy to fight the threat posed by SARS-CoV-2.
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Affiliation(s)
- Marcin Goławski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
- Correspondence:
| | - Piotr Lewandowski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
| | - Iwona Jabłońska
- Department of Biophysics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Marcin Delijewski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
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22
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Lin JJ, Tien CF, Kuo YP, Lin EJ, Tsai WH, Chen MY, Tsai PJ, Su YW, Pathak N, Yang JM, Yu CY, Chuang ZS, Wu HC, Tsai WT, Dai SS, Liao HC, Chai KM, Su YS, Chuang TH, Liu SJ, Chen HW, Dou HY, Chen FJ, Chen CT, Liao CL, Yu GY. Furin and TMPRSS2 Resistant Spike Induces Robust Humoral and Cellular Immunity Against SARS-CoV-2 Lethal Infection. Front Immunol 2022; 13:872047. [PMID: 35585971 PMCID: PMC9108258 DOI: 10.3389/fimmu.2022.872047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/24/2022] [Indexed: 12/23/2022] Open
Abstract
An effective COVID-19 vaccine against broad SARS-CoV-2 variants is still an unmet need. In the study, the vesicular stomatitis virus (VSV)-based vector was used to express the SARS-CoV-2 Spike protein to identify better vaccine designs. The replication-competent of the recombinant VSV-spike virus with C-terminal 19 amino acid truncation (SΔ19 Rep) was generated. A single dose of SΔ19 Rep intranasal vaccination is sufficient to induce protective immunity against SARS-CoV-2 infection in hamsters. All the clones isolated from the SΔ19 Rep virus contained R682G mutation located at the Furin cleavage site. An additional S813Y mutation close to the TMPRSS2 cleavage site was identified in some clones. The enzymatic processing of S protein was blocked by these mutations. The vaccination of the R682G-S813Y virus produced a high antibody response against S protein and a robust S protein-specific CD8+ T cell response. The vaccinated animals were protected from the lethal SARS-CoV-2 (delta variant) challenge. The S antigen with resistance to enzymatic processes by Furin and TMPRSS2 will provide better immunogenicity for vaccine design.
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Affiliation(s)
- Jhe-Jhih Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chih-Feng Tien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Ping Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - En-Ju Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Wei-Hsiang Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Ming-Yu Chen
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Pei-Ju Tsai
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Nikhil Pathak
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Jinn-Moon Yang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Zih-Shiuan Chuang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Wan-Ting Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Syong Dai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Hung-Chun Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Kit Man Chai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Siang Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Jen Liu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Wei Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chin-Len Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- *Correspondence: Guann-Yi Yu,
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23
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Beddingfield BJ, Rowe LA, Russell-Lodrigue KE, Doyle-Meyers LA, Golden N, Spencer S, Chirichella N, Blair RV, Maness NJ, Roy CJ. Breakthrough gastrointestinal COVID and intra-host evolution consequent to combination monoclonal antibody prophylaxis. J Infect Dis 2022; 226:1588-1592. [PMID: 35429402 PMCID: PMC9213849 DOI: 10.1093/infdis/jiac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/12/2022] [Indexed: 11/29/2022] Open
Abstract
Breakthrough gastrointestinal COVID-19 was observed after experimental SARS-CoV-2 upper mucosal infection in a rhesus macaque undergoing low-dose monoclonal antibody prophylaxis. High levels of viral RNA were detected in intestinal sites contrasting with minimal viral replication in upper respiratory mucosa. Sequencing of virus recovered from tissue in 3 gastrointestinal sites and rectal swab revealed loss of furin cleavage site deletions present in the inoculating virus stock and 2 amino acid changes in spike that were detected in 2 colon sites but not elsewhere, suggesting compartmentalized replication and intestinal viral evolution. This suggests suboptimal antiviral therapies promote viral sequestration in these anatomies.
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Affiliation(s)
| | - Lori A. Rowe
- Tulane National Primate Research Center, Covington, LA USA 70447
| | | | | | - Nadia Golden
- Tulane National Primate Research Center, Covington, LA USA 70447
| | - Skye Spencer
- Tulane National Primate Research Center, Covington, LA USA 70447
| | | | - Robert V. Blair
- Tulane National Primate Research Center, Covington, LA USA 70447
| | - Nicholas J. Maness
- Tulane National Primate Research Center, Covington, LA USA 70447
- Department of Microbiology & Immunology, Tulane School of Medicine, New Orleans, LA USA 70112
| | - Chad J. Roy
- Tulane National Primate Research Center, Covington, LA USA 70447
- Department of Microbiology & Immunology, Tulane School of Medicine, New Orleans, LA USA 70112
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24
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Barre A, Klonjkowski B, Benoist H, Rougé P. How Do Point Mutations Enhancing the Basic Character of the RBDs of SARS-CoV-2 Variants Affect Their Transmissibility and Infectivity Capacities? Viruses 2022; 14:783. [PMID: 35458513 PMCID: PMC9031512 DOI: 10.3390/v14040783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
The spread of SARS-CoV-2 variants in the population depends on their ability to anchor the ACE2 receptor in the host cells. Differences in the electrostatic potentials of the spike protein RBD (electropositive/basic) and ACE2 receptor (electronegative/acidic) play a key role in both the rapprochement and the recognition of the coronavirus by the cell receptors. Accordingly, point mutations that result in an increase in electropositively charged residues, e.g., arginine and lysine, especially in the RBD of spike proteins in the SARS-CoV-2 variants, could contribute to their spreading capacity by favoring their recognition by the electronegatively charged ACE2 receptors. All SARS-CoV-2 variants that have been recognized as being highly transmissible, such as the kappa (κ), delta (δ) and omicron (o) variants, which display an enhanced electropositive character in their RBDs associated with a higher number of lysine- or arginine-generating point mutations. Lysine and arginine residues also participate in the enhanced RBD-ACE2 binding affinity of the omicron variant, by creating additional salt bridges with aspartic and glutamic acid residues from ACE2. However, the effects of lysine- and arginine-generating point mutations on infectivity is more contrasted, since the overall binding affinity of omicron RBD for ACE2 apparently results from some epistasis among the whole set of point mutations.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Bernard Klonjkowski
- UMR Virologie, INRA, ANSES, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France;
| | - Hervé Benoist
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Pierre Rougé
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
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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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Prévost J, Medjahed H, Vézina D, Chen HC, Hahn BH, Smith AB, Finzi A. HIV-1 Envelope Glycoproteins Proteolytic Cleavage Protects Infected Cells from ADCC Mediated by Plasma from Infected Individuals. Viruses 2021; 13:2236. [PMID: 34835042 PMCID: PMC8625184 DOI: 10.3390/v13112236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) is synthesized in the endoplasmic reticulum as a trimeric gp160 precursor, which requires proteolytic cleavage by a cellular furin protease to mediate virus-cell fusion. Env is conformationally flexible but controls its transition from the unbound "closed" conformation (State 1) to downstream CD4-bound conformations (States 2/3), which are required for fusion. In particular, HIV-1 has evolved several mechanisms that reduce the premature "opening" of Env which exposes highly conserved epitopes recognized by non-neutralizing antibodies (nnAbs) capable of mediating antibody-dependent cellular cytotoxicity (ADCC). Env cleavage decreases its conformational transitions favoring the adoption of the "closed" conformation. Here we altered the gp160 furin cleavage site to impair Env cleavage and to examine its impact on ADCC responses mediated by plasma from HIV-1-infected individuals. We found that infected primary CD4+ T cells expressing uncleaved, but not wildtype, Env are efficiently recognized by nnAbs and become highly susceptible to ADCC responses mediated by plasma from HIV-1-infected individuals. Thus, HIV-1 limits the exposure of uncleaved Env at the surface of HIV-1-infected cells at least in part to escape ADCC responses.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (J.P.); (H.M.); (D.V.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Halima Medjahed
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (J.P.); (H.M.); (D.V.)
| | - Dani Vézina
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (J.P.); (H.M.); (D.V.)
| | - Hung-Ching Chen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA; (H.-C.C.); (A.B.S.III)
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA;
| | - Amos B. Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA; (H.-C.C.); (A.B.S.III)
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (J.P.); (H.M.); (D.V.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
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