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Synthetically recoded virus sCPD9 - A tool to accelerate SARS-CoV-2 research under biosafety level 2 conditions. Comput Struct Biotechnol J 2022; 20:4376-4380. [PMID: 35992535 PMCID: PMC9375251 DOI: 10.1016/j.csbj.2022.08.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/20/2022] Open
Abstract
Research with infectious SARS-CoV-2 is complicated because it must be conducted under biosafety level 3 (BSL-3) conditions. Recently, we constructed a live attenuated SARS-CoV-2 virus by rational design through partial recoding of the SARS-CoV-2 genome and showed that the attenuated virus, designated sCPD9, was highly attenuated in preclinical animal models. The recoded sequence was designed by codon pair deoptimization and is located at the distal end of gene ORF1ab. Codon pair deoptimization involves recoding of the viral sequence with underrepresented codon pairs but without altering the amino acid sequence of the encoded proteins. Thus, parental and attenuated viruses produce exactly the same proteins. In Germany, the live attenuated SARS-CoV-2 mutant sCPD9 was recently classified as a BSL-2 pathogen based on its genetic stability and strong attenuation in preclinical animal models. Despite its high attenuation in vivo, sCPD9 grows to high titers in common cell lines, making it suitable as substitute for virulent SARS-CoV-2 in many experimental setups. Consequently, sCPD9 can ease and accelerate SARS-CoV-2 research under BSL-2 conditions, particularly in experiments requiring replicating virus, such as diagnostics and development of antiviral drugs.
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202
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Ao Z, Ouyang MJ, Olukitibi TA, Yao X. SARS-CoV-2 Delta spike protein enhances the viral fusogenicity and inflammatory cytokine production. iScience 2022; 25:104759. [PMID: 35854977 PMCID: PMC9281453 DOI: 10.1016/j.isci.2022.104759] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/14/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022] Open
Abstract
The Delta variant had spread globally in 2021 and caused more serious disease than the original virus and Omicron variant. In this study, we investigated several virological features of Delta spike protein (SPDelta), including protein maturation, its impact on viral entry of pseudovirus and cell-cell fusion, and its induction of inflammatory cytokine production in human macrophages and dendritic cells. The results showed that SPΔCDelta exhibited enhanced S1/S2 cleavage in cells and pseudotyped virus-like particles (PVLPs). Further, SPΔCDelta elevated pseudovirus entry in human lung cell lines and significantly enhanced syncytia formation. Furthermore, we revealed that SPΔCDelta-PVLPs had stronger effects on stimulating NF-κB and AP-1 signaling in human monocytic THP1 cells and induced significantly higher levels of proinflammatory cytokine, such as TNF-α, IL-1β, and IL-6, released from human macrophages and dendritic cells. Overall, these studies provide evidence to support the important role of SPΔCDelta during virus infection, transmission, and pathogenesis.
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Affiliation(s)
- Zhujun Ao
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Maggie Jing Ouyang
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Titus Abiola Olukitibi
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Xiaojian Yao
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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203
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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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204
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Omidian N, Mohammadi P, Sadeghalvad M, Mohammadi-Motlagh HR. Cerebral microvascular complications associated with SARS-CoV-2 infection: How did it occur and how should it be treated? Biomed Pharmacother 2022; 154:113534. [PMID: 35994816 PMCID: PMC9381434 DOI: 10.1016/j.biopha.2022.113534] [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: 06/18/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 01/08/2023] Open
Abstract
Cerebral microvascular disease has been reported as a central feature of the neurological disorders in patients with SARS-CoV-2 infection that may be associated with an increased risk of ischemic stroke. The main pathomechanism in the development of cerebrovascular injury due to SARS-CoV-2 infection can be a consequence of endothelial cell dysfunction as a structural part of the blood-brain barrier (BBB), which may be accompanied by increased inflammatory response and thrombocytopenia along with blood coagulation disorders. In this review, we described the properties of the BBB, the neurotropism behavior of SARS-CoV-2, and the possible mechanisms of damage to the CNS microvascular upon SARS-CoV-2 infection.
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Affiliation(s)
- Neda Omidian
- Department of Physiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pantea Mohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mona Sadeghalvad
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamid-Reza Mohammadi-Motlagh
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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205
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Meng B, Datir R, Choi J, Bradley JR, Smith KGC, Lee JH, Gupta RK. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity. Cell Rep 2022; 40:111220. [PMID: 35963244 PMCID: PMC9346021 DOI: 10.1016/j.celrep.2022.111220] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike N-terminal domain (NTD) remains poorly characterized despite enrichment of mutations in this region across variants of concern (VOCs). Here, we examine the contribution of the NTD to infection and cell-cell fusion by constructing chimeric spikes bearing B.1.617 lineage (Delta and Kappa variants) NTDs and generating spike pseudotyped lentivirus. We find that the Delta NTD on a Kappa or wild-type (WT) background increases S1/S2 cleavage efficiency and virus entry, specifically in lung cells and airway organoids, through use of TMPRSS2. Delta exhibits increased cell-cell fusogenicity that could be conferred to WT and Kappa spikes by Delta NTD transfer. However, chimeras of Omicron BA.1 and BA.2 spikes with a Delta NTD do not show more efficient TMPRSS2 use or fusogenicity. We conclude that the NTD allosterically modulates S1/S2 cleavage and spike-mediated functions in a spike context-dependent manner, and allosteric interactions may be lost when combining regions from more distantly related VOCs.
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Affiliation(s)
- Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jinwook Choi
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK; NIHR Bioresource, Cambridge, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, South Africa.
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206
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Shuler G, Hagai T. Rapidly evolving viral motifs mostly target biophysically constrained binding pockets of host proteins. Cell Rep 2022; 40:111212. [PMID: 35977510 DOI: 10.1016/j.celrep.2022.111212] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/11/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022] Open
Abstract
Evolutionary changes in host-virus interactions can alter the course of infection, but the biophysical and regulatory constraints that shape interface evolution remain largely unexplored. Here, we focus on viral mimicry of host-like motifs that allow binding to host domains and modulation of cellular pathways. We observe that motifs from unrelated viruses preferentially target conserved, widely expressed, and highly connected host proteins, enriched with regulatory and essential functions. The interface residues within these host domains are more conserved and bind a larger number of cellular proteins than similar motif-binding domains that are not known to interact with viruses. In contrast, rapidly evolving viral-binding human proteins form few interactions with other cellular proteins and display high tissue specificity, and their interfaces have few inter-residue contacts. Our results distinguish between conserved and rapidly evolving host-virus interfaces and show how various factors limit host capacity to evolve, allowing for efficient viral subversion of host machineries.
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Affiliation(s)
- Gal Shuler
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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207
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Smither SJ, Kempster S, Priestnall SL, Suárez-Bonnet A, Stapleton H, Laws TR, Ferguson D, Almond N, Lever MS, Williamson ED. Early Isolates of SARS-CoV-2 Result in Different Pathogenesis in the Transduced Mouse Model of COVID-19. Viruses 2022; 14:v14081769. [PMID: 36016391 PMCID: PMC9414617 DOI: 10.3390/v14081769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
A transduced mouse model of SARS-CoV-2 infection was established using Balb/c mice. This was achieved through the adenovirus-vectored delivery of the hACE2 gene, to render the mice transiently susceptible to the virus. The model was characterised in terms of the dissemination of hACE2 receptor expression, the dissemination of three SARS-CoV-2 virus variants in vivo up to 10 days following challenge, the resulting histopathology and the clinical signs induced in the mice. In transduced mice, the infection was short-term, with a rapid loss in body weight starting at day 2 with maximum weight loss at day 4, followed by subsequent recovery until day 10. The induced expression of the hACE2 receptor was evident in the lungs, but, upon challenge, the SARS-CoV-2 virus disseminated beyond the lungs to spleen, liver and kidney, peaking at day 2 post infection. However, by day 10 post infection, the virus was undetectable. The lung histopathology was characterised by bronchial and alveolar inflammation, which was still present at day 10 post infection. Transduced mice had differential responses to viral variants ranking CVR-Glasgow 1 > Victoria-1 > England-2 isolates in terms of body weight loss. The transduced mouse model provides a consistent and manipulatable model of SARS-CoV-2 infection to screen viral variants for their relative virulence and possible interventions.
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Affiliation(s)
- Sophie J. Smither
- Chemical Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury SP4 0JQ, UK
- Correspondence: ; Tel.: +44-(0)1980-651-082
| | - Sarah Kempster
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms EN6 3QG, UK
| | - Simon L. Priestnall
- Department Pathobiology & Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK
| | - Alejandro Suárez-Bonnet
- Department Pathobiology & Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK
| | - Helen Stapleton
- Chemical Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury SP4 0JQ, UK
| | - Thomas R. Laws
- Chemical Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury SP4 0JQ, UK
| | - Deborah Ferguson
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms EN6 3QG, UK
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms EN6 3QG, UK
| | - Mark S. Lever
- Chemical Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury SP4 0JQ, UK
| | - E. Diane Williamson
- Chemical Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury SP4 0JQ, UK
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208
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Low JS, Jerak J, Tortorici MA, McCallum M, Pinto D, Cassotta A, Foglierini M, Mele F, Abdelnabi R, Weynand B, Noack J, Montiel-Ruiz M, Bianchi S, Benigni F, Sprugasci N, Joshi A, Bowen JE, Stewart C, Rexhepaj M, Walls AC, Jarrossay D, Morone D, Paparoditis P, Garzoni C, Ferrari P, Ceschi A, Neyts J, Purcell LA, Snell G, Corti D, Lanzavecchia A, Veesler D, Sallusto F. ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science 2022; 377:735-742. [PMID: 35857703 PMCID: PMC9348755 DOI: 10.1126/science.abq2679] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/03/2022] [Indexed: 12/14/2022]
Abstract
The coronavirus spike glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus spike proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors. These mAbs recognize the fusion peptide and acquire affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha- and betacoronaviruses, including animal coronaviruses WIV-1 and PDF-2180. Two selected mAbs also neutralize Omicron BA.1 and BA.2 authentic viruses and reduce viral burden and pathology in vivo. Structural and functional analyses showed that the fusion peptide-specific mAbs bound with different modalities to a cryptic epitope hidden in prefusion stabilized spike, which became exposed upon binding of angiotensin-converting enzyme 2 (ACE2) or ACE2-mimicking mAbs.
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Affiliation(s)
- Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
| | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
| | | | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Dora Pinto
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, B-3000 Leuven, Belgium
| | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Siro Bianchi
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Megi Rexhepaj
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Diego Morone
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Philipp Paparoditis
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; 6900 Lugano, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
- Department of Internal Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
- Global Virus Network, Baltimore, MD 21201, USA
| | | | | | - Davide Corti
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
- National Institute of Molecular Genetics, 20122 Milano, Italy
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
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209
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Frolova EI, Palchevska O, Lukash T, Dominguez F, Britt W, Frolov I. Acquisition of Furin Cleavage Site and Further SARS-CoV-2 Evolution Change the Mechanisms of Viral Entry, Infection Spread, and Cell Signaling. J Virol 2022; 96:e0075322. [PMID: 35876526 PMCID: PMC9364789 DOI: 10.1128/jvi.00753-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
Circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population leads to further viral evolution. The new variants that arise during this evolution are more infectious. Our data suggest that newer variants have shifted from utilizing both cathepsin/endosome- and TMPRSS2-mediated entry mechanisms to rely on a TMPRSS2-dependent entry pathway. Accordingly, only the early lineages of SARS-CoV-2 are capable of infecting and forming syncytia in Vero/ACE2 cells which lack TMPRSS2 expression. The presence of an intact multibasic furin cleavage site (FCS) in the S protein was a key requirement for cell-to-cell fusion. Deletion of FCS makes SARS-CoV-2 more infectious in vitro but renders it incapable of syncytium formation. Cell-to-cell fusion likely represents an alternative means of virus spread and is resistant to the presence of high levels of neutralizing monoclonal antibodies (MAbs) and immune sera in the media. In this study, we also noted that cells infected with SARS-CoV-2 with an intact FCS or alphavirus replicon expressing S protein (VEErep/S) released high levels of free S1 subunit. The released S1 is capable of activating the TLR4 receptor and inducing a pro-inflammatory response. Thus, S1 activation of TLR4 may be an important contributor to SARS-CoV-2-induced COVID-19 disease and needs to be considered in the design of COVID mRNA vaccines. Lastly, a VEErep/S-replicon was shown to produce large amounts of infectious, syncytium-forming pseudoviruses and thus could represent alternative experimental system for screening inhibitors of virus entry and syncytium formation. IMPORTANCE The results of this study demonstrate that the late lineages of SARS-CoV-2 evolved to more efficient use of the TMPRSS2-mediated entry pathway and gradually lost an ability to employ the cathepsins/endosome-mediated entry. The acquisition of a furin cleavage site (FCS) by SARS-CoV-2-specific S protein made the virus a potent producer of syncytia. Their formation is also determined by expression of ACE2 and TMPRSS2 and is resistant to neutralizing human MAbs and immune sera. Syncytium formation appears to be an alternative means of infection spread following the development of an adaptive immune response. Cells infected with SARS-CoV-2 with an intact FCS secrete high levels of the S1 subunit. The released S1 demonstrates an ability to activate the TLR4 receptor and induce pro-inflammatory cytokines, which represent a hallmark of SARS-CoV-2 pathogenesis. Alphavirus replicons encoding SARS-CoV-2 S protein cause spreading, syncytium-forming infection, and they can be applied as an experimental tool for studying the mechanism of syncytium formation.
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Affiliation(s)
- Elena I. Frolova
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Oksana Palchevska
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tetyana Lukash
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Francisco Dominguez
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - William Britt
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Pediatrics and Neurobiology, UAB School of Medicine, Birmingham, Alabama, USA
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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210
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Vu MN, Lokugamage KG, Plante JA, Scharton D, Bailey AO, Sotcheff S, Swetnam DM, Johnson BA, Schindewolf C, Alvarado RE, Crocquet-Valdes PA, Debbink K, Weaver SC, Walker DH, Russell WK, Routh AL, Plante KS, Menachery VD. QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis. Proc Natl Acad Sci U S A 2022; 119:e2205690119. [PMID: 35881779 PMCID: PMC9371735 DOI: 10.1073/pnas.2205690119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/26/2022] [Indexed: 02/08/2023] Open
Abstract
The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif (ΔQTQTN). Here, we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated, and disruption of its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site-the FCS, loop length, and glycosylation-are required for efficient SARS-CoV-2 replication and pathogenesis.
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Affiliation(s)
- Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
| | - Aaron O. Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Daniele M. Swetnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - R. Elias Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX
| | | | - Kari Debbink
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21211
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555
| | - William K. Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Andrew L. Routh
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555
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211
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Enjuanes L, Sola I, Zúñiga S, Honrubia JM, Bello-Pérez M, Sanz-Bravo A, González-Miranda E, Hurtado-Tamayo J, Requena-Platek R, Wang L, Muñoz-Santos D, Sánchez CM, Esteban A, Ripoll-Gómez J. Nature of viruses and pandemics: Coronaviruses. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:151-158. [PMID: 35966177 PMCID: PMC9359481 DOI: 10.1016/j.crimmu.2022.08.003] [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: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Coronaviruses (CoVs) have the largest genome among RNA viruses and store large amounts of information without genome integration as they replicate in the cell cytoplasm. The replication of the virus is a continuous process, whereas the transcription of the subgenomic mRNAs is a discontinuous one, involving a template switch, which resembles a high frequency recombination mechanism that may favor virus genome variability. The origin of the three deadly human CoVs SARS-CoV, MERS-CoV and SARS-CoV-2 are zoonotic events. SARS-CoV-2 has incorporated in its spike protein a furine proteolytic site that facilitates the activation of the virus in any tissue, making this CoV strain highly polytropic and pathogenic. Using MERS-CoV as a model, a propagation-deficient RNA replicon was generated by removing E protein gene (essential for viral morphogenesis and involved in virulence), and accessory genes 3, 4a, 4b and 5 (responsible for antagonism of the innate immune response) to attenuate the virus: MERS-CoV-Δ[3,4a,4b,5,E]. This RNA replicon is strongly attenuated and elicits sterilizing protection after a single immunization in transgenic mice with the receptor for MERS-CoV, making it a promising vaccine candidate for this virus and an interesting platform for vector-based vaccine development. A strategy could be developed for the design of RNA replicon vaccines for other human pathogenic coronaviruses.
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Affiliation(s)
- Luis Enjuanes
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Sonia Zúñiga
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - José M. Honrubia
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Melissa Bello-Pérez
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Alejandro Sanz-Bravo
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Ezequiel González-Miranda
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Jesús Hurtado-Tamayo
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Ricardo Requena-Platek
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Li Wang
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Carlos M. Sánchez
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Ana Esteban
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
| | - Jorge Ripoll-Gómez
- Department of Molecular and Cell Biology. National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid. Darwin 3, Madrid, Spain
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212
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Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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213
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Espeseth AS, Yuan M, Citron M, Reiserova L, Morrow G, Wilson A, Horton M, Rukhman M, Kinek K, Hou F, Li SL, Li F, Choi Y, Heidecker G, Luo B, Wu G, Zhang L, Strable E, DeStefano J, Secore S, Mukhopadhyay TK, Richardson DD, Sayeed E, Welch LS, Bett AJ, Feinberg MB, Gupta SB, Cooper CL, Parks CL. Preclinical immunogenicity and efficacy of a candidate COVID-19 vaccine based on a vesicular stomatitis virus-SARS-CoV-2 chimera. EBioMedicine 2022; 82:104203. [PMID: 35915046 PMCID: PMC9338221 DOI: 10.1016/j.ebiom.2022.104203] [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: 12/09/2021] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022] Open
Abstract
Background To investigate a vaccine technology with potential to protect against coronavirus disease 2019 (COVID-19) and reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a single vaccine dose, we developed a SARS-CoV-2 candidate vaccine using the live vesicular stomatitis virus (VSV) chimeric virus approach previously used to develop a licensed Ebola virus vaccine. Methods We generated a replication-competent chimeric VSV-SARS-CoV-2 vaccine candidate by replacing the VSV glycoprotein (G) gene with coding sequence for the SARS-CoV-2 Spike glycoprotein (S). Immunogenicity of the lead vaccine candidate (VSV∆G-SARS-CoV-2) was evaluated in cotton rats and golden Syrian hamsters, and protection from SARS-CoV-2 infection also was assessed in hamsters. Findings VSV∆G-SARS-CoV-2 delivered with a single intramuscular (IM) injection was immunogenic in cotton rats and hamsters and protected hamsters from weight loss following SARS-CoV-2 challenge. When mucosal vaccination was evaluated, cotton rats did not respond to the vaccine, whereas mucosal administration of VSV∆G-SARS-CoV-2 was found to be more immunogenic than IM injection in hamsters and induced immunity that significantly reduced SARS-CoV-2 challenge virus loads in both lung and nasal tissues. Interpretation VSV∆G-SARS-CoV-2 delivered by IM injection or mucosal administration was immunogenic in golden Syrian hamsters, and both vaccination methods effectively protected the lung from SARS-CoV-2 infection. Hamsters vaccinated by mucosal application of VSV∆G-SARS-CoV-2 also developed immunity that controlled SARS-CoV-2 replication in nasal tissue. Funding The study was funded by Merck Sharp & Dohme, Corp., a subsidiary of Merck & Co., Inc., Rahway, NJ, USA, and The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA. Parts of this research was supported by the Biomedical Advanced Research and Development Authority (BARDA) and the Defense Threat Reduction Agency (DTRA) of the US Department of Defense.
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Affiliation(s)
| | - Maoli Yuan
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Lucia Reiserova
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Gavin Morrow
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Aaron Wilson
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Mark Rukhman
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Fuxiang Hou
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Shui L Li
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Yesle Choi
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Bin Luo
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Guoxin Wu
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Lan Zhang
- Merck & Co., Inc., Rahway, New Jersey, USA
| | | | - Joanne DeStefano
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | | | | | - Eddy Sayeed
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Lisa S Welch
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA; Currently at Clover Biopharmaceuticals, Boston, Massachusetts, USA
| | | | - Mark B Feinberg
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Swati B Gupta
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Christopher L Cooper
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Christopher L Parks
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA.
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214
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Kumar A, Ladha A, Choudhury A, Ikbal AMA, Bhattacharjee B, Das T, Gupta G, Sharma C, Sarbajna A, Mandal SC, Choudhury MD, Ali N, Slama P, Rezaei N, Palit P, Tiwari ON. The chimera of S1 and N proteins of SARS-CoV-2: can it be a potential vaccine candidate for COVID-19? Expert Rev Vaccines 2022; 21:1071-1086. [PMID: 35604776 DOI: 10.1080/14760584.2022.2081156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the biggest global health issues. Spike protein (S) and nucleoprotein (N), the major immunogenic components of SARS-CoV-2, have been shown to be involved in the attachment and replication of the virus inside the host cell. AREAS COVERED Several investigations have shown that the SARS-CoV-2 nucleoprotein can elicit a cell-mediated immune response capable of regulating viral replication and lowering viral burden. However, the development of an effective vaccine that can stop the transmission of SARS-CoV-2 remains a matter of concern. Literature was retrieved using the keywords COVID-19 vaccine, role of nucleoprotein as vaccine candidate, spike protein, nucleoprotein immune responses against SARS-CoV-2, and chimera vaccine in PubMed, Google Scholar, and Google. EXPERT OPINION We have focussed on the use of chimera protein, consisting of N and S-1 protein components of SARS-CoV-2, as a potential vaccine candidate. This may act as a polyvalent mixed recombinant protein vaccine to elicit a strong T and B cell immune response, which will be capable of neutralizing the wild and mutated variants of SARS-CoV-2, and also restricting its attachment, replication, and budding in the host cell.
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Affiliation(s)
- Amresh Kumar
- Department of Life Sciences and Bioinformatics, Assam University, Silchar, India
| | - Amit Ladha
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Ankita Choudhury
- Department of Pharmaceutical Sciences, Allama TR College of Pharmacy, Hospital Rd, Srigouri, India
| | - Abu Md Ashif Ikbal
- Department of Pharmacy, Tripura University (A Central University), Suryamaninagar, Tripura (W), India
| | - Bedanta Bhattacharjee
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Tanmay Das
- Department of Business Administration, Assam University Silchar, India
| | - Gaurav Gupta
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India.,Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chhavi Sharma
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Adity Sarbajna
- Department of Zoology, Surendranath College, Kolkata, India
| | - Subhash C Mandal
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | | | - Nahid Ali
- Division of Immunology, Department of Infectious Diseases, INDIAN INSTITUTE OF CHEMICAL BIOLOGY, Kolkata, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, Brno, Czech Republic
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Partha Palit
- Department of Pharmaceutical Sciences Drug Discovery research Laboratory, Assam University, Silchar, India
| | - Onkar Nath Tiwari
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
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215
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Tiwari J, Tripathi N, Srivastava RS, Kumar S, Singh S, Jain S, Khattri A. Low expression of TMPRSS2–a SARS-CoV-2 internalization protease–associates with basal subtype of head and neck squamous cell carcinoma. Transl Oncol 2022; 22:101458. [PMID: 35607455 PMCID: PMC9117167 DOI: 10.1016/j.tranon.2022.101458] [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: 08/30/2021] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022] Open
Abstract
ACE2 and TMPRSS2, which are utilized for the COVID-19 entry into human cells, are expressed throughout the head and neck tissues. Different subtypes of HNSCC patients have different expression pattern of genes utilized by the COVID-19 to enter human cells. HPV-negative HNSCC patients have significantly lower expression of TMPRSS2 while significantly higher expression of ACE2 and FURIN. The basal subtype of HNSCC patients show significantly lower expression of TMPRSS2 but significantly higher expression of FURIN. We predict that the HNSCC patients of the basal subtype would be less susceptible to COVID-19 infection compared to the patients of other subtypes.
SARS-CoV-2 is a single-stranded RNA virus that has caused the ongoing COVID-19 pandemic. ACE2 and other genes utilized by SARS-CoV-2 to enter human cells have been shown to express in Head and Neck Squamous Cell Carcinoma (HNSCC) patients. However, their expression pattern in different subtypes has not been investigated. Hence, in the current study, we have analyzed the expression of ACE2, TMPRSS2 and FURIN in 649 HNSCC patients from two independent cohorts. Our analysis showed significantly lower expression of TMPRSS2 while significantly increased expression of ACE2 and FURIN in HPV-negative HNSCC. Comparison of expression of these genes in the three subtypes of HNSCC patients (basal, classical and inflamed/mesenchymal) showed no significant difference in the expression of ACE2 among the three subtypes; however, the basal subtype showed significantly reduced expression of TMPRSS2 but significantly increased expression of FURIN. Comparison of expression of these genes between the HPV-negative patients of basal subtype vs all others confirmed significantly lower expression of TMPRSS2 in HPV-negative patients of basal subtype as compared to all others. Our study shows that the different subtypes of HNSCC patients have different expression patterns of genes utilized by the SARS-CoV-2 to enter human cells, and hence, their susceptibility to SARS-CoV-2 may also be different. As the expression of TMPRSS2 is significantly lower in the HNSCC patients of the basal subtype, we predict that these patients would be less susceptible to SARS-CoV-2 infection than the patients of other subtypes. However, these findings need to be further validated.
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Affiliation(s)
- Jayesh Tiwari
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Nancy Tripathi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | | | - Sujeet Kumar
- Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
| | - Sanjay Singh
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Shreyans Jain
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Arun Khattri
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India.
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216
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Chen KWK, Tsung-Ning Huang D, Huang LM. SARS-CoV-2 variants - Evolution, spike protein, and vaccines. Biomed J 2022; 45:573-579. [PMID: 35526825 PMCID: PMC9072773 DOI: 10.1016/j.bj.2022.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/09/2022] [Accepted: 04/29/2022] [Indexed: 12/11/2022] Open
Abstract
Despite the rising natural and vaccines mediated immunity, several countries have experienced a resurgence of the Coronavirus disease of 2019 (COVID-19) due to the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. From Alpha to Omicron, the variants of concern (VOC) have evolved several spike protein mutations that may have an impact on virus characteristics, such as transmissibility and antigenicity. In this review, we describe the evolution of SARS-CoV-2, summarize current knowledge of epidemiological and clinical features of the variants, and discuss the response strategies in terms of vaccines to reduce the burden of COVID-19.
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Affiliation(s)
- Kai-Wei K Chen
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Daniel Tsung-Ning Huang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan; Department of Medicine, MacKay Medical College, Taipei, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Children's Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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217
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Mechrez G, Mani KA, Saha A, Lachman O, Luria N, Molad O, Kotliarevski L, Zelinger E, Smith E, Yaakov N, Stone DS, Reches M, Dombrovsky A. Platform for Active Vaccine Formulation Using a Two-Mode Enhancement Mechanism of Epitope Presentation by Pickering Emulsion. ACS APPLIED BIO MATERIALS 2022; 5:3859-3869. [PMID: 35913405 PMCID: PMC9382630 DOI: 10.1021/acsabm.2c00410] [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] [Indexed: 11/29/2022]
Abstract
The efficiency of epitope-based vaccination (subunit vaccines) is tightly correlated with heterogeneity and the high density of epitope presentation, which maximizes the potential antigenic determinants. Here, we developed a two-mode platform for intensifying the epitope presentation of subunit vaccines. The two-mode epitope presentation enhancement includes a covalent attachment of high concentrations of SARS-CoV-2-S1 peptide epitope to the surface of virus-like-particles (VLPs) and the subsequent assembly of VLP/epitope conjugates on the oil droplet surface at an oil/water interface of an emulsion as Pickering stabilizers. The resultant emulsions were stable for weeks in ambient conditions, and our platform was challenged using the epitope of the SARS-CoV-2-S1 peptide that served as a model epitope in this study. In vivo assays showed that the αSARS-CoV-2-S1 immunoglobulin G (IgG) titers of the studied mouse antisera, developed against the SARS-CoV-2-S1 peptide under different epitope preparation conditions, showed an order of magnitude higher IgG titers in the studied VLP-based emulsions than epitopes dissolved in water and epitopes administered with an adjuvant, thereby confirming the efficacy of the formulation. This VLP-based Pickering emulsion platform is a fully synthetic approach that can be readily applied for vaccine development to a wide range of pathogens.
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Affiliation(s)
- Guy Mechrez
- Department of Food Science, Institute of Postharvest and Food Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
| | - Karthik Ananth Mani
- Department of Food Science, Institute of Postharvest and Food Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel.,Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Abhijit Saha
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, India
| | - Oded Lachman
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
| | - Neta Luria
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
| | - Ori Molad
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
| | - Liliya Kotliarevski
- Department of Food Science, Institute of Postharvest and Food Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel.,Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Einat Zelinger
- The Interdepartmental Equipment Unit, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Elisheva Smith
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
| | - Noga Yaakov
- Department of Food Science, Institute of Postharvest and Food Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
| | | | - Meital Reches
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel
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218
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Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [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: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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219
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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] [Key Words] [Grants] [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, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Troy Dumenil
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Bing Tang
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Thuy T Le
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Cameron R Bishop
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Andreas Suhrbier
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, 300 Herston Road, Herston, 4029 and The University of Queensland, St Lucia, 4072, Australia
| | - Daniel J Rawle
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
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220
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Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Kurhade C, Plante JA, Bopp NE, Kalveram B, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi PY. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. Nat Commun 2022; 13:4337. [PMID: 35896528 PMCID: PMC9326133 DOI: 10.1038/s41467-022-31930-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/08/2022] [Indexed: 12/27/2022] Open
Abstract
We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcription regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (∆3678). The ∆3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The ∆3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the ∆3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the ∆3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter ∆3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that ∆3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio E Muruato
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Galveston National Laboratory, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte Kalveram
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander Bukreyev
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Galveston National Laboratory, Galveston, TX, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Tian Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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221
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Lubinski B, Jaimes JA, Whittaker GR. Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.20.488969. [PMID: 35923311 PMCID: PMC9347273 DOI: 10.1101/2022.04.20.488969] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. SARS-CoV-2 The variant B.1.1.529 (Omicron) emerged in late 2020 and has continued to evolve and is now present in several distinct sub-variants. Here, we analyzed the "furin cleavage site" of the spike protein of SARS-CoV-2 B.1.1.529 (Omicron variant) in vitro, to assess the role of two key mutations (spike, N679K and P681H) that are common across all subvariants compared to the ancestral B.1 virus and other notable lineages. We observed significantly increased intrinsic cleavability with furin compared to an original B lineage virus (Wuhan-Hu1), as well as to two variants, B.1.1.7 (Alpha) and B.1.617 (Delta) that subsequently had wide circulation. Increased furin-mediated cleavage was attributed to the N679K mutation, which lies outside the conventional furin binding pocket. Our findings suggest that B.1.1.529 (Omicron variant) has gained genetic features linked to intrinsic furin cleavability, in line with its evolution within the population as the COVID-19 pandemic has proceeded.
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Affiliation(s)
- Bailey Lubinski
- Graduate Field of Biological & Biomedical Sciences, Cornell University, Ithaca NY, 14853, USA
- Department of Microbiology & Immunology, 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
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca NY, 14853, USA
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222
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Singh S, Dahiya S, Singh YJ, Beeton K, Jain A, Sarkar R, Dubey A, Tehseen A, Sehrawat S. Robust anti-SARS-CoV2 single domain antibodies cross neutralize multiple viruses. iScience 2022; 25:104549. [PMID: 35702569 PMCID: PMC9181070 DOI: 10.1016/j.isci.2022.104549] [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: 02/22/2022] [Revised: 05/08/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
We report robust SARS-CoV2 neutralizing sdAbs targeting the viral peptides encompassing the polybasic cleavage site (CSP) and in the receptor binding domain (RBD) of the spike (S) protein. Both the sdAbs inhibited infectivity of the CoV2 S protein expressing pseudoviruses (LV-CoV2S). Both anti-CSP and RBD intrabodies (IB) inhibited the output of LV(CoV2 S). Anti-CSP IB altered the proteolytic processing and targeted the viral S protein for degradation. Because of cross-reactive CSPs in the entry mediators, the anti-CSP sdAb neutralized in vitro and in vivo the infectivity of SARS-CoV2 unrelated viruses such as herpes simplex virus 1 (HSV1) and pestes des petits ruminants virus (PPRV). Conversely, anti-HSV1 and anti-PPRV sera neutralized LV(CoV2 S) owing to the presence of CSP reactive antibodies indicating that a prior infection with such pathogens could impact on the pattern of COVID-19.
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Affiliation(s)
- Sudhakar Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Surbhi Dahiya
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Yuviana J. Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Komal Beeton
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Ayush Jain
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Roman Sarkar
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Abhishek Dubey
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Azeez Tehseen
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
| | - Sharvan Sehrawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar Knowledge City PO Manauli, Mohali, Punjab 140306, India
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223
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Yang L, Liang T, Pierson LM, Wang H, Fletcher JK, Wang S, Bao D, Zhang L, Huang Z, Zheng W, Zhang X, Park H, Li Y, Robinson JE, Feehan AK, Lyon CJ, Cao J, Morici LA, Li C, Roy CJ, Yu X, Hu T. SARS-CoV-2 Epitopes following Infection and Vaccination Overlap Known Neutralizing Antibody Sites. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9769803. [PMID: 35928300 PMCID: PMC9297724 DOI: 10.34133/2022/9769803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/27/2022] [Indexed: 11/06/2022]
Abstract
Identification of epitopes targeted following virus infection or vaccination can guide vaccine design and development of therapeutic interventions targeting functional sites, but can be laborious. Herein, we employed peptide microarrays to map linear peptide epitopes (LPEs) recognized following SARS-CoV-2 infection and vaccination. LPEs detected by nonhuman primate (NHP) and patient IgMs after SARS-CoV-2 infection extensively overlapped, localized to functionally important virus regions, and aligned with reported neutralizing antibody binding sites. Similar LPE overlap occurred after infection and vaccination, with LPE clusters specific to each stimulus, where strong and conserved LPEs mapping to sites known or likely to inhibit spike protein function. Vaccine-specific LPEs tended to map to sites known or likely to be affected by structural changes induced by the proline substitutions in the mRNA vaccine's S protein. Mapping LPEs to regions of known functional importance in this manner may accelerate vaccine evaluation and discovery of targets for site-specific therapeutic interventions.
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Affiliation(s)
- Li Yang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Te Liang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Lane M. Pierson
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jesse K. Fletcher
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Shu Wang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Lili Zhang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zhen Huang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Wenshu Zheng
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Heewon Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Yuwen Li
- Hayward Genetics Center, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - James E. Robinson
- Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Amy K. Feehan
- Infectious Disease Department, Ochsner Clinic Foundation, New Orleans, LA 70121, USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Jing Cao
- University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Lisa A. Morici
- Department of Microbiology & Immunology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Chenzhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Chad J. Roy
- Department of Microbiology & Immunology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Division of Microbiology, Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA 70433, USA
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
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Noval Rivas M, Porritt RA, Cheng MH, Bahar I, Arditi M. Multisystem Inflammatory Syndrome in Children and Long COVID: The SARS-CoV-2 Viral Superantigen Hypothesis. Front Immunol 2022; 13:941009. [PMID: 35874696 PMCID: PMC9300823 DOI: 10.3389/fimmu.2022.941009] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/09/2022] [Indexed: 12/19/2022] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a febrile pediatric inflammatory disease that may develop weeks after initial SARS-CoV-2 infection or exposure. MIS-C involves systemic hyperinflammation and multiorgan involvement, including severe cardiovascular, gastrointestinal (GI) and neurological symptoms. Some clinical attributes of MIS-C-such as persistent fever, rashes, conjunctivitis and oral mucosa changes (red fissured lips and strawberry tongue)-overlap with features of Kawasaki disease (KD). In addition, MIS-C shares striking clinical similarities with toxic shock syndrome (TSS), which is triggered by bacterial superantigens (SAgs). The remarkable similarities between MIS-C and TSS prompted a search for SAg-like structures in the SARS-CoV-2 virus and the discovery of a unique SAg-like motif highly similar to a Staphylococcal enterotoxin B (SEB) fragment in the SARS-CoV-2 spike 1 (S1) glycoprotein. Computational studies suggest that the SAg-like motif has a high affinity for binding T-cell receptors (TCRs) and MHC Class II proteins. Immunosequencing of peripheral blood samples from MIS-C patients revealed a profound expansion of TCR β variable gene 11-2 (TRBV11-2), which correlates with MIS-C severity and serum cytokine levels, consistent with a SAg-triggered immune response. Computational sequence analysis of SARS-CoV-2 spike further identified conserved neurotoxin-like motifs which may alter neuronal cell function and contribute to neurological symptoms in COVID-19 and MIS-C patients. Additionally, autoantibodies are detected during MIS-C, which may indicate development of post-SARS-CoV-2 autoreactive and autoimmune responses. Finally, prolonged persistence of SARS-CoV-2 RNA in the gut, increased gut permeability and elevated levels of circulating S1 have been observed in children with MIS-C. Accordingly, we hypothesize that continuous and prolonged exposure to the viral SAg-like and neurotoxin-like motifs in SARS-CoV-2 spike may promote autoimmunity leading to the development of post-acute COVID-19 syndromes, including MIS-C and long COVID, as well as the neurological complications resulting from SARS-CoV-2 infection.
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Affiliation(s)
- Magali Noval Rivas
- Department of Pediatrics, Division of Infectious Diseases and Immunology, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Infectious and Immunologic Diseases Research Center (IIDRC) and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Rebecca A Porritt
- Department of Pediatrics, Division of Infectious Diseases and Immunology, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Infectious and Immunologic Diseases Research Center (IIDRC) and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Moshe Arditi
- Department of Pediatrics, Division of Infectious Diseases and Immunology, Guerin Children's at Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Infectious and Immunologic Diseases Research Center (IIDRC) and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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225
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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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Zhang C, Meng X, Zhao H. Comparison of Cell Fusions Induced by Influenza Virus and SARS-CoV-2. Int J Mol Sci 2022; 23:ijms23137365. [PMID: 35806369 PMCID: PMC9266613 DOI: 10.3390/ijms23137365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/10/2022] Open
Abstract
Virus–cell fusion is the key step for viral infection in host cells. Studies on virus binding and fusion with host cells are important for understanding the virus–host interaction and viral pathogenesis for the discovery of antiviral drugs. In this review, we focus on the virus–cell fusions induced by the two major pandemic viruses, including the influenza virus and SARS-CoV-2. We further compare the cell fusions induced by the influenza virus and SARS-CoV-2, especially the pH-dependent fusion of the influenza virus and the fusion of SARS-CoV-2 in the type-II transmembrane serine protease 2 negative (TMPRSS2-) cells with syncytia formation. Finally, we present the development of drugs used against SARA-CoV-2 and the influenza virus through the discovery of anti-fusion drugs and the prevention of pandemic respiratory viruses.
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Affiliation(s)
- Chuyuan Zhang
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (C.Z.); (X.M.)
| | - Xinjie Meng
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (C.Z.); (X.M.)
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Hanjun Zhao
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (C.Z.); (X.M.)
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Correspondence: or ; Tel.: +852-2255-4892
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227
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Runft S, Färber I, Krüger J, Krüger N, Armando F, Rocha C, Pöhlmann S, Burigk L, Leitzen E, Ciurkiewicz M, Braun A, Schneider D, Baumgärtner L, Freisleben B, Baumgärtner W. Alternatives to animal models and their application in the discovery of species susceptibility to SARS-CoV-2 and other respiratory infectious pathogens: A review. Vet Pathol 2022; 59:565-577. [PMID: 35130766 DOI: 10.1177/03009858211073678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inspired rapid research efforts targeting the host range, pathogenesis and transmission mechanisms, and the development of antiviral strategies. Genetically modified mice, rhesus macaques, ferrets, and Syrian golden hamsters have been frequently used in studies of pathogenesis and efficacy of antiviral compounds and vaccines. However, alternatives to in vivo experiments, such as immortalized cell lines, primary respiratory epithelial cells cultured at an air-liquid interface, stem/progenitor cell-derived organoids, or tissue explants, have also been used for isolation of SARS-CoV-2, investigation of cytopathic effects, and pathogen-host interactions. Moreover, initial proof-of-concept studies for testing therapeutic agents can be performed with these tools, showing that animal-sparing cell culture methods could significantly reduce the need for animal models in the future, following the 3R principles of replace, reduce, and refine. So far, only few studies using animal-derived primary cells or tissues have been conducted in SARS-CoV-2 research, although natural infection has been shown to occur in several animal species. Therefore, the need for in-depth investigations on possible interspecies transmission routes and differences in susceptibility to SARS-CoV-2 is urgent. This review gives an overview of studies employing alternative culture systems like primary cell cultures, tissue explants, or organoids for investigations of the pathophysiology and reverse zoonotic potential of SARS-CoV-2 in animals. In addition, future possibilities of SARS-CoV-2 research in animals, including previously neglected methods like the use of precision-cut lung slices, will be outlined.
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Affiliation(s)
- Sandra Runft
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Iris Färber
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Johannes Krüger
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Nadine Krüger
- German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Federico Armando
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Cheila Rocha
- German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Stefan Pöhlmann
- German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Laura Burigk
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Eva Leitzen
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Hannover Medical School, Hannover, Germany
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228
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Abstract
The dramatic global consequences of the coronavirus disease 2019 (COVID-19) pandemic soon fueled quests for a suitable model that would facilitate the development and testing of therapies and vaccines. In contrast to other rodents, hamsters are naturally susceptible to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the Syrian hamster (Mesocricetus auratus) rapidly developed into a popular model. It recapitulates many characteristic features as seen in patients with a moderate, self-limiting course of the disease such as specific patterns of respiratory tract inflammation, vascular endothelialitis, and age dependence. Among 4 other hamster species examined, the Roborovski dwarf hamster (Phodopus roborovskii) more closely mimics the disease in highly susceptible patients with frequent lethal outcome, including devastating diffuse alveolar damage and coagulopathy. Thus, different hamster species are available to mimic different courses of the wide spectrum of COVID-19 manifestations in humans. On the other hand, fewer diagnostic tools and information on immune functions and molecular pathways are available than in mice, which limits mechanistic studies and inference to humans in several aspects. Still, under pandemic conditions with high pressure on progress in both basic and clinically oriented research, the Syrian hamster has turned into the leading non-transgenic model at an unprecedented pace, currently used in innumerable studies that all aim to combat the impact of the virus with its new variants of concern. As in other models, its strength rests upon a solid understanding of its similarities to and differences from the human disease, which we review here.
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229
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Abstract
SARS‐CoV‐2, the virus that causes coronavirus disease (COVID)‐19, has become a persistent global health threat. Individuals who are symptomatic for COVID‐19 frequently exhibit respiratory illness, which is often accompanied by neurological symptoms of anosmia and fatigue. Mounting clinical data also indicate that many COVID‐19 patients display long‐term neurological disorders postinfection such as cognitive decline, which emphasizes the need to further elucidate the effects of COVID‐19 on the central nervous system. In this review article, we summarize an emerging body of literature describing the impact of SARS‐CoV‐2 infection on central nervous system (CNS) health and highlight important areas of future investigation.
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Affiliation(s)
- Nick R Natale
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.,Center for Brain Immunology and Glia (BIG), Department of Neuroscience, University of Virginia, Charlottesville, Virginia, USA.,Neuroscience Graduate Program, University of Virginia, Charlottesville, Virginia, USA.,Global Biothreats Graduate Training Program, University of Virginia, Charlottesville, Virginia, USA
| | - John R Lukens
- Center for Brain Immunology and Glia (BIG), Department of Neuroscience, University of Virginia, Charlottesville, Virginia, USA.,Neuroscience Graduate Program, University of Virginia, Charlottesville, Virginia, USA.,Global Biothreats Graduate Training Program, University of Virginia, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.,Center for Brain Immunology and Glia (BIG), Department of Neuroscience, University of Virginia, Charlottesville, Virginia, USA.,Neuroscience Graduate Program, University of Virginia, Charlottesville, Virginia, USA.,Global Biothreats Graduate Training Program, University of Virginia, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA
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230
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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231
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The Cellular Characterization of SARS-CoV-2 Spike Protein in Virus-Infected Cells Using the Receptor Binding Domain Binding Specific Human Monoclonal Antibodies. J Virol 2022; 96:e0045522. [PMID: 35727030 PMCID: PMC9278116 DOI: 10.1128/jvi.00455-22] [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] [Indexed: 11/20/2022] Open
Abstract
A human monoclonal antibody panel (PD4, PD5, PD7, SC23, and SC29) was isolated from the B cells of convalescent patients and used to examine the S protein in SARS-CoV-2-infected cells. While all five antibodies bound conformational-specific epitopes within SARS-CoV-2 spike (S) protein, only PD5, PD7, and SC23 were able to bind to the receptor binding domain (RBD). Immunofluorescence microscopy was used to examine the S protein RBD in cells infected with the Singapore isolates SARS-CoV-2/0334 and SARS-CoV-2/1302. The RBD-binders exhibited a distinct cytoplasmic staining pattern that was primarily localized within the Golgi complex and was distinct from the diffuse cytoplasmic staining pattern exhibited by the non-RBD-binders (PD4 and SC29). These data indicated that the S protein adopted a conformation in the Golgi complex that enabled the RBD recognition by the RBD-binders. The RBD-binders also recognized the uncleaved S protein, indicating that S protein cleavage was not required for RBD recognition. Electron microscopy indicated high levels of cell-associated virus particles, and multiple cycle virus infection using RBD-binder staining provided evidence for direct cell-to-cell transmission for both isolates. Although similar levels of RBD-binder staining were demonstrated for each isolate, SARS-CoV-2/1302 exhibited slower rates of cell-to-cell transmission. These data suggest that a conformational change in the S protein occurs during its transit through the Golgi complex that enables RBD recognition by the RBD-binders and suggests that these antibodies can be used to monitor S protein RBD formation during the early stages of infection. IMPORTANCE The SARS-CoV-2 spike (S) protein receptor binding domain (RBD) mediates the attachment of SARS-CoV-2 to the host cell. This interaction plays an essential role in initiating virus infection, and the S protein RBD is therefore a focus of therapeutic and vaccine interventions. However, new virus variants have emerged with altered biological properties in the RBD that can potentially negate these interventions. Therefore, an improved understanding of the biological properties of the RBD in virus-infected cells may offer future therapeutic strategies to mitigate SARS- CoV-2 infection. We used physiologically relevant antibodies that were isolated from the B cells of convalescent COVID-19 patients to monitor the RBD in cells infected with SARS-CoV-2 clinical isolates. These immunological reagents specifically recognize the correctly folded RBD and were used to monitor the appearance of the RBD in SARS-CoV-2-infected cells and identified the site where the RBD first appears.
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232
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Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
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Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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233
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Eriksen AZ, Møller R, Makovoz B, tenOever BR, Blenkinsop TA. Protocols for SARS-CoV-2 infection in primary ocular cells and eye organoids. STAR Protoc 2022; 3:101383. [PMID: 35664254 PMCID: PMC9023348 DOI: 10.1016/j.xpro.2022.101383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Here, we describe a series of protocols detailing the steps for evaluating SARS-CoV-2 infection in models of the human eye. Included are protocols for whole eye organoid differentiation, SARS-CoV-2 infection, and processing organoids for single-cell RNA sequencing. Additional protocols describe how to dissect and culture adult human ocular cells from cadaver donor eyes and how to compare infection of SARS-CoV-2 and the presence of SARS-CoV-2 entry factors using qPCR, immunofluorescence, and plaque assays. For complete details on the use and execution of this protocol, please refer to Eriksen et al. (2021).
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Affiliation(s)
- Anne Zebitz Eriksen
- Department of Cell, Development and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Rasmus Møller
- Department of Microbiology, New York University, New York, NY 10016, USA
| | - Bar Makovoz
- Department of Cell, Development and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Timothy A. Blenkinsop
- Department of Cell, Development and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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234
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Douglas LEJ, Reihill JA, Ho MWY, Axten JM, Campobasso N, Schneck JL, Rendina AR, Wilcoxen KM, Martin SL. A highly selective, cell-permeable furin inhibitor BOS-318 rescues key features of cystic fibrosis airway disease. Cell Chem Biol 2022; 29:947-957.e8. [PMID: 35202587 DOI: 10.1016/j.chembiol.2022.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/14/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022]
Abstract
In cystic fibrosis (CF), excessive furin activity plays a critical role in the activation of the epithelial sodium channel (ENaC), dysregulation of which contributes to airway dehydration, ineffective mucociliary clearance (MCC), and mucus obstruction. Here, we report a highly selective, cell-permeable furin inhibitor, BOS-318, that derives selectivity by eliciting the formation of a new, unexpected binding pocket independent of the active site catalytic triad. Using human ex vivo models, BOS-318 showed significant suppression of ENaC, which led to enhanced airway hydration and an ∼30-fold increase in MCC rate. Furin inhibition also protected ENaC from subsequent activation by neutrophil elastase, a soluble protease dominant in CF airways. Additional therapeutic benefits include protection against epithelial cell death induced by Pseudomonas aeruginosa exotoxin A. Our findings demonstrate the utility of selective furin inhibition as a mutation-agnostic approach that can correct features of CF airway pathophysiology in a manner expected to deliver therapeutic value.
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Affiliation(s)
- Lisa E J Douglas
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - James A Reihill
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Melisa W Y Ho
- GlaxoSmithKline Research and Development, Collegeville, PA 19426, USA
| | - Jeffrey M Axten
- GlaxoSmithKline Research and Development, Collegeville, PA 19426, USA
| | - Nino Campobasso
- GlaxoSmithKline Research and Development, Collegeville, PA 19426, USA
| | - Jessica L Schneck
- GlaxoSmithKline Research and Development, Collegeville, PA 19426, USA
| | - Alan R Rendina
- GlaxoSmithKline Research and Development, Collegeville, PA 19426, USA
| | | | - S Lorraine Martin
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
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235
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Metalloproteinase-Dependent and TMPRSS2-Independent Cell Surface Entry Pathway of SARS-CoV-2 Requires the Furin Cleavage Site and the S2 Domain of Spike Protein. mBio 2022; 13:e0051922. [PMID: 35708281 PMCID: PMC9426510 DOI: 10.1128/mbio.00519-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ongoing global vaccination program to prevent SARS-CoV-2 infection, the causative agent of COVID-19, has had significant success. However, recently, virus variants that can evade the immunity in a host achieved through vaccination have emerged. Consequently, new therapeutic agents that can efficiently prevent infection from these new variants, and hence COVID-19 spread, are urgently required. To achieve this, extensive characterization of virus-host cell interactions to identify effective therapeutic targets is warranted. Here, we report a cell surface entry pathway of SARS-CoV-2 that exists in a cell type-dependent manner and is TMPRSS2 independent but sensitive to various broad-spectrum metalloproteinase inhibitors such as marimastat and prinomastat. Experiments with selective metalloproteinase inhibitors and gene-specific small interfering RNAS (siRNAs) revealed that a disintegrin and metalloproteinase 10 (ADAM10) is partially involved in the metalloproteinase pathway. Consistent with our finding that the pathway is unique to SARS-CoV-2 among highly pathogenic human coronaviruses, both the furin cleavage motif in the S1/S2 boundary and the S2 domain of SARS-CoV-2 spike protein are essential for metalloproteinase-dependent entry. In contrast, the two elements of SARS-CoV-2 independently contributed to TMPRSS2-dependent S2 priming. The metalloproteinase pathway is involved in SARS-CoV-2-induced syncytium formation and cytopathicity, leading us to theorize that it is also involved in the rapid spread of SARS-CoV-2 and the pathogenesis of COVID-19. Thus, targeting the metalloproteinase pathway in addition to the TMPRSS2 and endosomal pathways could be an effective strategy by which to cure COVID-19 in the future. IMPORTANCE To develop effective therapeutics against COVID-19, it is necessary to elucidate in detail the infection mechanism of the causative agent, SARS-CoV-2. SARS-CoV-2 binds to the cell surface receptor ACE2 via the spike protein, and then the spike protein is cleaved by host proteases to enable entry. Here, we found that the metalloproteinase-mediated pathway is important for SARS-CoV-2 infection in addition to the TMPRSS2-mediated pathway and the endosomal pathway. The metalloproteinase-mediated pathway requires both the prior cleavage of spike into two domains and a specific sequence in the second domain, S2, conditions met by SARS-CoV-2 but lacking in the related human coronavirus SARS-CoV. Besides the contribution of metalloproteinases to SARS-CoV-2 infection, inhibition of metalloproteinases was important in preventing cell death, which may cause organ damage. Our study provides new insights into the complex pathogenesis unique to COVID-19 and relevant to the development of effective therapies.
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236
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Bell EW, Schwartz JH, Freddolino PL, Zhang Y. PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. J Mol Biol 2022; 434:167530. [PMID: 35662463 PMCID: PMC8897833 DOI: 10.1016/j.jmb.2022.167530] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 03/03/2022] [Indexed: 01/31/2023]
Abstract
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of non-interactions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.
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Affiliation(s)
- Eric W Bell
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jacob H Schwartz
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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237
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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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Kung YA, Lee KM, Chiang HJ, Huang SY, Wu CJ, Shih SR. Molecular Virology of SARS-CoV-2 and Related Coronaviruses. Microbiol Mol Biol Rev 2022; 86:e0002621. [PMID: 35343760 PMCID: PMC9199417 DOI: 10.1128/mmbr.00026-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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239
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SARS-CoV-2 requires acidic pH to infect cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35702155 PMCID: PMC9196115 DOI: 10.1101/2022.06.09.495472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 cell entry starts with membrane attachment and ends with spike-protein (S) catalyzed membrane fusion depending on two cleavage steps, one usually by furin in producing cells and the second by TMPRSS2 on target cells. Endosomal cathepsins can carry out both. Using real-time 3D single virion tracking, we show fusion and genome penetration requires virion exposure to an acidic milieu of pH 6.2-6.8, even when furin and TMPRSS2 cleavages have occurred. We detect the sequential steps of S1-fragment dissociation, fusion, and content release from the cell surface in TMPRRS2 overexpressing cells only when exposed to acidic pH. We define a key role of an acidic environment for successful infection, found in endosomal compartments and at the surface of TMPRSS2 expressing cells in the acidic milieu of the nasal cavity. Significance Statement Infection by SARS-CoV-2 depends upon the S large spike protein decorating the virions and is responsible for receptor engagement and subsequent fusion of viral and cellular membranes allowing release of virion contents into the cell. Using new single particle imaging tools, to visualize and track the successive steps from virion attachment to fusion, combined with chemical and genetic perturbations of the cells, we provide the first direct evidence for the cellular uptake routes of productive infection in multiple cell types and their dependence on proteolysis of S by cell surface or endosomal proteases. We show that fusion and content release always require the acidic environment from endosomes, preceded by liberation of the S1 fragment which depends on ACE2 receptor engagement. One sentence summary Detailed molecular snapshots of the productive infectious entry pathway of SARS-CoV-2 into cells.
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SARS-CoV-2 Spike Furin Cleavage Site and S2' Basic Residues Modulate the Entry Process in a Host Cell-Dependent Manner. J Virol 2022; 96:e0047422. [PMID: 35678602 PMCID: PMC9278140 DOI: 10.1128/jvi.00474-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SARS-CoV-2 spike (S) envelope glycoprotein constitutes the main determinant of virus entry and the target of host immune response, thus being of great interest for antiviral research. It is constituted of S1 and S2 subunits, which are involved in ACE2 receptor binding and fusion between the viral envelope and host cell membrane, respectively. Induction of the fusion process requires S cleavage at the S1-S2 junction and the S2′ site located upstream of the fusion peptide. Interestingly, the SARS-CoV-2 spike harbors a 4-residue insertion at the S1-S2 junction that is absent in its closest relatives and constitutes a polybasic motif recognized by furin-like proteases. In addition, the S2′ site is characterized by the presence of conserved basic residues. Here, we sought to determine the importance of the furin cleavage site (FCS) and the S2′ basic residues for S-mediated entry functions. We determined the impact of mutations introduced at these sites on S processing, fusogenic activity, and its ability to mediate entry in different cellular backgrounds. Strikingly, mutation phenotypes were highly dependent on the host cell background. We confirmed that although the FCS was not absolutely required for virus entry, it contributed to extending the fusogenic potential of S. Cleavage site mutations, as well as inhibition of furin protease activity, affected the cell surface expression of S in a host cell-dependent manner. Finally, inhibition of furin activity differentially affected SARS-CoV-2 virus infectivity in the tested host cells, thereby confirming the host cell-dependent effect of spike processing for the viral life cycle. IMPORTANCE SARS-CoV-2 is responsible for the current global pandemic that has resulted in several million deaths. As the key determinant of virus entry into host cells and the main target of host immune response, the spike glycoprotein constitutes an attractive target for therapeutics development. Entry functions of spike rely on its processing at two sites by host cell proteases. While SARS-CoV-2 spike differs from its closest relatives by the insertion of a basic furin cleavage motif at the first site, it harbors conserved basic residues at the second cleavage site. Characterization of the importance of the basic sequences present at the two cleavage sites revealed that they were influencing spike processing, intracellular localization, induction of fusion, and entry in a host cell-dependent manner. Thus, our results revealed a high heterogeneity in spike sequence requirement for entry functions in the different host cells, in agreement with the high adaptability of the SARS-CoV-2 virus.
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Abstract
Infection with SARS-CoV-2, the causative agent of the COVID-19 pandemic, originated in China and quickly spread across the globe. Despite tremendous economic and healthcare devastation, research on this virus has contributed to a better understanding of numerous molecular pathways, including those involving γ-aminobutyric acid (GABA), that will positively impact medical science, including neuropsychiatry, in the post-pandemic era. SARS-CoV-2 primarily enters the host cells through the renin–angiotensin system’s component named angiotensin-converting enzyme-2 (ACE-2). Among its many functions, this protein upregulates GABA, protecting not only the central nervous system but also the endothelia, the pancreas, and the gut microbiota. SARS-CoV-2 binding to ACE-2 usurps the neuronal and non-neuronal GABAergic systems, contributing to the high comorbidity of neuropsychiatric illness with gut dysbiosis and endothelial and metabolic dysfunctions. In this perspective article, we take a closer look at the pathology emerging from the viral hijacking of non-neuronal GABA and summarize potential interventions for restoring these systems.
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242
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Troyano-Hernáez P, Reinosa R, Holguín Á. Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins. Int J Mol Sci 2022; 23:6394. [PMID: 35742840 PMCID: PMC9223475 DOI: 10.3390/ijms23126394] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.
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Affiliation(s)
| | | | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) in Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), 28034 Madrid, Spain; (P.T.-H.); (R.R.)
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243
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Li Z, Jiang J, Tong Y, Ruan X, Xu J. COVID-19 is a natural infectious disease. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022; 4:38-42. [PMID: 34927018 PMCID: PMC8664692 DOI: 10.1016/j.jobb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jiafu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Xiangdong Ruan
- Academy of Forest Inventory and Planning, State Forestry and Grassland Administration, Beijing 100714, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
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244
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Rayati Damavandi A, Dowran R, Al Sharif S, Kashanchi F, Jafari R. Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy. Med Microbiol Immunol 2022; 211:79-103. [PMID: 35235048 PMCID: PMC8889515 DOI: 10.1007/s00430-022-00729-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/09/2022] [Indexed: 12/30/2022]
Abstract
An ongoing pandemic of newly emerged SARS-CoV-2 has puzzled many scientists and health care policymakers around the globe. The appearance of the virus was accompanied by several distinct antigenic changes, specifically spike protein which is a key element for host cell entry of virus and major target of currently developing vaccines. Some of these mutations enable the virus to attach to receptors more firmly and easily. Moreover, a growing number of trials are demonstrating higher transmissibility and, in some of them, potentially more serious forms of illness related to novel variants. Some of these lineages, especially the Beta variant of concern, were reported to diminish the neutralizing activity of monoclonal and polyclonal antibodies present in both convalescent and vaccine sera. This could imply that these independently emerged variants could make antiviral strategies prone to serious threats. The rapid changes in the mutational profile of new clades, especially escape mutations, suggest the convergent evolution of the virus due to immune pressure. Nevertheless, great international efforts have been dedicated to producing efficacious vaccines with cutting-edge technologies. Despite the partial decrease in vaccines efficacy against worrisome clades, most current vaccines are still effective at preventing mild to severe forms of disease and hospital admission or death due to coronavirus disease 2019 (COVID-19). Here, we summarize existing evidence about newly emerged variants of SARS-CoV-2 and, notably, how well vaccines work against targeting new variants and modifications of highly flexible mRNA vaccines that might be required in the future.
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Affiliation(s)
- Amirmasoud Rayati Damavandi
- Students’ Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Razieh Dowran
- Students’ Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarah Al Sharif
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA USA
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA USA
| | - Reza Jafari
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
- Hematology, Immune Cell Therapy, and Stem Cell Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in 2020 and has led to an unprecedented global pandemic. Understanding the virology behind SARS-CoV-2 infection has provided key insights into our efforts to develop antiviral agents and control the COVID-19 pandemic. In this review, the authors focus on the genomic features of SARS-CoV-2, its intrahost and interhost evolution, viral dynamics in respiratory tract, and systemic dissemination.
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Affiliation(s)
- Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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246
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Kalveram B, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog 2022; 18:e1010627. [PMID: 35728038 PMCID: PMC9275689 DOI: 10.1371/journal.ppat.1010627] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022] Open
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral 'RG' motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2's continued adaptation to human infection.
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Affiliation(s)
- Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nathen Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Patricia Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Andrew L. Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
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247
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Abstract
Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing efforts have provided close to real-time tracking of the global spread and diversification of SARS-CoV-2 since its entry into the human population in late 2019. These data have underpinned analysis of its origins, epidemiology, and adaptations to the human population: principally immune evasion and increasing transmissibility. SARS-CoV-2, despite being a new human pathogen, was highly capable of human-to-human transmission. During its rapid spread in humans, SARS-CoV-2 has evolved independent new forms, the so-called "variants of concern," that are better optimized for human-to-human transmission. The most important adaptation of the bat coronavirus progenitor of both SARS-CoV-1 and SARS-CoV-2 for human infection (and other mammals) is the use of the angiotensin-converting enzyme 2 (ACE2) receptor. Relaxed structural constraints provide plasticity to SARS-related coronavirus spike protein permitting it to accommodate significant amino acid replacements of antigenic consequence without compromising the ability to bind to ACE2. Although the bulk of research has justifiably concentrated on the viral spike protein as the main determinant of antigenic evolution and changes in transmissibility, there is accumulating evidence for the contribution of other regions of the viral proteome to virus-host interaction. Whereas levels of community transmission of recombinants compromising genetically distinct variants are at present low, when divergent variants cocirculate, recombination between SARS-CoV-2 clades is being detected, increasing the risk that viruses with new properties emerge. Applying computational and machine learning methods to genome sequence data sets to generate experimentally verifiable predictions will serve as an early warning system for novel variant surveillance and will be important in future vaccine planning. Omicron, the latest SARS-CoV-2 variant of concern, has focused attention on step change antigenic events, "shift," as opposed to incremental "drift" changes in antigenicity. Both an increase in transmissibility and antigenic shift in Omicron led to it readily causing infections in the fully vaccinated and/or previously infected. Omicron's virulence, while reduced relative to the variant of concern it replaced, Delta, is very much premised on the past immune exposure of individuals with a clear signal that boosted vaccination protects from severe disease. Currently, SARS-CoV-2 has proven itself to be a dangerous new human respiratory pathogen with an unpredictable evolutionary capacity, leading to a risk of future variants too great not to ensure all regions of the world are screened by viral genome sequencing, protected through available and affordable vaccines, and have non-punitive strategies in place for detecting and responding to novel variants of concern.
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Affiliation(s)
- Amalio Telenti
- Vir Biotechnology, San Francisco, California 94158, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, USA
| | - Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
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Zahradník J, Nunvar J, Schreiber G. Perspectives: SARS-CoV-2 Spike Convergent Evolution as a Guide to Explore Adaptive Advantage. Front Cell Infect Microbiol 2022; 12:748948. [PMID: 35711666 PMCID: PMC9197234 DOI: 10.3389/fcimb.2022.748948] [Citation(s) in RCA: 10] [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: 07/28/2021] [Accepted: 04/19/2022] [Indexed: 01/22/2023] Open
Abstract
Viruses rapidly co-evolve with their hosts. The 9 million sequenced SARS-CoV-2 genomes by March 2022 provide a detailed account of viral evolution, showing that all amino acids have been mutated many times. However, only a few became prominent in the viral population. Here, we investigated the emergence of the same mutations in unrelated parallel lineages and the extent of such convergent evolution on the molecular level in the spike (S) protein. We found that during the first phase of the pandemic (until mid 2021, before mass vaccination) 31 mutations evolved independently ≥3-times within separated lineages. These included all the key mutations in SARS-CoV-2 variants of concern (VOC) at that time, indicating their fundamental adaptive advantage. The omicron added many more mutations not frequently seen before, which can be attributed to the synergistic nature of these mutations, which is more difficult to evolve. The great majority (24/31) of S-protein mutations under convergent evolution tightly cluster in three functional domains; N-terminal domain, receptor-binding domain, and Furin cleavage site. Furthermore, among the S-protein receptor-binding motif mutations, ACE2 affinity-improving substitutions are favoured. Next, we determined the mutation space in the S protein that has been covered by SARS-CoV-2. We found that all amino acids that are reachable by single nucleotide changes have been probed multiple times in early 2021. The substitutions requiring two nucleotide changes have recently (late 2021) gained momentum and their numbers are increasing rapidly. These provide a large mutation landscape for SARS-CoV-2 future evolution, on which research should focus now.
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Affiliation(s)
- Jiri Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jaroslav Nunvar
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Vestec, Czechia
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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249
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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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Cardiovascular Tropism and Sequelae of SARS-CoV-2 Infection. Viruses 2022; 14:v14061137. [PMID: 35746609 PMCID: PMC9228192 DOI: 10.3390/v14061137] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 01/18/2023] Open
Abstract
The extrapulmonary manifestation of coronavirus disease-19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), became apparent early in the ongoing pandemic. It is now recognized that cells of the cardiovascular system are targets of SARS-CoV-2 infection and associated disease pathogenesis. While some details are emerging, much remains to be understood pertaining to the mechanistic basis by which SARS-CoV-2 contributes to acute and chronic manifestations of COVID-19. This knowledge has the potential to improve clinical management for the growing populations of patients impacted by COVID-19. Here, we review the epidemiology and pathophysiology of cardiovascular sequelae of COVID-19 and outline proposed disease mechanisms, including direct SARS-CoV-2 infection of major cardiovascular cell types and pathogenic effects of non-infectious viral particles and elicited inflammatory mediators. Finally, we identify the major outstanding questions in cardiovascular COVID-19 research.
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