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Neil SJ. Pangolin merbecovirus gets down to (poly)basics. Cell 2023; 186:688-690. [PMID: 36803601 PMCID: PMC9933577 DOI: 10.1016/j.cell.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 02/18/2023]
Abstract
Trafficking of live mammals is considered a major risk for emergence of zoonotic viruses. SARS-CoV-2-related coronaviruses have previously been identified in pangolins, the world's most smuggled mammal. A new study identifies a MERS-related coronavirus in trafficked pangolins with broad mammalian tropism and a newly acquired furin cleavage site in Spike.
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Affiliation(s)
- Stuart J.D. Neil
- Department of Infectious Disease, King’s College London, London, UK,Corresponding author
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2
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Page R, Scourfield E, Ficarelli M, McKellar SW, Lee KL, Maguire TJ, Bouton C, Lista MJ, Neil SJ, Malim MH, Zuckerman M, Mischo HE, Martinez-Nunez RT. Homebrew: Protocol for glassmilk-based nucleic-acid extraction for SARS-CoV-2 diagnostics. STAR Protoc 2022; 3:101300. [PMID: 35479118 PMCID: PMC8938258 DOI: 10.1016/j.xpro.2022.101300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The gold standard protocol for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection detection remains reverse transcription quantitative polymerase chain reaction (qRT-PCR), which detects viral RNA more sensitively than any other approach. Here, we present Homebrew, a low-cost protocol to extract RNA using widely available reagents. Homebrew is as sensitive as commercially available RNA extraction kits. Homebrew allows for sample pooling and can be adapted for automation in high-throughput settings. For complete details on the use and execution of this protocol, please refer to Page et al. (2022).
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Affiliation(s)
- Robert Page
- ImmunoEngineering Lab, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Great Maze Pond, London SE1 9RT, UK
| | - Edward Scourfield
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mattia Ficarelli
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart W. McKellar
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Kwok Leung Lee
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Thomas J.A. Maguire
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Clement Bouton
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Maria Jose Lista
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart J.D. Neil
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Michael H. Malim
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mark Zuckerman
- South London Specialist Virology Centre, King’s College Hospital, London, UK
| | - Hannah E. Mischo
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Rocio T. Martinez-Nunez
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
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3
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Page R, Scourfield E, Ficarelli M, McKellar SW, Lee KL, Maguire TJ, Bouton C, Lista MJ, Neil SJ, Malim MH, Zuckerman M, Mischo HE, Martinez-Nunez RT. Homebrew: An economical and sensitive glassmilk-based nucleic-acid extraction method for SARS-CoV-2 diagnostics. Cell Rep Methods 2022; 2:100186. [PMID: 35262039 PMCID: PMC8890991 DOI: 10.1016/j.crmeth.2022.100186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/26/2021] [Accepted: 02/25/2022] [Indexed: 12/22/2022]
Abstract
Management of COVID-19 and other epidemics requires large-scale diagnostic testing. The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains reverse transcription quantitative PCR (qRT-PCR) analysis, which detects viral RNA more sensitively than any other method. However, the resource use and supply-chain requirements of RT-PCR have continued to challenge diagnostic laboratories worldwide. Here, we establish and characterize a low-cost method to detect SARS-CoV-2 in clinical combined nose and throat swabs, allowing for automation in high-throughput settings. This method inactivates virus material with sodium dodecylsulfate (SDS) and uses silicon dioxide as the RNA-binding matrix in combination with sodium chloride (NaCl) and isopropanol. With similar sensitivity for SARS-CoV-2 viral targets but a fraction of time and reagent expenditure compared with commercial kits, our method also enables sample pooling without loss of sensitivity. We suggest that this method will facilitate more economical widespread testing, particularly in resource-limited settings.
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Affiliation(s)
- Robert Page
- ImmunoEngineering Lab, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Great Maze Pond, London SE1 9RT, UK
| | - Edward Scourfield
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mattia Ficarelli
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart W. McKellar
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Kwok Leung Lee
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Thomas J.A. Maguire
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Clement Bouton
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Maria Jose Lista
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart J.D. Neil
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Michael H. Malim
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mark Zuckerman
- South London Specialist Virology Centre, King’s College Hospital London, London, UK
| | - Hannah E. Mischo
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Rocio T. Martinez-Nunez
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
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4
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Trevelin SC, Pickering S, Todd K, Bishop C, Pitcher M, Garrido Mesa J, Montorsi L, Spada F, Petrov N, Green A, Shankar-Hari M, Neil SJ, Spencer J. Disrupted Peyer's Patch Microanatomy in COVID-19 Including Germinal Centre Atrophy Independent of Local Virus. Front Immunol 2022; 13:838328. [PMID: 35251032 PMCID: PMC8893224 DOI: 10.3389/fimmu.2022.838328] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022] Open
Abstract
Confirmed SARS-coronavirus-2 infection with gastrointestinal symptoms and changes in microbiota associated with coronavirus disease 2019 (COVID-19) severity have been previously reported, but the disease impact on the architecture and cellularity of ileal Peyer's patches (PP) remains unknown. Here we analysed post-mortem tissues from throughout the gastrointestinal (GI) tract of patients who died with COVID-19. When virus was detected by PCR in the GI tract, immunohistochemistry identified virus in epithelium and lamina propria macrophages, but not in lymphoid tissues. Immunohistochemistry and imaging mass cytometry (IMC) analysis of ileal PP revealed depletion of germinal centres (GC), disruption of B cell/T cell zonation and decreased potential B and T cell interaction and lower nuclear density in COVID-19 patients. This occurred independent of the local viral levels. The changes in PP demonstrate that the ability to mount an intestinal immune response is compromised in severe COVID-19, which could contribute to observed dysbiosis.
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Affiliation(s)
- Silvia C. Trevelin
- Peter Gorer Department of Immunology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Katrina Todd
- National Institute for Health Research (NIHR) Guy’s and St. Thomas Biomedical Research Centre at Guy’s and St. Thomas NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Cynthia Bishop
- National Institute for Health Research (NIHR) Guy’s and St. Thomas Biomedical Research Centre at Guy’s and St. Thomas NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Michael Pitcher
- Peter Gorer Department of Immunology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jose Garrido Mesa
- National Institute for Health Research (NIHR) Guy’s and St. Thomas Biomedical Research Centre at Guy’s and St. Thomas NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Lucia Montorsi
- Peter Gorer Department of Immunology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Filomena Spada
- National Institute for Health Research (NIHR) Guy’s and St. Thomas Biomedical Research Centre at Guy’s and St. Thomas NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Nedyalko Petrov
- National Institute for Health Research (NIHR) Guy’s and St. Thomas Biomedical Research Centre at Guy’s and St. Thomas NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Anna Green
- Department of Histopathology, Guy’s and St. Thomas NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Manu Shankar-Hari
- Centre for Inflammation Research, Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stuart J.D. Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jo Spencer
- Peter Gorer Department of Immunology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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5
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Sertkaya H, Hidalgo L, Ficarelli M, Kmiec D, Signell AW, Ali S, Parker H, Wilson H, Neil SJ, Malim MH, Vink CA, Swanson CM. Minimal impact of ZAP on lentiviral vector production and transduction efficiency. Mol Ther Methods Clin Dev 2021; 23:147-157. [PMID: 34703838 PMCID: PMC8517000 DOI: 10.1016/j.omtm.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/24/2021] [Indexed: 11/29/2022]
Abstract
The antiviral protein ZAP binds CpG dinucleotides in viral RNA to inhibit replication. This has likely led to the CpG suppression observed in many RNA viruses, including retroviruses. Sequences added to retroviral vector genomes, such as internal promoters, transgenes, or regulatory elements, substantially increase CpG abundance. Because these CpGs could allow retroviral vector RNA to be targeted by ZAP, we analyzed whether it restricts vector production, transduction efficiency, and transgene expression. Surprisingly, even though CpG-high HIV-1 was efficiently inhibited by ZAP in HEK293T cells, depleting ZAP did not substantially increase lentiviral vector titer using several packaging and genome plasmids. ZAP overexpression also did not inhibit lentiviral vector titer. In addition, decreasing CpG abundance in a lentiviral vector genome did not increase its titer, and a gammaretroviral vector derived from murine leukemia virus was not substantially restricted by ZAP. Overall, we show that the increased CpG abundance in retroviral vectors relative to the wild-type retroviruses they are derived from does not intrinsically sensitize them to ZAP. Further understanding of how ZAP specifically targets transcripts to inhibit their expression may allow the development of CpG sequence contexts that efficiently recruit or evade this antiviral system.
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Affiliation(s)
- Helin Sertkaya
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Laura Hidalgo
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Mattia Ficarelli
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Dorota Kmiec
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Adrian W. Signell
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Sadfer Ali
- Cell & Gene Therapy Platform, Medicinal Science and Technology, GSK, Stevenage SG1 2NY, UK
| | - Hannah Parker
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Harry Wilson
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Stuart J.D. Neil
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Michael H. Malim
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
| | - Conrad A. Vink
- Cell & Gene Therapy Platform, Medicinal Science and Technology, GSK, Stevenage SG1 2NY, UK
| | - Chad M. Swanson
- Department of Infectious Diseases, King’s College London, London SE1 9RT, UK
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6
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Graham C, Seow J, Huettner I, Khan H, Kouphou N, Acors S, Winstone H, Pickering S, Galao RP, Lista MJ, Jimenez-Guardeno JM, Laing AG, Wu Y, Joseph M, Muir L, Ng WM, Duyvesteyn HME, Zhao Y, Bowden TA, Shankar-Hari M, Rosa A, Cherepanov P, McCoy LE, Hayday AC, Neil SJ, Malim MH, Doores KJ. Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike. bioRxiv 2021:2021.02.03.429355. [PMID: 33564766 PMCID: PMC7872354 DOI: 10.1101/2021.02.03.429355] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the ACE2 receptor on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, the N-terminal domain (NTD) and S2 subunits of Spike. To fully understand how these mutations affect the antigenicity of Spike, we have isolated and characterized neutralizing antibodies targeting epitopes beyond the already identified RBD epitopes. Using recombinant Spike as a sorting bait, we isolated >100 Spike-reactive monoclonal antibodies from SARS-CoV-2 infected individuals. ≈45% showed neutralizing activity of which ≈20% were NTD-specific. None of the S2-specific antibodies showed neutralizing activity. Competition ELISA revealed that NTD-specific mAbs formed two distinct groups: the first group was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Importantly, mutations present in B.1.1.7 Spike frequently conferred resistance to neutralization by the NTD-specific neutralizing antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes need to be considered when investigating antigenic drift in emerging variants.
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Affiliation(s)
- Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Jose M Jimenez-Guardeno
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Adam G. Laing
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Yin Wu
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
- The Francis Crick Institute, UK
| | - Magdalene Joseph
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Luke Muir
- Division of Infection and Immunity, University College London, London, UK
| | - Weng M. Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M. E. Duyvesteyn
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | | | | | - Laura E. McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Adrian C. Hayday
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Stuart J.D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Genotype-to-Phenotype UK National Virology Consortium
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Genotype-to-Phenotype UK National Virology Consortium
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
- Genotype-to-Phenotype UK National Virology Consortium
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Abstract
One cannot spend >5 min on social media at the moment without finding a link to some conspiracy theory or other regarding the origin of SARS-CoV2, the coronavirus responsible for the COVID-19 pandemic. From the virus being deliberately released as a bioweapon to pharmaceutical companies blocking the trials of natural remedies to boost their dangerous drugs and vaccines, the Internet is rife with far-fetched rumors. And predictably, now that the first immunization trials have started, the antivaccine lobby has latched on to most of them. In the last week, the trailer for a new "bombshell documentary" Plandemic has been doing the rounds, gaining notoriety for being repeatedly removed from YouTube and Facebook. We usually would not pay much heed to such things, but for retrovirologists like us, the name associated with these claims is unfortunately too familiar: Dr. Judy Mikovits.
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Affiliation(s)
- Stuart J.D. Neil
- Department of Infectious Disease, School of Immunobiology and Microbial Sciences, King's College London, London, United Kingdom
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
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