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Daniels A, Padariya M, Fletcher S, Ball K, Singh A, Carragher N, Hupp T, Tait-Burkard C, Kalathiya U. Molecules targeting a novel homotrimer cavity of Spike protein attenuate replication of SARS-CoV-2. Antiviral Res 2024; 228:105949. [PMID: 38942150 DOI: 10.1016/j.antiviral.2024.105949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
The SARS-CoV-2 Spike glycoprotein (S) utilizes a unique trimeric conformation to interact with the ACE2 receptor on host cells, making it a prime target for inhibitors that block viral entry. We have previously identified a novel proteinaceous cavity within the Spike protein homotrimer that could serve as a binding site for small molecules. However, it is not known whether these molecules would inhibit, stimulate, or have no effect on viral replication. To address this, we employed structural-based screening to identify small molecules that dock into the trimer cavity and assessed their impact on viral replication. Our findings show that a cohort of identified small molecules binding to the Spike trimer cavity effectively reduces the replication of various SARS-CoV-2 variants. These molecules exhibited inhibitory effects on B.1 (European original, D614G, EDB2) and B.1.617.2 (δ) variants, while showing moderate activity against the B.1.1.7 (α) variant. We further categorized these molecules into distinct groups based on their structural similarities. Our experiments demonstrated a dose-dependent viral replication inhibitory activity of these compounds, with some, like BCC0040453 exhibiting no adverse effects on cell viability even at high concentrations. Further investigation revealed that pre-incubating virions with compounds like BCC0031216 at different temperatures significantly inhibited viral replication, suggesting their specificity towards the S protein. Overall, our study highlights the inhibitory impact of a diverse set of chemical molecules on the biological activity of the Spike protein. These findings provide valuable insights into the role of the trimer cavity in the viral replication cycle and aid drug discovery programs aimed at targeting the coronavirus family.
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Affiliation(s)
- Alison Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland
| | - Sarah Fletcher
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Kathryn Ball
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ashita Singh
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Neil Carragher
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland.
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2
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Pennisi I, Cavuto ML, Miglietta L, Malpartida-Cardenas K, Stringer OW, Mantikas KT, Reid R, Frise R, Moser N, Randell P, Davies F, Bolt F, Barclay W, Holmes A, Georgiou P, Rodriguez-Manzano J. Rapid, Portable, and Electricity-free Sample Extraction Method for Enhanced Molecular Diagnostics in Resource-Limited Settings. Anal Chem 2024; 96:11181-11188. [PMID: 38967089 PMCID: PMC11256010 DOI: 10.1021/acs.analchem.4c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The COVID-19 pandemic has highlighted the need for rapid and reliable diagnostics that are accessible in resource-limited settings. To address this pressing issue, we have developed a rapid, portable, and electricity-free method for extracting nucleic acids from respiratory swabs (i.e. nasal, nasopharyngeal and buccal swabs), successfully demonstrating its effectiveness for the detection of SARS-CoV-2 in residual clinical specimens. Unlike traditional approaches, our solution eliminates the need for micropipettes or electrical equipment, making it user-friendly and requiring little to no training. Our method builds upon the principles of magnetic bead extraction and revolves around a low-cost plastic magnetic lid, called SmartLid, in combination with a simple disposable kit containing all required reagents conveniently prealiquoted. Here, we clinically validated the SmartLid sample preparation method in comparison to the gold standard QIAamp Viral RNA Mini Kit from QIAGEN, using 406 clinical isolates, including 161 SARS-CoV-2 positives, using the SARS-CoV-2 RT-qPCR assays developed by the US Centers for Disease Control and Prevention (CDC). The SmartLid method showed an overall sensitivity of 95.03% (95% CI: 90.44-97.83%) and a specificity of 99.59% (95% CI: 97.76-99.99%), with a positive agreement of 97.79% (95% CI: 95.84-98.98%) when compared to QIAGEN's column-based extraction method. There are clear benefits to using the SmartLid sample preparation kit: it enables swift extraction of viral nucleic acids, taking less than 5 min, without sacrificing significant accuracy when compared to more expensive and time-consuming alternatives currently available on the market. Moreover, its simplicity makes it particularly well-suited for the point-of-care where rapid results and portability are crucial. By providing an efficient and accessible means of nucleic acid extraction, our approach aims to introduce a step-change in diagnostic capabilities for resource-limited settings.
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Affiliation(s)
- Ivana Pennisi
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Matthew L. Cavuto
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Luca Miglietta
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | | | - Oliver W. Stringer
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Katerina-Theresa Mantikas
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Ruth Reid
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Rebecca Frise
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Nicolas Moser
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Paul Randell
- Department
of Infectious Diseases, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London W6 8RP, U.K.
| | - Frances Davies
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
- Department
of Infectious Diseases, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London W6 8RP, U.K.
| | - Frances Bolt
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Wendy Barclay
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Alison Holmes
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Pantelis Georgiou
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Jesus Rodriguez-Manzano
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
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3
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Zorzoli A, MacLean A, Nicholson S, Daniels A, Hughes S, Bennet-Slater S, Tait-Burkard C, Sakka NE, Gunson R, Templeton K. Transitioning from Triton X-100 to Tergitol 15-S-9: impacts on diagnostic assays using viral PCR sample solution. Biotechniques 2024:1-4. [PMID: 38706171 DOI: 10.1080/07366205.2024.2342172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/08/2024] [Indexed: 05/07/2024] Open
Abstract
In 2019, the European Union banned Triton X-100, a detergent widely used in laboratory diagnostics, including the Viral PCR Sample Solution (VPSS), and urged manufacturers to find environmentally sustainable alternatives. Tergitol 15-S-9 (VPSS2) has been proposed as an alternative surfactant. This multicenter study evaluated the effectiveness of VPSS2, a Tergitol-based viral solution, as a replacement for VPSS. Our results show the equivalent performance of VPSS2 to VPSS for nucleic acid extraction and viral stability over time at different temperatures. The new VPSS formulation was also tested against external quality assurance panels and clinical samples. The results of this work support adopting this modified viral PCR sample solution to replace Triton X-100-containing viral transport solutions.
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Affiliation(s)
- Azul Zorzoli
- Department of Clinical Microbiology, NHS Lothian, Edinburgh, UK
| | - Alasdair MacLean
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, UK
| | - Scott Nicholson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, UK
| | - Alison Daniels
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Stephen Hughes
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, UK
| | - Susan Bennet-Slater
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, UK
| | - Christine Tait-Burkard
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Noha El Sakka
- Department of Medical Microbiology, NHS Grampian, Aberdeen, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, UK
| | - Kate Templeton
- Department of Clinical Microbiology, NHS Lothian, Edinburgh, UK
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4
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Rahn KL, Osman SY, Pollak QG, Anand RK. Electrokinetic focusing of SARS-CoV-2 spike protein via ion concentration polarization in a paper-based lateral flow assay. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 16:91-104. [PMID: 38086621 DOI: 10.1039/d3ay00990d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The COVID-19 pandemic highlighted the importance of designing sensitive and selective point-of-care (POC) diagnostic sensors for early and rapid detection of infection. Paper-based lateral flow assays (LFAs) are easy to use, inexpensive, and rapid, but they lack sensitivity. Preconcentration techniques can improve the sensitivity of LFAs by increasing the local concentration of the analyte before detection. Here, ion concentration polarization (ICP) is used to focus the analyte, SARS-CoV-2 Spike protein (S-protein), directly over a test line composed of angiotensin converting enzyme 2 (ACE2) capture probes. ICP is the enrichment and depletion of electrolyte ions at opposing ends of an ion-selective membrane under a voltage bias. The ion depleted zone (IDZ) establishes a steep gradient in electric field strength along its boundary. Enrichment of charged species (such as a biomolecule analyte) occurs at an axial location along this electric field gradient in the presence of a fluid flow that counteracts migration of those species - a phenomenon called ICP focusing. In this paper, running buffer composition and pretreatment solutions for ICP focusing in a paper-based LFA are evaluated, and the method of voltage application for ICP-enrichment is optimized. With a power consumption of 1.8 mW, S-protein is concentrated by a factor of 21-fold, leading to a 2.9-fold increase in the signal from the LFA compared to a LFA without ICP-enrichment. The described ICP-enhanced LFA is significant because the preconcentration strategy is amenable to POC applications and can be applied to existing LFAs for improvement in sensitivity.
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Affiliation(s)
- Kira L Rahn
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, IA 50011-1021, USA.
| | - Sommer Y Osman
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, IA 50011-1021, USA.
| | - Quinlan G Pollak
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, IA 50011-1021, USA.
| | - Robbyn K Anand
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, IA 50011-1021, USA.
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5
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Kurkowiak M, Fletcher S, Daniels A, Mozolewski P, Silvestris DA, Król E, Marek-Trzonkowska N, Hupp T, Tait-Burkard C. Differential RNA editing landscapes in host cell versus the SARS-CoV-2 genome. iScience 2023; 26:108031. [PMID: 37876814 PMCID: PMC10590966 DOI: 10.1016/j.isci.2023.108031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/09/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The SARS-CoV-2 pandemic was defined by the emergence of new variants formed through virus mutation originating from random errors not corrected by viral proofreading and/or the host antiviral response introducing mutations into the viral genome. While sequencing information hints at cellular RNA editing pathways playing a role in viral evolution, here, we use an in vitro human cell infection model to assess RNA mutation types in two SARS-CoV-2 strains representing the original and the alpha variants. The variants showed both different cellular responses and mutation patterns with alpha showing higher mutation frequency with most substitutions observed being C-U, indicating an important role for apolipoprotein B mRNA editing catalytic polypeptide-like editing. Knockdown of select APOBEC3s through RNAi increased virus production in the original virus, but not in alpha. Overall, these data suggest a deaminase-independent anti-viral function of APOBECs in SARS-CoV-2 while the C-U editing itself might function to enhance genetic diversity enabling evolutionary adaptation.
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Affiliation(s)
- Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Sarah Fletcher
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Alison Daniels
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
- Infection Medicine, University of Edinburgh, Little France Crescent, UK
| | - Paweł Mozolewski
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | | | - Ewelina Król
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine Medical University of Gdańsk, Gdańsk, Poland
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Cell Signalling Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Christine Tait-Burkard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
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6
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Daniels A, Fletcher S, Kerr HEM, Kratzel A, Pinto RM, Kriplani N, Craig N, Hastie CJ, Davies P, Digard P, Thiel V, Tait-Burkard C. One for all-human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses. J Virol 2023; 97:e0055523. [PMID: 37668370 PMCID: PMC10537734 DOI: 10.1128/jvi.00555-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 09/06/2023] Open
Abstract
In vitro investigations of host-virus interactions are reliant on suitable cell and tissue culture models. Results are only as good as the model they are generated in. However, choosing cell models for in vitro work often depends on availability and previous use alone. Despite the vast increase in coronavirus research over the past few years, scientists are still heavily reliant on: non-human, highly heterogeneous or not fully differentiated, or naturally unsusceptible cells requiring overexpression of receptors and other accessory factors. Complex primary or stem cell models are highly representative of human tissues but are expensive and time-consuming to develop and maintain with limited suitability for high-throughput experiments.Using tissue-specific expression patterns, we identified human kidney cells as an ideal target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and broader coronavirus infection. We show the use of the well-characterized human kidney cell line Caki-1 for infection with three human coronaviruses (hCoVs): Betacoronaviruses SARS-CoV-2 and Middle Eastern respiratory syndrome coronavirus and Alphacoronavirus hCoV 229E. Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cell lines for the cultivation of the respective virus. Antibody staining against SARS-CoV-2 N protein shows comparable replication rates. A panel of 26 custom antibodies shows the location of SARS-CoV-2 proteins during replication using immunocytochemistry. In addition, Caki-1 cells were found to be susceptible to two other human respiratory viruses, influenza A virus and respiratory syncytial virus, making them an ideal model for cross-comparison for a broad range of respiratory viruses. IMPORTANCE Cell lines remain the backbone of virus research, but results are only as good as their originating model. Despite increased research into human coronaviruses following the COVID-19 pandemic, researchers continue to rely on suboptimal cell line models of: non-human origin, incomplete differentiation, or lacking active interferon responses. We identified the human kidney Caki-1 cell line as a potential target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This cell line could be shown to be infectable with a wide range of coronaviruses including common cold virus hCoV-229E, epidemic virus MERS-CoV, and SARS-CoV-2 as well as other important respiratory viruses influenza A virus and respiratory syncytial virus. We could show the localization of 26 SARS-CoV-2 proteins in Caki-1 cells during natural replication and the cells are competent of forming a cellular immune response. Together, this makes Caki-1 cells a unique tool for cross-virus comparison in one cell line.
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Affiliation(s)
- Alison Daniels
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- Infection Medicine, University of Edinburgh, Little France Crescent, United Kingdom
| | - Sarah Fletcher
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Holly E. M. Kerr
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rute Maria Pinto
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nisha Kriplani
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nicky Craig
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - C. James Hastie
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Digard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christine Tait-Burkard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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7
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Mache C, Schulze J, Holland G, Bourquain D, Gensch JM, Oh DY, Nitsche A, Dürrwald R, Laue M, Wolff T. SARS-CoV-2 Omicron variant is attenuated for replication in a polarized human lung epithelial cell model. Commun Biol 2022; 5:1138. [PMID: 36302956 PMCID: PMC9610361 DOI: 10.1038/s42003-022-04068-3] [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: 02/16/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 and its emerging variants of concern remain a major threat for global health. Here we introduce an infection model based upon polarized human Alveolar Epithelial Lentivirus immortalized (hAELVi) cells grown at the air-liquid interface to estimate replication and epidemic potential of respiratory viruses in the human lower respiratory tract. hAELVI cultures are highly permissive for different human coronaviruses and seasonal influenza A virus and upregulate various mediators following virus infection. Our analysis revealed a significantly reduced capacity of SARS-CoV-2 Omicron BA.1 and BA.2 variants to propagate in this human model compared to earlier D614G and Delta variants, which extends early risk assessments from epidemiological and animal studies suggesting a reduced pathogenicity of Omicron.
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Affiliation(s)
- Christin Mache
- Influenza and other Respiratory Viruses (Unit 17), Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Jessica Schulze
- Influenza and other Respiratory Viruses (Unit 17), Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Gudrun Holland
- Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Daniel Bourquain
- Highly Pathogenic Viruses (ZBS 1), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Jean-Marc Gensch
- Influenza and other Respiratory Viruses (Unit 17), Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Djin-Ye Oh
- Influenza and other Respiratory Viruses (Unit 17), Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses (ZBS 1), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and other Respiratory Viruses (Unit 17), Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Thorsten Wolff
- Influenza and other Respiratory Viruses (Unit 17), Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
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8
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Thiopurines inhibit coronavirus Spike protein processing and incorporation into progeny virions. PLoS Pathog 2022; 18:e1010832. [PMID: 36121863 PMCID: PMC9522307 DOI: 10.1371/journal.ppat.1010832] [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: 03/31/2022] [Revised: 09/29/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022] Open
Abstract
There is an outstanding need for broadly acting antiviral drugs to combat emerging viral diseases. Here, we report that thiopurines inhibit the replication of the betacoronaviruses HCoV-OC43 and SARS-CoV-2. 6-Thioguanine (6-TG) disrupted early stages of infection, limiting accumulation of full-length viral genomes, subgenomic RNAs and structural proteins. In ectopic expression models, we observed that 6-TG increased the electrophoretic mobility of Spike from diverse betacoronaviruses, matching the effects of enzymatic removal of N-linked oligosaccharides from Spike in vitro. SARS-CoV-2 virus-like particles (VLPs) harvested from 6-TG-treated cells were deficient in Spike. 6-TG treatment had a similar effect on production of lentiviruses pseudotyped with SARS-CoV-2 Spike, yielding pseudoviruses deficient in Spike and unable to infect ACE2-expressing cells. Together, these findings from complementary ectopic expression and infection models strongly indicate that defective Spike trafficking and processing is an outcome of 6-TG treatment. Using biochemical and genetic approaches we demonstrated that 6-TG is a pro-drug that must be converted to the nucleotide form by hypoxanthine phosphoribosyltransferase 1 (HPRT1) to achieve antiviral activity. This nucleotide form has been shown to inhibit small GTPases Rac1, RhoA, and CDC42; however, we observed that selective chemical inhibitors of these GTPases had no effect on Spike processing or accumulation. By contrast, the broad GTPase agonist ML099 countered the effects of 6-TG, suggesting that the antiviral activity of 6-TG requires the targeting of an unknown GTPase. Overall, these findings suggest that small GTPases are promising targets for host-targeted antivirals. The COVID-19 pandemic has ignited efforts to repurpose existing drugs as safe and effective antivirals. Rather than directly inhibiting viral enzymes, host-targeted antivirals inhibit host cell processes to indirectly impede viral replication and/or stimulate antiviral responses. Here, we describe a new antiviral mechanism of action for an FDA-approved thiopurine known as 6-thioguanine (6-TG). We demonstrate that 6-TG is a pro-drug that must be metabolized by host enzymes to gain antiviral activity. We show that it can inhibit the replication of human coronaviruses, including SARS-CoV-2, at least in part by interfering with the processing and accumulation of Spike glycoproteins, thereby impeding assembly of infectious progeny viruses. We provide evidence implicating host cell GTPase enzymes in the antiviral mechanism of action.
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9
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Gregorova P, Heinonen MMK, Sarin LP. An improved RT-qPCR method for direct quantification of enveloped RNA viruses. MethodsX 2022; 9:101737. [PMID: 35669085 PMCID: PMC9162933 DOI: 10.1016/j.mex.2022.101737] [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: 02/11/2022] [Accepted: 05/10/2022] [Indexed: 11/23/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) has emerged as the gold standard for virus detection and quantification, being utilized in numerous diagnostic and research applications. However, the direct detection of viruses has so far posed a challenge as the viral genome is often encapsidated by a proteinaceous layer surrounded by a lipid envelope. This necessitates an additional and undesired RNA extraction step prior to RT-qPCR amplification. To circumvent this limitation, we have developed a direct RT-qPCR method for the detection of RNA viruses. In our method, we provide a proof-of-concept using phage phi6, a safe-to-use proxy for pathogenic enveloped RNA viruses that is commonly utilized in e.g. aerosolization studies. First, the phage phi6 envelope is removed by 1% chloroform treatment and the virus is then directly quantified by RT-qPCR. To identify false negative results, firefly luciferase is included as a synthetic external control. Thanks to the duplex format, our direct RT-qPCR method reduces the reagents needed and provides an easy to implement and broadly applicable, fast, and cost-effective tool for the quantitative analysis of enveloped RNA viruses.One-step direct RT-qPCR quantification of phage phi6 virus without prior RNA isolation. Reduced reaction volume for sustainable and cost-effective analysis.
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